ORG.Asm issues
https://git.metabarcoding.org/org-asm/org-asm/-/issues
2017-09-20T20:43:56Z
https://git.metabarcoding.org/org-asm/org-asm/-/issues/48
Error during orgasm installation on Ubuntu 16.04
2017-09-20T20:43:56Z
André Marques
Error during orgasm installation on Ubuntu 16.04
marques@marques:~/Documents/Plastome-assembly/org-asm$ sudo python3 setup.py --serenity install
[sudo] password for marques:
['/home/marques/Documents/Plastome-assembly/org-asm', '/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/usr/local/lib/python3.5/dist-packages', '/usr/lib/python3/dist-packages', '/home/marques/Documents/Plastome-assembly/org-asm/distutils.ext', '/home/marques/Documents/Plastome-assembly/org-asm/python']
Installing ORG.asm (1.0.00-alpha3) in serenity mode
You are running the good python
Restarting installation within the ORG.asm-1.0.00-alpha3 virtualenv
Install script restarting...
['/home/marques/Documents/Plastome-assembly/org-asm', '/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages', '/home/marques/Documents/Plastome-assembly/org-asm/distutils.ext', '/home/marques/Documents/Plastome-assembly/org-asm/python']
Installing ORG.asm (1.0.00-alpha3) in serenity mode
You are running the good python
ORG.asm will be installed with python : /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/python
Required packages for the installation :
Look for package pip (>=8.0) : ok version 8.1.1 installed
Look for package Cython (>=0.24) : ok version 0.25.2 installed
Look for package Sphinx (>=1.3) : ok version 1.5.1 installed
You are running the good python
Required packages for the installation :
Look for package pip (>=8.0) : ok version 8.1.1 installed
Look for package Cython (>=0.24) : ok version 0.25.2 installed
Look for package Sphinx (>=1.3) : ok version 1.5.1 installed
Required packages for the installation :
Look for package pip (>=8.0) : ok version 8.1.1 installed
Look for package Cython (>=0.24) : ok version 0.25.2 installed
Look for package Sphinx (>=1.3) : ok version 1.5.1 installed
Cython module : ['src/_sse.h', 'src/buffer.c', 'src/buildindex.c', '@code16bits.c', '@codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/debug.h', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/orgasm.h', 'src/sort.c', 'src/fgetln.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.h', 'src/orgasm.h']
Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h']
Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h']
Cython module : ['src/orgasm.h', 'fiboheap/fibo.h']
Cython module : ['src/orgasm.h']
Cython module : ['fiboheap/fibo.h', 'src/orgasm.h', '@expand8bits.c']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.h', 'src/orgasm.h']
Cython module : []
Cython module : []
running install
running build
running littlebigman
building 'littlebigman' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c distutils.ext/src/littlebigman.c -o build/temp.linux-x86_64-3.5/distutils.ext/src/littlebigman.o -msse2
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/distutils.ext/src/littlebigman.o -o build/temp.linux-x86_64-3.5/littlebigman
Your CPU is in mode : -DLITTLE_END
running build_py
running build_ext
Look for CPU architecture... [('LITTLE_END', None)]
running build_files
running build_ctools
building 'buildcomplement' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcomplement.c -o build/temp.linux-x86_64-3.5/src/buildcomplement.o -msse2
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildcomplement.o -o build/temp.linux-x86_64-3.5/buildcomplement
building 'buildcode' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcode.c -o build/temp.linux-x86_64-3.5/src/buildcode.o -msse2
src/buildcode.c: In function ‘main’:
src/buildcode.c:44:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", *((uint64_t*)nu
^
src/buildcode.c:44:19: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", *((uint64_t*)nu
^
src/buildcode.c:46:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", *((uint64_t*)nu
^
src/buildcode.c:46:19: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", *((uint64_t*)nu
^
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildcode.o -o build/temp.linux-x86_64-3.5/buildcode
building 'buildexpand8bits' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildexpand8bits.c -o build/temp.linux-x86_64-3.5/src/buildexpand8bits.o -msse2
src/buildexpand8bits.c: In function ‘main’:
src/buildexpand8bits.c:40:1: warning: multi-line comment [-Wcomment]
// *((uint32_t*)nuc) = *((uint32_t*)nuc) >> 24 | \
^
src/buildexpand8bits.c:47:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," 0x%08XUL, // %04X\n", *((uint32_t*)nuc),code);
^
src/buildexpand8bits.c:49:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," 0x%08XUL // %04X\n", *((uint32_t*)nuc),code);
^
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildexpand8bits.o -o build/temp.linux-x86_64-3.5/buildexpand8bits
Building file : codecomp.c
--> build/temp.linux-x86_64-3.5/buildcomplement > build/temp.linux-x86_64-3.5/codecomp.c
Done.
Building file : code16bits.c
--> build/temp.linux-x86_64-3.5/buildcode > build/temp.linux-x86_64-3.5/code16bits.c
Done.
Building file : expand8bits.c
--> build/temp.linux-x86_64-3.5/buildexpand8bits > build/temp.linux-x86_64-3.5/expand8bits.c
Done.
running build_cexe
Look for CPU architecture... [('LITTLE_END', None)]
orgasmi :-> src/orgasmi.c ok
orgasmi :-> src/buffer.c ok
orgasmi :-> src/buildindex.c ok
orgasmi :-> @code16bits.c changed to build/temp.linux-x86_64-3.5/code16bits.c
orgasmi :-> @codecomp.c changed to build/temp.linux-x86_64-3.5/codecomp.c
orgasmi :-> src/compsort.c ok
orgasmi :-> src/debug.c ok
orgasmi :-> src/decode.c ok
orgasmi :-> src/encode.c ok
orgasmi :-> src/fastq.c ok
orgasmi :-> src/indexinput.c ok
orgasmi :-> src/indexoutput.c ok
orgasmi :-> src/load.c ok
orgasmi :-> src/lookfor.c ok
orgasmi :-> src/malloc.c ok
orgasmi :-> src/fgetln.c ok
orgasmi :-> src/sort.c ok
building 'orgasmi' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/orgasmi.c -o build/temp.linux-x86_64-3.5/src/orgasmi.o -msse2
src/orgasmi.c:27:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
static void PrintHelp()
^
src/orgasmi.c:62:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
static void ExitUsage(stat)
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buffer.c -o build/temp.linux-x86_64-3.5/src/buffer.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildindex.c -o build/temp.linux-x86_64-3.5/src/buildindex.o -msse2
src/buildindex.c: In function ‘buildIndex’:
src/buildindex.c:44:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ofx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.5/code16bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.5/codecomp.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/compsort.c -o build/temp.linux-x86_64-3.5/src/compsort.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/debug.c -o build/temp.linux-x86_64-3.5/src/debug.o -msse2
src/debug.c: In function ‘int2bin’:
src/debug.c:23:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
u = *(unsigned *)&i;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/decode.c -o build/temp.linux-x86_64-3.5/src/decode.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/encode.c -o build/temp.linux-x86_64-3.5/src/encode.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fastq.c -o build/temp.linux-x86_64-3.5/src/fastq.o -msse2
src/fastq.c: In function ‘readFastq’:
src/fastq.c:42:11: warning: implicit declaration of function ‘fgetln’ [-Wimplicit-function-declaration]
buffer = fgetln(in,&lseq);
^
src/fastq.c:42:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:45:10: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:59:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:60:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexinput.c -o build/temp.linux-x86_64-3.5/src/indexinput.o -msse2
src/indexinput.c: In function ‘loadGeneralData’:
src/indexinput.c:57:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(buffer,1,sizeof(buffer_t),input);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexoutput.c -o build/temp.linux-x86_64-3.5/src/indexoutput.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/load.c -o build/temp.linux-x86_64-3.5/src/load.o -msse2
src/load.c: In function ‘loadIndexedReads’:
src/load.c:34:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ogx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/lookfor.c -o build/temp.linux-x86_64-3.5/src/lookfor.o -msse2
src/lookfor.c: In function ‘shiftKey’:
src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable]
uint8_t rmask;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/malloc.c -o build/temp.linux-x86_64-3.5/src/malloc.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fgetln.c -o build/temp.linux-x86_64-3.5/src/fgetln.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/sort.c -o build/temp.linux-x86_64-3.5/src/sort.o -msse2
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/orgasmi.o build/temp.linux-x86_64-3.5/src/buffer.o build/temp.linux-x86_64-3.5/src/buildindex.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o build/temp.linux-x86_64-3.5/src/compsort.o build/temp.linux-x86_64-3.5/src/debug.o build/temp.linux-x86_64-3.5/src/decode.o build/temp.linux-x86_64-3.5/src/encode.o build/temp.linux-x86_64-3.5/src/fastq.o build/temp.linux-x86_64-3.5/src/indexinput.o build/temp.linux-x86_64-3.5/src/indexoutput.o build/temp.linux-x86_64-3.5/src/load.o build/temp.linux-x86_64-3.5/src/lookfor.o build/temp.linux-x86_64-3.5/src/malloc.o build/temp.linux-x86_64-3.5/src/fgetln.o build/temp.linux-x86_64-3.5/src/sort.o -o build/scripts-3.5/orgasmi
orgasm.indexer._orgasm :-> python/orgasm/indexer/_orgasm.pyx ok
orgasm.indexer._orgasm :-> src/buffer.c ok
orgasm.indexer._orgasm :-> src/buildindex.c ok
orgasm.indexer._orgasm :-> @code16bits.c changed to build/temp.linux-x86_64-3.5/code16bits.c
orgasm.indexer._orgasm :-> @codecomp.c changed to build/temp.linux-x86_64-3.5/codecomp.c
orgasm.indexer._orgasm :-> src/compsort.c ok
orgasm.indexer._orgasm :-> src/debug.c ok
orgasm.indexer._orgasm :-> src/decode.c ok
orgasm.indexer._orgasm :-> src/encode.c ok
orgasm.indexer._orgasm :-> src/fastq.c ok
orgasm.indexer._orgasm :-> src/indexinput.c ok
orgasm.indexer._orgasm :-> src/indexoutput.c ok
orgasm.indexer._orgasm :-> src/load.c ok
orgasm.indexer._orgasm :-> src/lookfor.c ok
orgasm.indexer._orgasm :-> src/malloc.c ok
orgasm.indexer._orgasm :-> src/sort.c ok
orgasm.indexer._orgasm :-> src/fgetln.c ok
orgasm.indexer.fakereads :-> python/orgasm/indexer/fakereads.pyx ok
orgasm.apps.command :-> python/orgasm/apps/command.pyx ok
orgasm.apps.progress :-> python/orgasm/apps/progress.pyx ok
orgasm.apps.config :-> python/orgasm/apps/config.pyx ok
orgasm.apps.logging :-> python/orgasm/apps/logging.pyx ok
orgasm.apps.counter :-> python/orgasm/apps/counter.pyx ok
orgasm.apps.arguments :-> python/orgasm/apps/arguments.pyx ok
orgasm.graph._graphmultiedge :-> python/orgasm/graph/_graphmultiedge.pyx ok
orgasm.graph._fibointheap :-> python/orgasm/graph/_fibointheap.pyx ok
orgasm.graph._fibointheap :-> fiboheap/fibo.c ok
orgasm.graph._fibominintheap :-> python/orgasm/graph/_fibominintheap.pyx ok
orgasm.graph._fibominintheap :-> fiboheap/fibo.c ok
orgasm.graph._fibomaxintheap :-> python/orgasm/graph/_fibomaxintheap.pyx ok
orgasm.graph._fibomaxintheap :-> fiboheap/fibo.c ok
orgasm.graph._graph :-> python/orgasm/graph/_graph.pyx ok
orgasm.assembler._assembler :-> python/orgasm/assembler/_assembler.pyx ok
orgasm.assembler._asmbgraph :-> python/orgasm/assembler/_asmbgraph.pyx ok
orgasm.assembler._tango :-> python/orgasm/assembler/_tango.pyx ok
orgasm.utils._progress :-> python/orgasm/utils/_progress.pyx ok
orgasm.utils.dna :-> python/orgasm/utils/dna.pyx ok
orgasm.multialign._dynamic :-> python/orgasm/multialign/_dynamic.pyx ok
orgasm.multialign._multi :-> python/orgasm/multialign/_multi.pyx ok
orgasm.backtranslate._bitvector :-> python/orgasm/backtranslate/_bitvector.pyx ok
orgasm.backtranslate._ahocorasick :-> python/orgasm/backtranslate/_ahocorasick.pyx ok
orgasm.backtranslate._ahocorasick :-> @expand8bits.c changed to build/temp.linux-x86_64-3.5/expand8bits.c
orgasm.fiboheap._fiboheap :-> python/orgasm/fiboheap/_fiboheap.pyx ok
orgasm.fiboheap._fiboheap :-> fiboheap/fibo.c ok
orgasm.reads._sequences :-> python/orgasm/reads/_sequences.pyx ok
orgasm.reads._fastq :-> python/orgasm/reads/_fastq.pyx ok
orgasm.reads._fasta :-> python/orgasm/reads/_fasta.pyx ok
orgasm.files.uncompress :-> python/orgasm/files/uncompress.pyx ok
orgasm.files.universalopener :-> python/orgasm/files/universalopener.pyx ok
orgasm.files.linebuffer :-> python/orgasm/files/linebuffer.pyx ok
orgasm.indexer._orgasm :-> ['python/orgasm/indexer/_orgasm.pyx', 'src/buffer.c', 'src/buildindex.c', 'build/temp.linux-x86_64-3.5/code16bits.c', 'build/temp.linux-x86_64-3.5/codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/sort.c', 'src/fgetln.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c' Cython extension (up-to-date)
building 'orgasm.indexer._orgasm' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c: In function ‘__pyx_f_6orgasm_7indexer_7_orgasm_5Index_getIds’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c:289:40: warning: ‘__pyx_v_t’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c:8981:7: note: ‘__pyx_v_t’ was declared here
int __pyx_v_t;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/buffer.c -o build/temp.linux-x86_64-3.5/src/buffer.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/buildindex.c -o build/temp.linux-x86_64-3.5/src/buildindex.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/buildindex.c: In function ‘buildIndex’:
src/buildindex.c:44:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ofx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/code16bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/codecomp.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/compsort.c -o build/temp.linux-x86_64-3.5/src/compsort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/debug.c -o build/temp.linux-x86_64-3.5/src/debug.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/debug.c: In function ‘int2bin’:
src/debug.c:23:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
u = *(unsigned *)&i;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/decode.c -o build/temp.linux-x86_64-3.5/src/decode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/encode.c -o build/temp.linux-x86_64-3.5/src/encode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/fastq.c -o build/temp.linux-x86_64-3.5/src/fastq.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/fastq.c: In function ‘readFastq’:
src/fastq.c:42:11: warning: implicit declaration of function ‘fgetln’ [-Wimplicit-function-declaration]
buffer = fgetln(in,&lseq);
^
src/fastq.c:42:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:45:10: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:59:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:60:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/indexinput.c -o build/temp.linux-x86_64-3.5/src/indexinput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/indexinput.c: In function ‘loadGeneralData’:
src/indexinput.c:57:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(buffer,1,sizeof(buffer_t),input);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/indexoutput.c -o build/temp.linux-x86_64-3.5/src/indexoutput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/load.c -o build/temp.linux-x86_64-3.5/src/load.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/load.c: In function ‘loadIndexedReads’:
src/load.c:34:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ogx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/lookfor.c -o build/temp.linux-x86_64-3.5/src/lookfor.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/lookfor.c: In function ‘shiftKey’:
src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable]
uint8_t rmask;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/malloc.c -o build/temp.linux-x86_64-3.5/src/malloc.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/sort.c -o build/temp.linux-x86_64-3.5/src/sort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/fgetln.c -o build/temp.linux-x86_64-3.5/src/fgetln.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.o build/temp.linux-x86_64-3.5/src/buffer.o build/temp.linux-x86_64-3.5/src/buildindex.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o build/temp.linux-x86_64-3.5/src/compsort.o build/temp.linux-x86_64-3.5/src/debug.o build/temp.linux-x86_64-3.5/src/decode.o build/temp.linux-x86_64-3.5/src/encode.o build/temp.linux-x86_64-3.5/src/fastq.o build/temp.linux-x86_64-3.5/src/indexinput.o build/temp.linux-x86_64-3.5/src/indexoutput.o build/temp.linux-x86_64-3.5/src/load.o build/temp.linux-x86_64-3.5/src/lookfor.o build/temp.linux-x86_64-3.5/src/malloc.o build/temp.linux-x86_64-3.5/src/sort.o build/temp.linux-x86_64-3.5/src/fgetln.o -o build/lib.linux-x86_64-3.5/orgasm/indexer/_orgasm.cpython-35m-x86_64-linux-gnu.so
orgasm.indexer.fakereads :-> ['python/orgasm/indexer/fakereads.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/fakereads.c' Cython extension (up-to-date)
orgasm.apps.command :-> ['python/orgasm/apps/command.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/command.c' Cython extension (up-to-date)
orgasm.apps.progress :-> ['python/orgasm/apps/progress.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/progress.c' Cython extension (up-to-date)
orgasm.apps.config :-> ['python/orgasm/apps/config.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/config.c' Cython extension (up-to-date)
orgasm.apps.logging :-> ['python/orgasm/apps/logging.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/logging.c' Cython extension (up-to-date)
orgasm.apps.counter :-> ['python/orgasm/apps/counter.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/counter.c' Cython extension (up-to-date)
orgasm.apps.arguments :-> ['python/orgasm/apps/arguments.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/arguments.c' Cython extension (up-to-date)
orgasm.graph._graphmultiedge :-> ['python/orgasm/graph/_graphmultiedge.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graphmultiedge.c' Cython extension (up-to-date)
orgasm.graph._fibointheap :-> ['python/orgasm/graph/_fibointheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibointheap.c' Cython extension (up-to-date)
orgasm.graph._fibominintheap :-> ['python/orgasm/graph/_fibominintheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibominintheap.c' Cython extension (up-to-date)
orgasm.graph._fibomaxintheap :-> ['python/orgasm/graph/_fibomaxintheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibomaxintheap.c' Cython extension (up-to-date)
orgasm.graph._graph :-> ['python/orgasm/graph/_graph.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c' Cython extension (up-to-date)
orgasm.assembler._assembler :-> ['python/orgasm/assembler/_assembler.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_assembler.c' Cython extension (up-to-date)
orgasm.assembler._asmbgraph :-> ['python/orgasm/assembler/_asmbgraph.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c' Cython extension (up-to-date)
orgasm.assembler._tango :-> ['python/orgasm/assembler/_tango.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_tango.c' Cython extension (up-to-date)
orgasm.utils._progress :-> ['python/orgasm/utils/_progress.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/utils/_progress.c' Cython extension (up-to-date)
orgasm.utils.dna :-> ['python/orgasm/utils/dna.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/utils/dna.c' Cython extension (up-to-date)
orgasm.multialign._dynamic :-> ['python/orgasm/multialign/_dynamic.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/multialign/_dynamic.c' Cython extension (up-to-date)
orgasm.multialign._multi :-> ['python/orgasm/multialign/_multi.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/multialign/_multi.c' Cython extension (up-to-date)
orgasm.backtranslate._bitvector :-> ['python/orgasm/backtranslate/_bitvector.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_bitvector.c' Cython extension (up-to-date)
orgasm.backtranslate._ahocorasick :-> ['python/orgasm/backtranslate/_ahocorasick.pyx', 'build/temp.linux-x86_64-3.5/expand8bits.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c' Cython extension (up-to-date)
building 'orgasm.backtranslate._ahocorasick' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_11AhoCorasick_simpleMatch’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:6063:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
__pyx_v_nextstate = (__pyx_v_table[__pyx_v_letter]);
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_addSequence’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:8959:8: warning: variable ‘__pyx_v_letter’ set but not used [-Wunused-but-set-variable]
char __pyx_v_letter[2];
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_scanIndex’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:289:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:9993:7: note: ‘__pyx_v_locmax’ was declared here
int __pyx_v_locmax;
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_14NucAhoCorasick_scanIndex’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:289:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:12390:7: note: ‘__pyx_v_locmax’ was declared here
int __pyx_v_locmax;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/expand8bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/expand8bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/expand8bits.o -o build/lib.linux-x86_64-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-x86_64-linux-gnu.so
orgasm.fiboheap._fiboheap :-> ['python/orgasm/fiboheap/_fiboheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/fiboheap/_fiboheap.c' Cython extension (up-to-date)
orgasm.reads._sequences :-> ['python/orgasm/reads/_sequences.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_sequences.c' Cython extension (up-to-date)
orgasm.reads._fastq :-> ['python/orgasm/reads/_fastq.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_fastq.c' Cython extension (up-to-date)
orgasm.reads._fasta :-> ['python/orgasm/reads/_fasta.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_fasta.c' Cython extension (up-to-date)
orgasm.files.uncompress :-> ['python/orgasm/files/uncompress.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/uncompress.c' Cython extension (up-to-date)
orgasm.files.universalopener :-> ['python/orgasm/files/universalopener.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/universalopener.c' Cython extension (up-to-date)
orgasm.files.linebuffer :-> ['python/orgasm/files/linebuffer.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/linebuffer.c' Cython extension (up-to-date)
running build_scripts
running build_sphinx
Running Sphinx v1.5.1
WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler".
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised:
Traceback (most recent call last):
File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in <module>
from orgasm.assembler import tango, getusedreads # @UnresolvedImport
ImportError: cannot import name 'getusedreads'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] userapi
generating indices... genindex py-modindex
highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages... search
copying downloadable files... [100%] ../../samples/butterfly.mito.intermediate.gml
copying static files... WARNING: html_static_path entry '/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 8 warnings.
Running Sphinx v1.5.1
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden
WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [epub]: targets for 0 source files that are out of date
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler".
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised:
Traceback (most recent call last):
File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in <module>
from orgasm.assembler import tango, getusedreads # @UnresolvedImport
ImportError: cannot import name 'getusedreads'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] userapi
generating indices... genindex py-modindex
highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages...
copying static files... WARNING: html_static_path entry '/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/_static' does not exist
done
copying extra files... done
writing mimetype file...
writing META-INF/container.xml file...
writing content.opf file...
writing nav.xhtml file...
writing toc.ncx file...
writing OrganelleAssembler.epub file...
build succeeded, 16 warnings.
Running Sphinx v1.5.1
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden
WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [man]: all manpages
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler".
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised:
Traceback (most recent call last):
File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in <module>
from orgasm.assembler import tango, getusedreads # @UnresolvedImport
ImportError: cannot import name 'getusedreads'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree
done
writing... organelleassembler.1 { install oa preparing commands/index assembling commands/seeds commands/buildgraph finishing commands/fillgaps commands/cutlow unfolding commands/unfold commands/unfoldrdna commands/path commands/fasta utilities commands/list commands/compact fasta fastq embl mitochondrion algorithms algorithms/seedselection algorithms/graphextension algorithms/graphcleanning algorithms/gapfilling algorithms/graphunfolding } /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --length ###
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --estimate-length #.##
build succeeded, 17 warnings.
running install_lib
copying build/lib.linux-x86_64-3.5/orgasm/indexer/_orgasm.cpython-35m-x86_64-linux-gnu.so -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/orgasm/indexer
copying build/lib.linux-x86_64-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-x86_64-linux-gnu.so -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/orgasm/backtranslate
running install_scripts
copying build/scripts-3.5/orgasmi -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin
changing mode of /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/orgasmi to 755
changing mode of /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/oa to 755
exporting file /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/orgasmi -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/bin/orgasmi
exporting file /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/oa -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/bin/oa
running install_egg_info
Removing /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/ORG.asm-1.0.00_alpha3.egg-info
Writing /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/ORG.asm-1.0.00_alpha3.egg-info
running install_sphinx
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/index.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/genindex.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/py-modindex.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/searchindex.js -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/.buildinfo -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/search.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/basic.css -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/pygments.css -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/searchtools.js -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/doctools.js -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/nature.css -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/userapi.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/objects.inv -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_modules/index.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_modules
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/man/organelleassembler.1 -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/man/man1
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/epub/OrganelleAssembler.epub -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share
marques@marques:~/Documents/Plastome-assembly/org-asm$
It seems that there is something wrong with sphinx installation, but I cannot figure out the problem.
marques@marques:~/Documents/Plastome-assembly/org-asm$ sudo python3 setup.py --serenity install
[sudo] password for marques:
['/home/marques/Documents/Plastome-assembly/org-asm', '/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/usr/local/lib/python3.5/dist-packages', '/usr/lib/python3/dist-packages', '/home/marques/Documents/Plastome-assembly/org-asm/distutils.ext', '/home/marques/Documents/Plastome-assembly/org-asm/python']
Installing ORG.asm (1.0.00-alpha3) in serenity mode
You are running the good python
Restarting installation within the ORG.asm-1.0.00-alpha3 virtualenv
Install script restarting...
['/home/marques/Documents/Plastome-assembly/org-asm', '/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages', '/home/marques/Documents/Plastome-assembly/org-asm/distutils.ext', '/home/marques/Documents/Plastome-assembly/org-asm/python']
Installing ORG.asm (1.0.00-alpha3) in serenity mode
You are running the good python
ORG.asm will be installed with python : /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/python
Required packages for the installation :
Look for package pip (>=8.0) : ok version 8.1.1 installed
Look for package Cython (>=0.24) : ok version 0.25.2 installed
Look for package Sphinx (>=1.3) : ok version 1.5.1 installed
You are running the good python
Required packages for the installation :
Look for package pip (>=8.0) : ok version 8.1.1 installed
Look for package Cython (>=0.24) : ok version 0.25.2 installed
Look for package Sphinx (>=1.3) : ok version 1.5.1 installed
Required packages for the installation :
Look for package pip (>=8.0) : ok version 8.1.1 installed
Look for package Cython (>=0.24) : ok version 0.25.2 installed
Look for package Sphinx (>=1.3) : ok version 1.5.1 installed
Cython module : ['src/_sse.h', 'src/buffer.c', 'src/buildindex.c', '@code16bits.c', '@codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/debug.h', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/orgasm.h', 'src/sort.c', 'src/fgetln.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.h', 'src/orgasm.h']
Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h']
Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h']
Cython module : ['src/orgasm.h', 'fiboheap/fibo.h']
Cython module : ['src/orgasm.h']
Cython module : ['fiboheap/fibo.h', 'src/orgasm.h', '@expand8bits.c']
Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h']
Cython module : ['fiboheap/fibo.h', 'src/orgasm.h']
Cython module : []
Cython module : []
running install
running build
running littlebigman
building 'littlebigman' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c distutils.ext/src/littlebigman.c -o build/temp.linux-x86_64-3.5/distutils.ext/src/littlebigman.o -msse2
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/distutils.ext/src/littlebigman.o -o build/temp.linux-x86_64-3.5/littlebigman
Your CPU is in mode : -DLITTLE_END
running build_py
running build_ext
Look for CPU architecture... [('LITTLE_END', None)]
running build_files
running build_ctools
building 'buildcomplement' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcomplement.c -o build/temp.linux-x86_64-3.5/src/buildcomplement.o -msse2
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildcomplement.o -o build/temp.linux-x86_64-3.5/buildcomplement
building 'buildcode' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcode.c -o build/temp.linux-x86_64-3.5/src/buildcode.o -msse2
src/buildcode.c: In function ‘main’:
src/buildcode.c:44:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", *((uint64_t*)nu
^
src/buildcode.c:44:19: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", *((uint64_t*)nu
^
src/buildcode.c:46:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", *((uint64_t*)nu
^
src/buildcode.c:46:19: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", *((uint64_t*)nu
^
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildcode.o -o build/temp.linux-x86_64-3.5/buildcode
building 'buildexpand8bits' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildexpand8bits.c -o build/temp.linux-x86_64-3.5/src/buildexpand8bits.o -msse2
src/buildexpand8bits.c: In function ‘main’:
src/buildexpand8bits.c:40:1: warning: multi-line comment [-Wcomment]
// *((uint32_t*)nuc) = *((uint32_t*)nuc) >> 24 | \
^
src/buildexpand8bits.c:47:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," 0x%08XUL, // %04X\n", *((uint32_t*)nuc),code);
^
src/buildexpand8bits.c:49:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
fprintf(stdout," 0x%08XUL // %04X\n", *((uint32_t*)nuc),code);
^
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildexpand8bits.o -o build/temp.linux-x86_64-3.5/buildexpand8bits
Building file : codecomp.c
--> build/temp.linux-x86_64-3.5/buildcomplement > build/temp.linux-x86_64-3.5/codecomp.c
Done.
Building file : code16bits.c
--> build/temp.linux-x86_64-3.5/buildcode > build/temp.linux-x86_64-3.5/code16bits.c
Done.
Building file : expand8bits.c
--> build/temp.linux-x86_64-3.5/buildexpand8bits > build/temp.linux-x86_64-3.5/expand8bits.c
Done.
running build_cexe
Look for CPU architecture... [('LITTLE_END', None)]
orgasmi :-> src/orgasmi.c ok
orgasmi :-> src/buffer.c ok
orgasmi :-> src/buildindex.c ok
orgasmi :-> @code16bits.c changed to build/temp.linux-x86_64-3.5/code16bits.c
orgasmi :-> @codecomp.c changed to build/temp.linux-x86_64-3.5/codecomp.c
orgasmi :-> src/compsort.c ok
orgasmi :-> src/debug.c ok
orgasmi :-> src/decode.c ok
orgasmi :-> src/encode.c ok
orgasmi :-> src/fastq.c ok
orgasmi :-> src/indexinput.c ok
orgasmi :-> src/indexoutput.c ok
orgasmi :-> src/load.c ok
orgasmi :-> src/lookfor.c ok
orgasmi :-> src/malloc.c ok
orgasmi :-> src/fgetln.c ok
orgasmi :-> src/sort.c ok
building 'orgasmi' program
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/orgasmi.c -o build/temp.linux-x86_64-3.5/src/orgasmi.o -msse2
src/orgasmi.c:27:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
static void PrintHelp()
^
src/orgasmi.c:62:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
static void ExitUsage(stat)
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buffer.c -o build/temp.linux-x86_64-3.5/src/buffer.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildindex.c -o build/temp.linux-x86_64-3.5/src/buildindex.o -msse2
src/buildindex.c: In function ‘buildIndex’:
src/buildindex.c:44:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ofx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.5/code16bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.5/codecomp.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/compsort.c -o build/temp.linux-x86_64-3.5/src/compsort.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/debug.c -o build/temp.linux-x86_64-3.5/src/debug.o -msse2
src/debug.c: In function ‘int2bin’:
src/debug.c:23:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
u = *(unsigned *)&i;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/decode.c -o build/temp.linux-x86_64-3.5/src/decode.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/encode.c -o build/temp.linux-x86_64-3.5/src/encode.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fastq.c -o build/temp.linux-x86_64-3.5/src/fastq.o -msse2
src/fastq.c: In function ‘readFastq’:
src/fastq.c:42:11: warning: implicit declaration of function ‘fgetln’ [-Wimplicit-function-declaration]
buffer = fgetln(in,&lseq);
^
src/fastq.c:42:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:45:10: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:59:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:60:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexinput.c -o build/temp.linux-x86_64-3.5/src/indexinput.o -msse2
src/indexinput.c: In function ‘loadGeneralData’:
src/indexinput.c:57:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(buffer,1,sizeof(buffer_t),input);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexoutput.c -o build/temp.linux-x86_64-3.5/src/indexoutput.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/load.c -o build/temp.linux-x86_64-3.5/src/load.o -msse2
src/load.c: In function ‘loadIndexedReads’:
src/load.c:34:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ogx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/lookfor.c -o build/temp.linux-x86_64-3.5/src/lookfor.o -msse2
src/lookfor.c: In function ‘shiftKey’:
src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable]
uint8_t rmask;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/malloc.c -o build/temp.linux-x86_64-3.5/src/malloc.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fgetln.c -o build/temp.linux-x86_64-3.5/src/fgetln.o -msse2
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/sort.c -o build/temp.linux-x86_64-3.5/src/sort.o -msse2
x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/orgasmi.o build/temp.linux-x86_64-3.5/src/buffer.o build/temp.linux-x86_64-3.5/src/buildindex.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o build/temp.linux-x86_64-3.5/src/compsort.o build/temp.linux-x86_64-3.5/src/debug.o build/temp.linux-x86_64-3.5/src/decode.o build/temp.linux-x86_64-3.5/src/encode.o build/temp.linux-x86_64-3.5/src/fastq.o build/temp.linux-x86_64-3.5/src/indexinput.o build/temp.linux-x86_64-3.5/src/indexoutput.o build/temp.linux-x86_64-3.5/src/load.o build/temp.linux-x86_64-3.5/src/lookfor.o build/temp.linux-x86_64-3.5/src/malloc.o build/temp.linux-x86_64-3.5/src/fgetln.o build/temp.linux-x86_64-3.5/src/sort.o -o build/scripts-3.5/orgasmi
orgasm.indexer._orgasm :-> python/orgasm/indexer/_orgasm.pyx ok
orgasm.indexer._orgasm :-> src/buffer.c ok
orgasm.indexer._orgasm :-> src/buildindex.c ok
orgasm.indexer._orgasm :-> @code16bits.c changed to build/temp.linux-x86_64-3.5/code16bits.c
orgasm.indexer._orgasm :-> @codecomp.c changed to build/temp.linux-x86_64-3.5/codecomp.c
orgasm.indexer._orgasm :-> src/compsort.c ok
orgasm.indexer._orgasm :-> src/debug.c ok
orgasm.indexer._orgasm :-> src/decode.c ok
orgasm.indexer._orgasm :-> src/encode.c ok
orgasm.indexer._orgasm :-> src/fastq.c ok
orgasm.indexer._orgasm :-> src/indexinput.c ok
orgasm.indexer._orgasm :-> src/indexoutput.c ok
orgasm.indexer._orgasm :-> src/load.c ok
orgasm.indexer._orgasm :-> src/lookfor.c ok
orgasm.indexer._orgasm :-> src/malloc.c ok
orgasm.indexer._orgasm :-> src/sort.c ok
orgasm.indexer._orgasm :-> src/fgetln.c ok
orgasm.indexer.fakereads :-> python/orgasm/indexer/fakereads.pyx ok
orgasm.apps.command :-> python/orgasm/apps/command.pyx ok
orgasm.apps.progress :-> python/orgasm/apps/progress.pyx ok
orgasm.apps.config :-> python/orgasm/apps/config.pyx ok
orgasm.apps.logging :-> python/orgasm/apps/logging.pyx ok
orgasm.apps.counter :-> python/orgasm/apps/counter.pyx ok
orgasm.apps.arguments :-> python/orgasm/apps/arguments.pyx ok
orgasm.graph._graphmultiedge :-> python/orgasm/graph/_graphmultiedge.pyx ok
orgasm.graph._fibointheap :-> python/orgasm/graph/_fibointheap.pyx ok
orgasm.graph._fibointheap :-> fiboheap/fibo.c ok
orgasm.graph._fibominintheap :-> python/orgasm/graph/_fibominintheap.pyx ok
orgasm.graph._fibominintheap :-> fiboheap/fibo.c ok
orgasm.graph._fibomaxintheap :-> python/orgasm/graph/_fibomaxintheap.pyx ok
orgasm.graph._fibomaxintheap :-> fiboheap/fibo.c ok
orgasm.graph._graph :-> python/orgasm/graph/_graph.pyx ok
orgasm.assembler._assembler :-> python/orgasm/assembler/_assembler.pyx ok
orgasm.assembler._asmbgraph :-> python/orgasm/assembler/_asmbgraph.pyx ok
orgasm.assembler._tango :-> python/orgasm/assembler/_tango.pyx ok
orgasm.utils._progress :-> python/orgasm/utils/_progress.pyx ok
orgasm.utils.dna :-> python/orgasm/utils/dna.pyx ok
orgasm.multialign._dynamic :-> python/orgasm/multialign/_dynamic.pyx ok
orgasm.multialign._multi :-> python/orgasm/multialign/_multi.pyx ok
orgasm.backtranslate._bitvector :-> python/orgasm/backtranslate/_bitvector.pyx ok
orgasm.backtranslate._ahocorasick :-> python/orgasm/backtranslate/_ahocorasick.pyx ok
orgasm.backtranslate._ahocorasick :-> @expand8bits.c changed to build/temp.linux-x86_64-3.5/expand8bits.c
orgasm.fiboheap._fiboheap :-> python/orgasm/fiboheap/_fiboheap.pyx ok
orgasm.fiboheap._fiboheap :-> fiboheap/fibo.c ok
orgasm.reads._sequences :-> python/orgasm/reads/_sequences.pyx ok
orgasm.reads._fastq :-> python/orgasm/reads/_fastq.pyx ok
orgasm.reads._fasta :-> python/orgasm/reads/_fasta.pyx ok
orgasm.files.uncompress :-> python/orgasm/files/uncompress.pyx ok
orgasm.files.universalopener :-> python/orgasm/files/universalopener.pyx ok
orgasm.files.linebuffer :-> python/orgasm/files/linebuffer.pyx ok
orgasm.indexer._orgasm :-> ['python/orgasm/indexer/_orgasm.pyx', 'src/buffer.c', 'src/buildindex.c', 'build/temp.linux-x86_64-3.5/code16bits.c', 'build/temp.linux-x86_64-3.5/codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/sort.c', 'src/fgetln.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c' Cython extension (up-to-date)
building 'orgasm.indexer._orgasm' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c: In function ‘__pyx_f_6orgasm_7indexer_7_orgasm_5Index_getIds’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c:289:40: warning: ‘__pyx_v_t’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c:8981:7: note: ‘__pyx_v_t’ was declared here
int __pyx_v_t;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/buffer.c -o build/temp.linux-x86_64-3.5/src/buffer.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/buildindex.c -o build/temp.linux-x86_64-3.5/src/buildindex.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/buildindex.c: In function ‘buildIndex’:
src/buildindex.c:44:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ofx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/code16bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/codecomp.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/compsort.c -o build/temp.linux-x86_64-3.5/src/compsort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/debug.c -o build/temp.linux-x86_64-3.5/src/debug.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/debug.c: In function ‘int2bin’:
src/debug.c:23:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
u = *(unsigned *)&i;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/decode.c -o build/temp.linux-x86_64-3.5/src/decode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/encode.c -o build/temp.linux-x86_64-3.5/src/encode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/fastq.c -o build/temp.linux-x86_64-3.5/src/fastq.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/fastq.c: In function ‘readFastq’:
src/fastq.c:42:11: warning: implicit declaration of function ‘fgetln’ [-Wimplicit-function-declaration]
buffer = fgetln(in,&lseq);
^
src/fastq.c:42:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:45:10: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:59:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
src/fastq.c:60:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
buffer = fgetln(in,&lseq);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/indexinput.c -o build/temp.linux-x86_64-3.5/src/indexinput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/indexinput.c: In function ‘loadGeneralData’:
src/indexinput.c:57:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(buffer,1,sizeof(buffer_t),input);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/indexoutput.c -o build/temp.linux-x86_64-3.5/src/indexoutput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/load.c -o build/temp.linux-x86_64-3.5/src/load.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/load.c: In function ‘loadIndexedReads’:
src/load.c:34:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration]
asprintf(&indexFileName,"%s.ogx",indexname);
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/lookfor.c -o build/temp.linux-x86_64-3.5/src/lookfor.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
src/lookfor.c: In function ‘shiftKey’:
src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable]
uint8_t rmask;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/malloc.c -o build/temp.linux-x86_64-3.5/src/malloc.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/sort.c -o build/temp.linux-x86_64-3.5/src/sort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/fgetln.c -o build/temp.linux-x86_64-3.5/src/fgetln.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.o build/temp.linux-x86_64-3.5/src/buffer.o build/temp.linux-x86_64-3.5/src/buildindex.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o build/temp.linux-x86_64-3.5/src/compsort.o build/temp.linux-x86_64-3.5/src/debug.o build/temp.linux-x86_64-3.5/src/decode.o build/temp.linux-x86_64-3.5/src/encode.o build/temp.linux-x86_64-3.5/src/fastq.o build/temp.linux-x86_64-3.5/src/indexinput.o build/temp.linux-x86_64-3.5/src/indexoutput.o build/temp.linux-x86_64-3.5/src/load.o build/temp.linux-x86_64-3.5/src/lookfor.o build/temp.linux-x86_64-3.5/src/malloc.o build/temp.linux-x86_64-3.5/src/sort.o build/temp.linux-x86_64-3.5/src/fgetln.o -o build/lib.linux-x86_64-3.5/orgasm/indexer/_orgasm.cpython-35m-x86_64-linux-gnu.so
orgasm.indexer.fakereads :-> ['python/orgasm/indexer/fakereads.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/fakereads.c' Cython extension (up-to-date)
orgasm.apps.command :-> ['python/orgasm/apps/command.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/command.c' Cython extension (up-to-date)
orgasm.apps.progress :-> ['python/orgasm/apps/progress.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/progress.c' Cython extension (up-to-date)
orgasm.apps.config :-> ['python/orgasm/apps/config.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/config.c' Cython extension (up-to-date)
orgasm.apps.logging :-> ['python/orgasm/apps/logging.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/logging.c' Cython extension (up-to-date)
orgasm.apps.counter :-> ['python/orgasm/apps/counter.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/counter.c' Cython extension (up-to-date)
orgasm.apps.arguments :-> ['python/orgasm/apps/arguments.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/arguments.c' Cython extension (up-to-date)
orgasm.graph._graphmultiedge :-> ['python/orgasm/graph/_graphmultiedge.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graphmultiedge.c' Cython extension (up-to-date)
orgasm.graph._fibointheap :-> ['python/orgasm/graph/_fibointheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibointheap.c' Cython extension (up-to-date)
orgasm.graph._fibominintheap :-> ['python/orgasm/graph/_fibominintheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibominintheap.c' Cython extension (up-to-date)
orgasm.graph._fibomaxintheap :-> ['python/orgasm/graph/_fibomaxintheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibomaxintheap.c' Cython extension (up-to-date)
orgasm.graph._graph :-> ['python/orgasm/graph/_graph.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c' Cython extension (up-to-date)
orgasm.assembler._assembler :-> ['python/orgasm/assembler/_assembler.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_assembler.c' Cython extension (up-to-date)
orgasm.assembler._asmbgraph :-> ['python/orgasm/assembler/_asmbgraph.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c' Cython extension (up-to-date)
orgasm.assembler._tango :-> ['python/orgasm/assembler/_tango.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_tango.c' Cython extension (up-to-date)
orgasm.utils._progress :-> ['python/orgasm/utils/_progress.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/utils/_progress.c' Cython extension (up-to-date)
orgasm.utils.dna :-> ['python/orgasm/utils/dna.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/utils/dna.c' Cython extension (up-to-date)
orgasm.multialign._dynamic :-> ['python/orgasm/multialign/_dynamic.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/multialign/_dynamic.c' Cython extension (up-to-date)
orgasm.multialign._multi :-> ['python/orgasm/multialign/_multi.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/multialign/_multi.c' Cython extension (up-to-date)
orgasm.backtranslate._bitvector :-> ['python/orgasm/backtranslate/_bitvector.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_bitvector.c' Cython extension (up-to-date)
orgasm.backtranslate._ahocorasick :-> ['python/orgasm/backtranslate/_ahocorasick.pyx', 'build/temp.linux-x86_64-3.5/expand8bits.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c' Cython extension (up-to-date)
building 'orgasm.backtranslate._ahocorasick' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_11AhoCorasick_simpleMatch’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:6063:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
__pyx_v_nextstate = (__pyx_v_table[__pyx_v_letter]);
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_addSequence’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:8959:8: warning: variable ‘__pyx_v_letter’ set but not used [-Wunused-but-set-variable]
char __pyx_v_letter[2];
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_scanIndex’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:289:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:9993:7: note: ‘__pyx_v_locmax’ was declared here
int __pyx_v_locmax;
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_14NucAhoCorasick_scanIndex’:
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:289:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^
build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:12390:7: note: ‘__pyx_v_locmax’ was declared here
int __pyx_v_locmax;
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/expand8bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/expand8bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/expand8bits.o -o build/lib.linux-x86_64-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-x86_64-linux-gnu.so
orgasm.fiboheap._fiboheap :-> ['python/orgasm/fiboheap/_fiboheap.pyx', 'fiboheap/fibo.c']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/fiboheap/_fiboheap.c' Cython extension (up-to-date)
orgasm.reads._sequences :-> ['python/orgasm/reads/_sequences.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_sequences.c' Cython extension (up-to-date)
orgasm.reads._fastq :-> ['python/orgasm/reads/_fastq.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_fastq.c' Cython extension (up-to-date)
orgasm.reads._fasta :-> ['python/orgasm/reads/_fasta.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_fasta.c' Cython extension (up-to-date)
orgasm.files.uncompress :-> ['python/orgasm/files/uncompress.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/uncompress.c' Cython extension (up-to-date)
orgasm.files.universalopener :-> ['python/orgasm/files/universalopener.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/universalopener.c' Cython extension (up-to-date)
orgasm.files.linebuffer :-> ['python/orgasm/files/linebuffer.pyx']
skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/linebuffer.c' Cython extension (up-to-date)
running build_scripts
running build_sphinx
Running Sphinx v1.5.1
WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler".
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised:
Traceback (most recent call last):
File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in <module>
from orgasm.assembler import tango, getusedreads # @UnresolvedImport
ImportError: cannot import name 'getusedreads'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] userapi
generating indices... genindex py-modindex
highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages... search
copying downloadable files... [100%] ../../samples/butterfly.mito.intermediate.gml
copying static files... WARNING: html_static_path entry '/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 8 warnings.
Running Sphinx v1.5.1
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden
WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [epub]: targets for 0 source files that are out of date
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler".
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised:
Traceback (most recent call last):
File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in <module>
from orgasm.assembler import tango, getusedreads # @UnresolvedImport
ImportError: cannot import name 'getusedreads'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] userapi
generating indices... genindex py-modindex
highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages...
copying static files... WARNING: html_static_path entry '/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/_static' does not exist
done
copying extra files... done
writing mimetype file...
writing META-INF/container.xml file...
writing content.opf file...
writing nav.xhtml file...
writing toc.ncx file...
writing OrganelleAssembler.epub file...
build succeeded, 16 warnings.
Running Sphinx v1.5.1
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden
WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden
WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [man]: all manpages
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler".
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised:
Traceback (most recent call last):
File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in <module>
from orgasm.assembler import tango, getusedreads # @UnresolvedImport
ImportError: cannot import name 'getusedreads'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree
done
writing... organelleassembler.1 { install oa preparing commands/index assembling commands/seeds commands/buildgraph finishing commands/fillgaps commands/cutlow unfolding commands/unfold commands/unfoldrdna commands/path commands/fasta utilities commands/list commands/compact fasta fastq embl mitochondrion algorithms algorithms/seedselection algorithms/graphextension algorithms/graphcleanning algorithms/gapfilling algorithms/graphunfolding } /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --length ###
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --estimate-length #.##
build succeeded, 17 warnings.
running install_lib
copying build/lib.linux-x86_64-3.5/orgasm/indexer/_orgasm.cpython-35m-x86_64-linux-gnu.so -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/orgasm/indexer
copying build/lib.linux-x86_64-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-x86_64-linux-gnu.so -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/orgasm/backtranslate
running install_scripts
copying build/scripts-3.5/orgasmi -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin
changing mode of /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/orgasmi to 755
changing mode of /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/oa to 755
exporting file /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/orgasmi -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/bin/orgasmi
exporting file /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/oa -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/bin/oa
running install_egg_info
Removing /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/ORG.asm-1.0.00_alpha3.egg-info
Writing /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/ORG.asm-1.0.00_alpha3.egg-info
running install_sphinx
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/index.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/genindex.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html
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marques@marques:~/Documents/Plastome-assembly/org-asm$
It seems that there is something wrong with sphinx installation, but I cannot figure out the problem.
https://git.metabarcoding.org/org-asm/org-asm/-/issues/45
X in protein probe
2017-09-20T20:43:57Z
Pierre Taberlet
X in protein probe
When downloading a whole mtDNA from genbank
When downloading a whole mtDNA from genbank
https://git.metabarcoding.org/org-asm/org-asm/-/issues/44
No indexing of sequence with the --estimate-length option
2017-09-20T20:43:57Z
Eric Coissac
No indexing of sequence with the --estimate-length option
When running `oa index` with the `--estimate-length` option the indexing never end.
Actually the indexer correctly estimate the indexing size. The C indexing software is correctly launched but no sequence is provided to it.
It seems that this bug only occurs on Mac platform
When running `oa index` with the `--estimate-length` option the indexing never end.
Actually the indexer correctly estimate the indexing size. The C indexing software is correctly launched but no sequence is provided to it.
It seems that this bug only occurs on Mac platform
Eric Coissac
Eric Coissac
https://git.metabarcoding.org/org-asm/org-asm/-/issues/43
No fasta output and problem with --estimate-length option
2017-09-20T20:43:57Z
Ghost User
No fasta output and problem with --estimate-length option
Hello,
After running ORG.asm following the tutorial on the sample data, two scaffolds are printed in the terminal but no fasta output is generated. I tried on other datasets but I experienced the same trouble.
Moreover, on all my data set, when i used the -estimate-length=0.9 option, ORG.asm output strange stats : Counter({100: 5663614, 77: 1997, 76: 1102, 91: 557, 74: 527, 30: 419, 87: 349, 90: 245, 35: 231, 39: 223, 43: 218, 19: 174, 47: 153, 54: 150, 38: 108, 78: 97, 14: 94, 73: 93, 17: 78, 55: 69, 42: 59, 53: 50, 20: 49, 34: 49, 13: 40, 33: 38, 45: 37, 15: 35, 28: 35, 50: 35, 89: 32, 18: 31, 56: 25, 16: 18, 48: 17, 61: 16, 32: 13, 75: 13, 26: 9, 29: 9, 37: 9, 21: 6, 31: 6, 57: 5, 25: 4, 58: 4, 12: 3, 27: 2, 9: 1, 23: 1, 59: 1}) but I checked with the FASTQC software and all my reads are 100 bp longer. After indexing, ORG.asm is blocked at 290000 indexed reads (for days). In contrast, indexing reads works well when i don't use the --estimate-length parameter
(ORG.asm-0.2.07) oa unfold test test.mito
Loading global data...
Done.
Reading indexed sequence reads...
94742 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-09-15 08:05:03,155 [INFO ] No new probe set specified
2016-09-15 08:05:03,155 [INFO ] No new probe set specified
2016-09-15 08:05:03,160 [INFO ] Load matches from previous run : 1 probe sets restored
2016-09-15 08:05:03,160 [INFO ] ==> A total of : 10724
2016-09-15 08:05:03,160 [INFO ] Match list :
2016-09-15 08:05:03,163 [INFO ] nd3 : 1497 (422.2x)
2016-09-15 08:05:03,163 [INFO ] nd4L : 981 (337.2x)
2016-09-15 08:05:03,163 [INFO ] atp6 : 1765 (257.7x)
2016-09-15 08:05:03,163 [INFO ] cox3 : 1615 (203.4x)
2016-09-15 08:05:03,163 [INFO ] nd1 : 1679 (177.6x)
2016-09-15 08:05:03,163 [INFO ] cytB : 1772 (153.1x)
2016-09-15 08:05:03,163 [INFO ] nd6 : 714 (133.1x)
2016-09-15 08:05:03,163 [INFO ] cox1 : 1586 (102.6x)
2016-09-15 08:05:03,163 [INFO ] nd4 : 731 ( 54.1x)
2016-09-15 08:05:03,163 [INFO ] cox2 : 222 ( 32.3x)
2016-09-15 08:05:03,163 [INFO ] atp8 : 5 ( 3.0x)
2016-09-15 08:05:03,163 [INFO ] nd5 : 39 ( 2.2x)
2016-09-15 08:05:03,163 [INFO ] nd2 : 2 ( 0.2x)
2016-09-15 08:05:03,491 [INFO ] Evaluate fragment length
2016-09-15 08:05:03,704 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:03,704 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:03,845 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:03,847 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:03,856 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:03,996 [INFO ] Fragment length estimated : 100.000000 pb (sd: 0.000000)
2016-09-15 08:05:03,996 [INFO ] Evaluate pair-end constraints
2016-09-15 08:05:04,205 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:04,205 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:04,351 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:04,352 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:04,362 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:04,393 [INFO ] Select the good connected components
2016-09-15 08:05:04,393 [INFO ] Print the result as a fasta file
Coverage 1x = 396
2016-09-15 08:05:04,641 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:04,642 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:04,786 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:04,788 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:04,798 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:04,940 [INFO ] Path is circular
>test.mito_1 seq_length=15184; coverage=393.0; circular=True; 1 : ATAAT->(15184)->TTTTT [393].{connection: 1}
ATAATAAATATTAAATACCTAAATTGCTATATAAAATTTTAAAAACTAAAAAATTATAAT
ATATTAATTTATATATTAATAAATTAAATATTTTTATTATATTATTAAATATATTAATAT
ATTAAATTTTTAATATATATATATATATATTACTAAAAAAATTTAAAAACCTTAATTTTT
TTTTTACTATTAATAATTTATATAATATTTTTATTTTTTTACTAAACCATTCCATATAAA
TATTTATATAAATAAAAAAAAATAAAATTAAAAATAAGCTAAAATAAGCTTTTGGGTTCA
TACCCCAAATATAAAGGAAATCCCTTTTTTTTAAAAATAAAGTGCCTGATTAAAGGATTA
TTCTGATAGGATAAATTAAGTAGAATTCTACCTTTATTATATTTTATAGAATTTAACTAT
ATCTAATAATATCAAAAATTATTGTGCCCCTACACTAAAATATATAAATATAAATAAATT
ATATTAAATTTTTAATTTAATTTAATTCCCCCATTTTAAATTTTTTTAAATATTAATTCA
AATAAAATATTTTTTTATTTTATTTTAATTTTTAGAACTTTAATTTCAATTTCTTCTAAT
TCTTGATTAGGGTGTTGGATTGGACTTGAAATTAATTTACTTAGATTTATCCCCCTAATT
TCTAGGTATAAAAATCTTTTATCTTCTGAAGCAGCACTAAAATATTTTTTAACACAAGCT
ATTGCTTCTATTAATTTTTTGTTTTCTATTCTAATTAAAATAATTTTATTAAAAAATTTT
GAAATTAATAATTTAATTTCAATTATAATTGATTCTTCATTATTAATAAAAATAGGATCT
GCCCCATTTCACTTTTGATTCCCCAATATTGTTGAAGGTTTATCCTGAATTAATTGTTTT
ATATTAATAACTTGACAAAAAATTTCCCCTATAATTTTACTTTCCTATTATATAAATAAT
AATTTTTTAATAATAATTATAATTATTAATGTTATTATTGGTGTTCTAGGGGGTATTAAT
CAAACTTCTTTACGTAAATTAATATCTTTTTCTTCAATTAATAATTTAGGTTGAATATTA
GCTGCTTTAATAATTAGAGAAAATTTATGAATATTTTATTTAATTATATATTCCTTTTTA
ATTAGAATTATATGTTTTATATTCAATTTAATAAATACTTATTTTTTAAATCAATTATTT
ATCATTAATATAAATCCTATTATTAAAATTTCTTTATTAATTAATTTTTTATCATTAGGA
GGATTACCTCCATTCTTAGGATTTTTTCCTAAATGAATTACTATTAATTTTTTAATCACA
AATAATTTTTTTATAATTACATTTATTTTTATTATAATAAGATTAATTATATTATTTTTA
TATATTCGAATTATTTATTCTTCAATTACATTTAATTATTTAAAATTAAAATGATTTAAA
TTTTATTTAAAAAATAATTCAATATTAATTATTAATTTTTCTAGAATAATTTCATTATTA
GGTATAATTATTAGAACTTTTGTCTATCTATAAGGTTTTAAGTTATAATAAACTAATAAT
CTTCAAAATTATAAAAAAAGAAATTCTTTAAGCCTTAGTAATTTATTATTATACTCCTTA
AAATTTGCAATTTTATATCATAATTGACTATAAAGCTTAATAAAAGAGATTTTTCTCATA
AATAAATTTACAATTTATCGCTTATAATTCAGCCATTTTATTAGCGAAAATGACTTTATT
CAACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGTATTTGAGCAAGTATAT
TAGGAACTTCTCTTAGTTTATTAATTCGAACTGAATTAGGAACACCAGGTTCATTAATTG
GAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCTTTTATTATAATTTTTTTTA
TAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAATTCCTTTAATATTGGGAG
CCCCTGACATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCTCCTTCAT
TAACTCTTTTAATTTCAAGAATAATTGTAGAAAATGGAGCTGGAACTGGTTGAACTGTTT
ACCCCCCTCTCTCTTCTAACATTGCACATGGAAGAAGATCAGTAGATTTAGTTATTTTTT
CTTTACATTTAGCAGGTATCTCATCAATTTTAGGAGCAATTAATTTCATCACAACAATTA
TTAATATACGTATTAATAATATATCATTTGATCAAATACCTTTATTTGTTTGAGCTGTTG
GAATTACAGCTTTATTATTACTTCTTTCCTTACCAGTTTTAGCTGGAGCTATTACTATAT
TATTAACAGATCGAAATTTAAATACTTCTTTTTTTGATCCTGCTGGGGGAGGAGATCCTA
TTTTATACCAACATTTATTTTGATTTTTTGGGCACCCAGAAGTTTACATTTTAATTTTAC
CTGGATTTGGAATAATTTCTCATATTATTTCCCAAGAAAGAGGGAAAAAAGAAACATTTG
GATGTTTAGGAATAATTTATGCAATAATAGCAATTGGTTTATTAGGATTTATTGTTTGAG
CTCATCATATATTTACTGTAGGAATAGATACGGATACTCGAGCTTATTTTACTTCAGCAA
CAATAATTATTGCAGTTCCTACAGGTATTAAAATTTTTAGTTGATTAGCTACTTTCCATG
GAACACAAATCAATTACAGTCCATCAATTCTATGAAGATTAGGATTTGTTTTTCTTTTTA
CAGTAGGAGGATTAACTGGTGTAATTCTTGCTAATTCATCTATTGATGTAACATTACATG
ATACTTATTATGTAGTAGCTCACTTTCATTATGTTTTATCTATAGGAGCTGTATTTGCTA
TTATAGGAAGATTTATTCATTGATATCCTTTATTTACTGGACTTTCATTAAATTCATATT
ATTTAAAAATCCAATTTTTTACTATATTTATTGGAGTTAATTTAACTTTTTTCCCTCAAC
ATTTTTTAGGGTTAGCAGGTATACCTCGTCGTTATTCTGATTACCCAGATAATTATATAT
CTTGAAATATTTTATCTTCTTTTGGATCATATATTTCTTTATTATCTTTTATAATAATAA
TAATAATTATTTGAGAATCATTTATTAATCAACGAATTATTTTATTTTCTCTTAATATAC
CTTCTTCTATTGAATGATTACAAAATTTACCACCTGCTGAACATTCATATAATGAACTTC
CTATTTTAAGAAACTTCTAATATGACAGATTATATGTAATGGATTTAAACCCCATCAATA
AAGGTTTATCCTTTTTTTAGAAATGGCTACTTGATCTAATTTTAATCTTCAAAATAGAGC
TTCTCCTTTAATAGAACAAATTATTTTTTTTCATGACCATACTTTAATTATTTTAATTAT
AATTACTATTTTAGTAGGTTACTTAATAATTAATTTATTTTTTAACAAATATATTAATCG
TTTTTTACTAGAAGGACAAATAATTGAATTAATTTGAACTATTATTCCTACTATTACTTT
AATTTTTATTGCTCTTCCTTCATTACGCTTATTATATTTATTAGATGAACTAAATAATCC
TTTAATTACACTAAAATCAATTGGTCATCAATGATATTGAAGTTATGAATATTCTGATTT
TAATAATGTAGAATTCGATTCTTATATAATTAATTATGATAATTCTAATATTAATAATTT
TCGATTATTAGATGTTGATAATCGAATTATTTTACCTATAAATAATCAAATTCGAATTAT
AGTTACCGCTACAGATGTTATTCATTCATGAACCATCCCCTCTTTAGGGGTTAAAATTGA
CGCTAATCCTGGTCGATTAAATCAAACTAATTTATTTATTAATCGACCAGGTATTTTTTT
TGGTCAATGTTCAGAAATTTGTGGGGCTAATCACAGATTTATGCCTATTATAATTGAAAG
AATTTCAATTAAAAATTTTATTAATTGAATTAATAATTATTCCTCATTAGATGACTGAAA
GCAAGTACTGGTCTCTTAAACCATTTTATAGTAAATTAGCAATTACTTCTAATGAAAGAA
TTAGTTAAAATATAACATAAATATGTCAAATTTAAATTATTACTCTAGTAATATTCTTTT
ATCCCTCAAATAATACCAATTAACTGAATTCTTTCTTTTATTTTATTTATTGTAATTTTT
ATTATTTTTAATATTATAAACTATTATATTTTTATTAATAATAATAATAATATATTAAAT
AATAAATTCATTAATAAAAATTTTAACAATTTAAATTGAAAATGATAAATAATTTATTTT
CTATTTTTGATCCTTCTACTAATATTTTTAACTTATCGTTAAATTGAATTAGAACATTTA
TTGGATTATTATTTATTCCTTACTCTTTTTGACTTATTCCAAATCGACAATTTATTTTTT
GAAATTTTATTCTTAACAAACTTCACAATGAATTTAAAATATTATTAGGAAATAATAAAC
TTAATAAAGGATCAACTTTTATTTTTATCTCCTTATTTTCTTTTATCTTATTTAATAATT
TTTTAGGATTATTTCCCTATATTTTTACAAGAACTAGACATCTTACTATCTCTTTATCTA
TTTCTCTTTCTTTATGATTAAGATTTATATTATATGGTTGAATTAATAACTATCAACATA
TATTTATCCATATAATCCCGCAAGGAACTCCTTCAATTTTAATGCCTTTTATAGTAATAA
TTGAAACAATTAGAAATATTATTCGTCCTGGAACATTAGCTGTTCGTCTATCTGCTAATA
TAATTGCCGGTCATTTATTATTAACTCTTCTAAGAAGAACTAGTAATAGTTTATCATTTT
ATTTATTATTTATTTTAATTTTTATACAAATTTTATTATTAATTTTAGAATCAGCAGTTG
CAGTTATTCAAGCCTATGTAATTTCTATTTTAAGAACACTATATTCTAGAGAAGTTAATT
AATAACTAATGTCAATAAATAACAACCACCCTTTTCACTTAGTAGATTATAGTCCTTGAC
CATTAACTGGAGCAATTGGTGTAATAACATTAGTTACAGGAATAATTAAATGATTTCATG
AATTTAACATAAATTTAATAATTTTAGGTTATATAATTATTTTATTAACTATATATCAAT
GATGACGAGATATTTGTCGAGAAGGAACATATCAAGGTAGTCATACTATTTTAGTTTCGA
AAGGATTACGATGAGGAATAATTTTATTTATTATCTCTGAAATTTTTTTTTTTATTTCTT
TTTTTTGAGCTTTTTTTCATAGAAGTTTATCCCCTAATATTGATATTGGAGCTATATGAC
CTCCTTCTAGAATTATTCCTTTTAACCCCTTTCAAATTCCCCTTCTAAATACTATTATTC
TAATTACATCAGGAGTTTCAGTAACTTGAGCTCATCATGCAATTATAGAAAATAATTTCT
CCCAAACTACCCAAGGATTATTTATTACTATTATCTTAGGAATTTATTTTACTATTCTTC
AAGCTTATGAATACATTGAAGCTCCATTTACTATTGCCGATTCAATTTATGGATCAACTT
TTTTTATAGCTACTGGATTCCACGGACTTCATGTAATTATTGGAACAATTTTTTTATTTA
TTTGTTTTTTACGTCATTTATCAGCACATTTTTCTAATAAACATCACTTTGGATTTGAAG
CAGCAGCATGATATTGACATTTTGTAGATGTAGTTTGATTATTCCTTTATATTTCTATTT
ACTGATGAGGTAATTAATTTATTTATATAATATATTTAGTATATTTGATTTCCAATCAAA
AAGTTTAATTTAAATTAATATAAATAATTATTTTCTTATTTATTATTTCAATTTTAATTA
TTTTAATTTCTAATATTATTATATTTTTAACAATTATCTTATCTAAGAAATCATTTATAG
ACCGAGAAAAAAATTCCCCATTTGAATGTGGATTCGACCCTAAATCTTCAGCACGAATTC
CATTTTCATTGCATTTTTTTTTAATTACAGTAATTTTTTTAATTTTTGATGTAGAAATTG
CCTTAATTTTCCCAATAATTTATTCTTTTAATTTAGTAAACTTTTATTCATTAATAAAAA
TTAGATTTTTTTTTTTAATTATACTTTTAATTGGACTTTACCATGAATGAAATCAAAATA
TATTAAATTGAACAAATTAGGATTATAGTTTATTTAAAACATTTGATTTGCATTCAAAAA
ATATTGAAATCAATTTATCTTAAATATGAAGCAATATCATGCATTTAATTTCGACTTAAA
AGAAAGAGTATTTTACTCCATATTTATTAATTGAAACCAAATAGAGGTATATCACTGTTA
ATGATATTAATGAATTTTTATTCCAATTAAAGAAATATAAAAATTAAGCTTCTAACTTAA
AATATAGTAGAAAATATCTATTAATATTTCTATTTATATAGTTTATTTAAAACATTACAT
TTTCATTGTAAAAATAAAAAGAATTTTTTTTATAAATATTTAAAGATTTAACAATCTCCT
TAATATCTTCAATATTATGCTCTAATTATAAGCTATTTAAATTTTATAATAATAATAATA
TTAAATAAAAAATTATTAATCAAAAAAAAAATCTAAATAAATAAATTTTAAAATTATTTA
TTTGATAAAAATTATAAAAAACAGAATAATTTTTGATAATATTAAATATACCTTGTCCTC
TATATAATTCTCTTCATCCTATATCAATATTCTTTAATAAACTTTGCCCTATTTTTAAAA
AATAAATATTTAATCCATAAGTAGAGAGATTTGGTATAAATCATATTAAACACAGAAAAT
TTCTTAAATTATAAGTCATTAAAAACTTATTAATTGAATAAATTTTTATATTTCTAATTA
AATACCCTAAAAATAAACCCATTAATATTACATAAATAACTATTATTTTTATATTAATAG
GTAAATAAATTATATAAGGATAATTAAAAATTATTCAACTTAAAAATCTACCTACAACTA
AACTTATAAATAATAACATAAATATTCTTTTTAATATTACATAATCTTCATCATATAAAT
TATAAACAACTATTAAATTATAATCATTTACTATTAAATAAAATAATAAACGAACAGTAT
AAAATATAGTTAATCCTGTTGAAAAATAATATAAAAAAAAAATTATTAAATTTAAATTTC
TTATTCTTACTATTTCTAAAATTATGTCCTTTGAATAAAACCCAGCTAAAAATGGAATAC
CACATAAAGCTAAATTTGAAATATTTAAACATAAACTTGTTAAAGGAATATAAAATCTAA
TTCCCCCTATATATCGAATATCTTGAATATCATTCATTATATGAATTACTACTCCAGCAC
ATATAAATAATAAAGCCTTAAATATAGCATGAGTTAATAAATGAAAAAAAGCTAAATCTG
GTATTCCTATTCTTAAAATTCTTATTATCAAACCTAATTGTCTTAATGTTGATAAAGCAA
TAATTTTCTTTAAATCAAACTCATAATTAGCGGAAATTCCCGCTATAAACATTGTTAAAC
CCGATAATAACAACAAAAACTTTAAAAAAATTATATCTACTAATATTATATTAAATCGAA
TTAATAAATAAACTCCCGCAGTTACTAGCGTTGAAGAATGAACTAAAGCTGAAACAGGAG
TAGGAGCTGCTATAGCAGCAGGTAATCACGATCTAAAAGGAATTTGAGCTCTTTTAGTTA
TAGCAGCAATAATTAATAAAAAACTAATAATTTTTATTATAAAATCATTATTTATAAAAT
TTAAAAAAAAAATATAATTTCATCTCCCATAATTTATTATTCAAGAAAATACTATTAAAA
TTATTACATCTCCAATTCGATTTGATAAAGCAGTTAATATACCAGCATTATAAGACTTAA
TATTTTGATAATAAATAACTAAACAATAAGAAACTAAGCCCAATCCATCTCAACCTAAAA
AAATTCTAATTATATTAGGTCTAATAATTAATAAAATTATAGAAAATACAAACAATAACA
CTAAAATAATAAAACGATTTAAGTTTAATTCTGAAGATATATATCTTTTTCTATAATAAA
TTACTGAAGATGAAATCATAGTTACAAATATTATAAATAATAATGATATTCAATCCAATA
AAATAGATATTACAATTTTTATAGAATTAAAAGAAATAATTTCTCACTCTAAAAAAAAAA
ATACATTTTCCATAATAAAATAAATCATAAAAAAAAAATTTATTATTCTAAAAAAAAATA
AAAAAAAAAAACTAATAAAACAAATTGAAAAATTTTTTATTTTAAATGAAACCTCATATT
TTTGATTCCACAAATCAATATTTTTACTTAAATTATTTAAATTAAAATCAAATTATAAAA
AAATCAATTTTTAAAATTAATAAATTTAATGGTAATCAATGTAATATTAATATTAAATAT
TCACGAGATACTCCAGTATAAAATCTATAAATTCTTATATTATATTTCCCATGTTGTGTA
TAAGAATATAAGTATAATCTATAACCAGCTCTAAAAAATGAAATCATAATAAGAATAATT
ATTGTTAAATAAGATCATCTAATAACTCTATTAATTAATCTAATTTCCCCTATTAAATTC
ATAGATGGAGGAGCTGCTATATTTGATGATATAATTAAAAATCACCATAAACTTATTGAA
GGCATAAAATTTATCATCCCCTTATTTATAAATAATCTACGACTATGTAATCGTTCGTAA
TTAATATTTGCCAAACAAAATATCCCTGAAGAACATAACCCATGTCCAATTATTATTACA
TATGAACCTAAATAACCTCAATAATTTATAGTTATAATCCCACAAATTACCAATCTTATA
TGAGCTACAGATGAATAAGCAATTAATGATTTCATGTCAACTTGGCAAAAACAATTTAAT
CTAATATATAAACCCCCTAATAATCTAATAATTACTCAAATTAATCTATATTTTATATTA
ATTTTTTGAAAAATAATTATAACTCGAAAAAGTCCATAACCACCTAATTTCAATATAATT
CCAGCTAAAATTATTGACCCTGAAACAGGAGCCTCCACATGAGCTTTTGGTAATCATAAA
TGAACAAAATATATAGGTATTTTAACTAAAAAAGCTAAAATTATTGATAAATATAATAAA
AAAAAATTCATATTATAAAACTTAAAAAAATATATAATCATACAATTATAATTATAAAAA
ATAAAAAAAATTCCTATTAATATTGGTAAAGAAGCAAATAAAGTATAAAATAATAAATAT
ATTCCTGCTTGAATTCGTTCTGGTTGATATCCTCACCCAATAATTAATATTAACGTAGGA
ATTAAACTCCCCTCAAAAAATAAATAAAACATAAATAAATTTAATACTCTAAAAGTTAAG
TATAACATAATTAATAAAATAATAATATTAAATATAAAAAAATTAATATAAAAATTTATC
TTATTTAAATTTTCTCTTGCTATAATTATCAATAAACAAATTCAAATTCTTAATAAAATT
AAGCCATAAGAAATTATATCACATCCTATCATATATGAAAGATTACAAAAATTTATAATA
TTTATATTTATATTTATAAATATAAATATTAATAATAATAAAAATATTTGAACCATTCAA
AATATATTATTTAAAAAACATAAAGGAATTATAAAAATTATCATTATTAAAAATTTTATC
ATTATAATATATTAAATCTTTGAAAATAATCATTTCCATGTGTCCGAATTATAGAAACTA
AAATTGATAAACCTAAAGCTCCTTCACAAACAGAAAATAATAAAAAAATTATTAATATAT
ATATGTCATATTCAATATAATTTAAATAAATAAGTATTAAAAAAAAAATTCTTAAAACAA
TAAATTCTAATCTTAATAAAACAATTAATAAATGTTTATGCTTAGAAATAAAAATTACAT
TACCAATAATAAATATTATAATAATAATTAATCATATATTTAATATTATCATTAGTTTTT
ATAGTTTAAATAAAACATTGGTCTTGTAAATCAAAAATAAGATTTTTCTTTAAAAACTTC
AAAGAAAAAGAACTTCTTTATCTATAATCTCCAAAATTATTATTTTTTATAAACTATTCT
TTGAAATAATAAAAATATTTCTTTCTTTATTAATTATTATATTTTCTATTATTATATTAT
TTTTAAATCATCCTTTATCTATAGGATTAATAATTTTAATTCAAACTCTTGTTATTTGTC
TTTTATCAGGAATATTAATTAACTCTTATTGATTTTCTTATATTTTATTCTTAGTATTTT
TAGGAGGCTTATTAGTTTTATTTATTTACGTTTCTAGAGTAGCCTCTAATGAATTATTTA
ATATAAATTTTTCTCTAAAAAATATTATATTTTTTCTTTTAATTATATCATTATTTTTAA
GATTTAACTATATAAATAATTTAAATTGACTAAATTTTTCATTTAACTACGAAATAAAAA
ACATAATAAATTTTTTTATTTTTTTTAATAATGAAAATAAAATTAATTTATCTAAATTAT
ATAATAATCAAAATTATATATTAATAATAATATTAATTACCTATTTATTTATTACTTTAG
TAGCTATTGTAAAAATTACAAATATTTTTTATGGTCCTATTCGATCTATCAATTACTAAT
TACTAATGATAAATAAATTTCCCCCATTACGAAAAACTCACCCATTATTTAAAATTATTA
ATAACTCATTAATTGATTTACCTTCTCCGTCTAATATTTCAGCTTGATGAAATTTTGGCT
CTCTTTTAGCATTATGTTTAATTATTCAAATTATTACAGGATTATTTTTAACTATATATT
ATACAGCTAATATTGAATTAGCTTTTTACAGAGTTAATTATATTTGTCGTAATGTTAATT
ACGGCTGATTAATTCGTACTCTTCATGCAAATGGAGCTTCTTTTTTCTTTATTTGTATTT
ACCTTCATATTGGACGAGGAATTTATTATGAATCCTTTAATCTAAAATATACATGAATAG
TAGGAATTATTATTTTATTTATTTTAATAGCAACAGCTTTTATAGGTTATGTCTTACCTT
GAGGACAAATATCTTTTTGAGGGGCTACAGTAATTACTAATTTACTTTCAGCTATTCCTT
ATTTAGGATCTATACTAGTTAATTGAATTTGAGGGGGATTTGCTATTGATAATGCAACCT
TAACACGATTTTATTCTTTCCATTTTCTATTCCCCTTTATTATTATAATATTAACTATAA
TTCATTTATTATTTTTACACCAAACTGGTTCTAATAACCCATTAGGATTAAATAGAAATT
TAGATAAAATTCCATTTCATCCTTTTTTTACTTTTAAGGACTTAATTGGATTTATTTTTT
TATTATTTTTTTTAAGATTATTAACTTTAACTAATCCTTATTTATTGGGAGATCCTGATA
ATTTTATACCTGCCAATCCTTTAGTTACTCCCATTCATATTCAACCTGAATGATATTTTT
TATTTGCATATGCTATTCTACGATCAATTCCTAATAAACTAGGAGGAGTTATTGCTTTAG
TTATATCTATTTTAATTTTAATTATTTTACCTTTAACTTTTAATAAAAAAATTCAAGGAA
TCCAATTCTATCCATTAAATCAATTTTTATTTTGATCTATAGTTACTACTATTATTCTTC
TTACTTGAGCCGGAGCCCGACCAGTAGAAGAACCTTATATTTTTACTAGCCAACTATTAA
CTTTATTATATTTCTCTTATTTTATTATTAACCCAATTATTAATAAATACTGAGATAATT
TAATTTTTAAATAATTATTAATTAATGAGCTTGTTAAAGCATTTGTTTTGAAAACTTAAG
AAAGAATCTTATATTCTATTAATTTATACTAAAAATATTAACTATTTAAAAAAAATTTTT
AATCCTAAAAAAAATAATAAAAAATTTAAAGAAACTGGTAAATATCTCTTTCAAGATAAA
TATATTAATTTATCGTAACGATAACGAGGTAAAGTCCCTCGAATTCAAACAAATATAAAA
GAAATAAATGATAATTTTAAATAAAAAATTAATCTTAGTCTATATCCTCCCATATATAAT
AAAATAAATAGTATACTTATAAAAAGAATTCTAGAATATTCAGATAAAAAAATTAAAGTA
AATCCCCCTCTTCTATACTCAACATTAAATCCTGAAACTAACTCTCTTTCCCCCTCAGCA
AAATCAAAAGGTGTTCGATTAGTTTCTGCCAATCTTGAAGATAATCAACACAATCTTAAA
GGTATTATTAAAAAAAAAAATCAAATAATTTCTTGATAAAAAAAAAAATCAATTATATTA
AAACTCATAATTATAATAATTCTTGATAATATAATTAAAGATAATCTAACTTCATATGAA
ATCGTTTGAGCTACAGCTCGTAATCCCCCTAATAAAGCATAATTTGAATTTGAAGACCAT
CCTGCAATTATTACTGTAAATACCCCAATTCTTGTACAACATAAAAAAAATAAAACTCCT
AAATTAAATCTAATTATATTAAAATAATAAGGAATTAATAATCAAGTTATTAAAGTAACG
ACTAATCTTACGACTGGAGAAAAATAATAAGCTATATAATTTGAATAATTAGGGAAAGTT
TGTTCTTTGACAAATAATTTAATAACATCAGCAAATGGTTGTAAAATTCCTATATATCCA
ACTTTATTAGGACCTTTTCGAATTTGAATATAACCTAAAGCTTGACGCTCTAATAAAGTT
AAAAAAGCAACCCCCACTATTACCCCAATAACCATAATTAACACTCCAATAATATATATA
TAAATATCATTTAATATCATTTACTATATATATAATAAATTATATATTTATGACTTCTAA
AATCATTACATTTTTCTGCCAAAATAGTTTTATAAATATTATTAATAATATTCATTTTTA
TAAAATTATTTTTAATATTTGATCCTTTCGTACTAAAATATTATTTTTATTTAAAGATAG
AAACCAACCTGGCTCACACCGGTTTGAACTCAGATCATGTAAGATTTTAATGATCGAACA
GATCAAAATTTTAAACTTTTGCATTTAAATTTTATTTTAATCCAACATCGAGGTCGCAAA
CTTTTTTTCCTATTTGAACTAAAAAAAAAAATTACGCTGTTATCCCTAAGGTAATTTTTT
CTTTTAATCAATATTAATGGATCATTTATTCATAAATTAATGTTAATTATTTAAAAAAGT
TAATTTAATTTTTCTGTCACCCCAACAAAATAATTTATTTAATTTTAATTTTAAAATTTA
CATATTAAAAAGAACCAAATAAATTATAAAACTCTTTAGGGTCTTCCCGTCTTTTAAAAT
TATTTAAGCTTTTTTACTAAAAAATTAGATTTTAAAAATTAATTACAGACAGTTTATATT
TCATCCAATCTTTCATACAGGTCCCCAATTAAAAGACAAAGGATGATGCTACCTTTGTAC
AGCCAAAATACTGCAGCCCTTTAAAATATTTATCAGGGGGCAGATTAAACTTTAAATTAT
TTCCAAAAAGACATGTTTTTGATAAACAAGTGAATATATAATTTTGCCGAATTCCTTTAA
TTAATTTTTAATAAATCATTATTTTTATAATTTTTATATACTAATTTTATCATTATATTT
AATTTTATCTTATTAAAATATATTTTTTTATAAAAATTTAAATTTTATATTAAATTTTAA
TTAAAATTAAATTATTTGTAAAAAATTATAATTTATTTAACAATTTAAATTTTAAAATTT
TAATTTTTTTTATTATTATTAATTATAAAAATTTATTTTAAAGCTTATCCCTTAAAATAT
TTAATATTAATTATTAAAATTTTTATTAATAAAATTTTAAAATATAATATTTAAAATTAA
ATTTTTTTCTAAAAAAACTAGATATTTTTAAAAACGATTAACATTTCATTTCTAATTAAT
TATTAAAAATAATTATTCTACATTAACTTTTATAATTAATTAACTCTTTTAAATTCGAGA
AATTTATATTTAGAAAATTTTATTAATAAACTCTGATACACAAGATACAATAAATTAAAT
TTACTTTTTTATAATTTTTATACTTATTTCAAAATTCTCTTACAATACTATTTCACTATA
AATTTTAAAATTTTTCCTATATATATACTCTAACCCCCATTAAAATATACCTTAAAAATT
TTTTTATTATTTTTTTTTTATTAATTTTTCCCCTCAAATTAATTAAATTTAATATCTTTT
CAATGTAAATGAAATACTTATTCAAGCTCTAATTTGTTCTTTCTAGAAACACTTTCCAGT
ACTTCTACTTTGTTACGACTTATTCCAATTTATAAATGAAAGCGACGGGCAATATGTACA
TATTTCAATTTTTAATCATTTTATCAAATTAAATAAAATTACATTTAAATCCACCTTCAA
ATATATATTAAAATATATTATTCATTTAATCATTTCTTATTGTAATCCATTATATTCTTA
ATTATAATCTGCATCTTGATCTGAATTAATTTAATTTTAAAATTTTTAAATATTATTTTT
ATTAAAAAATATTTTTTTAACAACGATATACAAAATATATAAATTAAGTAAATTTATTCG
TGGATTATCAATTATTAAACAGATTCCTCTAAATGAACTAAAATACCGCCAAATTATTTA
AGTTTCTATAAATAATTATATACTATTTTAGTATTTTTTATTTAATTTTTAATAATAGAG
TATCTAATTCTAGTTTTTTATAAAATTTAATAAATCATATTATTTATTAAAATTTTAATT
AAATTAAAATTTCACCTAATAATTTAATATTTAATTTAATCTATTAATATTTATTATTTA
CTAATAAAATTTATTTAAATGAAATTTATTAACTTTTTTATCTTTAAAAGATTTTTTTTT
TTGAGAATTTTCTCTGAGGGTGTTTTTTTAAATTTTAAAAAATATTTTTTTTTTAAAAAT
TATATAAATAGTGGAAAAAAATATAAATGTTTTTTGGTGTTGATAGGTTTAGTAAAATTT
TATTTATTCTGGGAAATTTTCGGGTGGTTTTTTAAATTTTTTAATTTTTAAAAAAATCCC
CTTTTATAAAATTTTTTATTAGGCCCTTATTAAACCCTTAAATAATTTTTTTTTTTTTTT
TTTT
Coverage 1x = 396
2016-09-15 08:05:05,201 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:05,202 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:05,344 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:05,346 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:05,356 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:05,496 [INFO ] Path is circular
>test.mito_2 seq_length=15184; coverage=393.0; circular=True; -1 : ACCCG->(15184)->AAAAC [393].{connection: 1}
ACCCGAAAATTTCCCAGAATAAATAAAATTTTACTAAACCTATCAACACCAAAAAACATT
TATATTTTTTTCCACTATTTATATAATTTTTAAAAAAAAAATATTTTTTAAAATTTAAAA
AAACACCCTCAGAGAAAATTCTCAAAAAAAAAAATCTTTTAAAGATAAAAAAGTTAATAA
ATTTCATTTAAATAAATTTTATTAGTAAATAATAAATATTAATAGATTAAATTAAATATT
AAATTATTAGGTGAAATTTTAATTTAATTAAAATTTTAATAAATAATATGATTTATTAAA
TTTTATAAAAAACTAGAATTAGATACTCTATTATTAAAAATTAAATAAAAAATACTAAAA
TAGTATATAATTATTTATAGAAACTTAAATAATTTGGCGGTATTTTAGTTCATTTAGAGG
AATCTGTTTAATAATTGATAATCCACGAATAAATTTACTTAATTTATATATTTTGTATAT
CGTTGTTAAAAAAATATTTTTTAATAAAAATAATATTTAAAAATTTTAAAATTAAATTAA
TTCAGATCAAGATGCAGATTATAATTAAGAATATAATGGATTACAATAAGAAATGATTAA
ATGAATAATATATTTTAATATATATTTGAAGGTGGATTTAAATGTAATTTTATTTAATTT
GATAAAATGATTAAAAATTGAAATATGTACATATTGCCCGTCGCTTTCATTTATAAATTG
GAATAAGTCGTAACAAAGTAGAAGTACTGGAAAGTGTTTCTAGAAAGAACAAATTAGAGC
TTGAATAAGTATTTCATTTACATTGAAAAGATATTAAATTTAATTAATTTGAGGGGAAAA
ATTAATAAAAAAAAAATAATAAAAAAATTTTTAAGGTATATTTTAATGGGGGTTAGAGTA
TATATATAGGAAAAATTTTAAAATTTATAGTGAAATAGTATTGTAAGAGAATTTTGAAAT
AAGTATAAAAATTATAAAAAAGTAAATTTAATTTATTGTATCTTGTGTATCAGAGTTTAT
TAATAAAATTTTCTAAATATAAATTTCTCGAATTTAAAAGAGTTAATTAATTATAAAAGT
TAATGTAGAATAATTATTTTTAATAATTAATTAGAAATGAAATGTTAATCGTTTTTAAAA
ATATCTAGTTTTTTTAGAAAAAAATTTAATTTTAAATATTATATTTTAAAATTTTATTAA
TAAAAATTTTAATAATTAATATTAAATATTTTAAGGGATAAGCTTTAAAATAAATTTTTA
TAATTAATAATAATAAAAAAAATTAAAATTTTAAAATTTAAATTGTTAAATAAATTATAA
TTTTTTACAAATAATTTAATTTTAATTAAAATTTAATATAAAATTTAAATTTTTATAAAA
AAATATATTTTAATAAGATAAAATTAAATATAATGATAAAATTAGTATATAAAAATTATA
AAAATAATGATTTATTAAAAATTAATTAAAGGAATTCGGCAAAATTATATATTCACTTGT
TTATCAAAAACATGTCTTTTTGGAAATAATTTAAAGTTTAATCTGCCCCCTGATAAATAT
TTTAAAGGGCTGCAGTATTTTGGCTGTACAAAGGTAGCATCATCCTTTGTCTTTTAATTG
GGGACCTGTATGAAAGATTGGATGAAATATAAACTGTCTGTAATTAATTTTTAAAATCTA
ATTTTTTAGTAAAAAAGCTTAAATAATTTTAAAAGACGGGAAGACCCTAAAGAGTTTTAT
AATTTATTTGGTTCTTTTTAATATGTAAATTTTAAAATTAAAATTAAATAAATTATTTTG
TTGGGGTGACAGAAAAATTAAATTAACTTTTTTAAATAATTAACATTAATTTATGAATAA
ATGATCCATTAATATTGATTAAAAGAAAAAATTACCTTAGGGATAACAGCGTAATTTTTT
TTTTTAGTTCAAATAGGAAAAAAAGTTTGCGACCTCGATGTTGGATTAAAATAAAATTTA
AATGCAAAAGTTTAAAATTTTGATCTGTTCGATCATTAAAATCTTACATGATCTGAGTTC
AAACCGGTGTGAGCCAGGTTGGTTTCTATCTTTAAATAAAAATAATATTTTAGTACGAAA
GGATCAAATATTAAAAATAATTTTATAAAAATGAATATTATTAATAATATTTATAAAACT
ATTTTGGCAGAAAAATGTAATGATTTTAGAAGTCATAAATATATAATTTATTATATATAT
AGTAAATGATATTAAATGATATTTATATATATATTATTGGAGTGTTAATTATGGTTATTG
GGGTAATAGTGGGGGTTGCTTTTTTAACTTTATTAGAGCGTCAAGCTTTAGGTTATATTC
AAATTCGAAAAGGTCCTAATAAAGTTGGATATATAGGAATTTTACAACCATTTGCTGATG
TTATTAAATTATTTGTCAAAGAACAAACTTTCCCTAATTATTCAAATTATATAGCTTATT
ATTTTTCTCCAGTCGTAAGATTAGTCGTTACTTTAATAACTTGATTATTAATTCCTTATT
ATTTTAATATAATTAGATTTAATTTAGGAGTTTTATTTTTTTTATGTTGTACAAGAATTG
GGGTATTTACAGTAATAATTGCAGGATGGTCTTCAAATTCAAATTATGCTTTATTAGGGG
GATTACGAGCTGTAGCTCAAACGATTTCATATGAAGTTAGATTATCTTTAATTATATTAT
CAAGAATTATTATAATTATGAGTTTTAATATAATTGATTTTTTTTTTTATCAAGAAATTA
TTTGATTTTTTTTTTTAATAATACCTTTAAGATTGTGTTGATTATCTTCAAGATTGGCAG
AAACTAATCGAACACCTTTTGATTTTGCTGAGGGGGAAAGAGAGTTAGTTTCAGGATTTA
ATGTTGAGTATAGAAGAGGGGGATTTACTTTAATTTTTTTATCTGAATATTCTAGAATTC
TTTTTATAAGTATACTATTTATTTTATTATATATGGGAGGATATAGACTAAGATTAATTT
TTTATTTAAAATTATCATTTATTTCTTTTATATTTGTTTGAATTCGAGGGACTTTACCTC
GTTATCGTTACGATAAATTAATATATTTATCTTGAAAGAGATATTTACCAGTTTCTTTAA
ATTTTTTATTATTTTTTTTAGGATTAAAAATTTTTTTTAAATAGTTAATATTTTTAGTAT
AAATTAATAGAATATAAGATTCTTTCTTAAGTTTTCAAAACAAATGCTTTAACAAGCTCA
TTAATTAATAATTATTTAAAAATTAAATTATCTCAGTATTTATTAATAATTGGGTTAATA
ATAAAATAAGAGAAATATAATAAAGTTAATAGTTGGCTAGTAAAAATATAAGGTTCTTCT
ACTGGTCGGGCTCCGGCTCAAGTAAGAAGAATAATAGTAGTAACTATAGATCAAAATAAA
AATTGATTTAATGGATAGAATTGGATTCCTTGAATTTTTTTATTAAAAGTTAAAGGTAAA
ATAATTAAAATTAAAATAGATATAACTAAAGCAATAACTCCTCCTAGTTTATTAGGAATT
GATCGTAGAATAGCATATGCAAATAAAAAATATCATTCAGGTTGAATATGAATGGGAGTA
ACTAAAGGATTGGCAGGTATAAAATTATCAGGATCTCCCAATAAATAAGGATTAGTTAAA
GTTAATAATCTTAAAAAAAATAATAAAAAAATAAATCCAATTAAGTCCTTAAAAGTAAAA
AAAGGATGAAATGGAATTTTATCTAAATTTCTATTTAATCCTAATGGGTTATTAGAACCA
GTTTGGTGTAAAAATAATAAATGAATTATAGTTAATATTATAATAATAAAGGGGAATAGA
AAATGGAAAGAATAAAATCGTGTTAAGGTTGCATTATCAATAGCAAATCCCCCTCAAATT
CAATTAACTAGTATAGATCCTAAATAAGGAATAGCTGAAAGTAAATTAGTAATTACTGTA
GCCCCTCAAAAAGATATTTGTCCTCAAGGTAAGACATAACCTATAAAAGCTGTTGCTATT
AAAATAAATAAAATAATAATTCCTACTATTCATGTATATTTTAGATTAAAGGATTCATAA
TAAATTCCTCGTCCAATATGAAGGTAAATACAAATAAAGAAAAAAGAAGCTCCATTTGCA
TGAAGAGTACGAATTAATCAGCCGTAATTAACATTACGACAAATATAATTAACTCTGTAA
AAAGCTAATTCAATATTAGCTGTATAATATATAGTTAAAAATAATCCTGTAATAATTTGA
ATAATTAAACATAATGCTAAAAGAGAGCCAAAATTTCATCAAGCTGAAATATTAGACGGA
GAAGGTAAATCAATTAATGAGTTATTAATAATTTTAAATAATGGGTGAGTTTTTCGTAAT
GGGGGAAATTTATTTATCATTAGTAATTAGTAATTGATAGATCGAATAGGACCATAAAAA
ATATTTGTAATTTTTACAATAGCTACTAAAGTAATAAATAAATAGGTAATTAATATTATT
ATTAATATATAATTTTGATTATTATATAATTTAGATAAATTAATTTTATTTTCATTATTA
AAAAAAATAAAAAAATTTATTATGTTTTTTATTTCGTAGTTAAATGAAAAATTTAGTCAA
TTTAAATTATTTATATAGTTAAATCTTAAAAATAATGATATAATTAAAAGAAAAAATATA
ATATTTTTTAGAGAAAAATTTATATTAAATAATTCATTAGAGGCTACTCTAGAAACGTAA
ATAAATAAAACTAATAAGCCTCCTAAAAATACTAAGAATAAAATATAAGAAAATCAATAA
GAGTTAATTAATATTCCTGATAAAAGACAAATAACAAGAGTTTGAATTAAAATTATTAAT
CCTATAGATAAAGGATGATTTAAAAATAATATAATAATAGAAAATATAATAATTAATAAA
GAAAGAAATATTTTTATTATTTCAAAGAATAGTTTATAAAAAATAATAATTTTGGAGATT
ATAGATAAAGAAGTTCTTTTTCTTTGAAGTTTTTAAAGAAAAATCTTATTTTTGATTTAC
AAGACCAATGTTTTATTTAAACTATAAAAACTAATGATAATATTAAATATATGATTAATT
ATTATTATAATATTTATTATTGGTAATGTAATTTTTATTTCTAAGCATAAACATTTATTA
ATTGTTTTATTAAGATTAGAATTTATTGTTTTAAGAATTTTTTTTTTAATACTTATTTAT
TTAAATTATATTGAATATGACATATATATATTAATAATTTTTTTATTATTTTCTGTTTGT
GAAGGAGCTTTAGGTTTATCAATTTTAGTTTCTATAATTCGGACACATGGAAATGATTAT
TTTCAAAGATTTAATATATTATAATGATAAAATTTTTAATAATGATAATTTTTATAATTC
CTTTATGTTTTTTAAATAATATATTTTGAATGGTTCAAATATTTTTATTATTATTAATAT
TTATATTTATAAATATAAATATAAATATTATAAATTTTTGTAATCTTTCATATATGATAG
GATGTGATATAATTTCTTATGGCTTAATTTTATTAAGAATTTGAATTTGTTTATTGATAA
TTATAGCAAGAGAAAATTTAAATAAGATAAATTTTTATATTAATTTTTTTATATTTAATA
TTATTATTTTATTAATTATGTTATACTTAACTTTTAGAGTATTAAATTTATTTATGTTTT
ATTTATTTTTTGAGGGGAGTTTAATTCCTACGTTAATATTAATTATTGGGTGAGGATATC
AACCAGAACGAATTCAAGCAGGAATATATTTATTATTTTATACTTTATTTGCTTCTTTAC
CAATATTAATAGGAATTTTTTTTATTTTTTATAATTATAATTGTATGATTATATATTTTT
TTAAGTTTTATAATATGAATTTTTTTTTATTATATTTATCAATAATTTTAGCTTTTTTAG
TTAAAATACCTATATATTTTGTTCATTTATGATTACCAAAAGCTCATGTGGAGGCTCCTG
TTTCAGGGTCAATAATTTTAGCTGGAATTATATTGAAATTAGGTGGTTATGGACTTTTTC
GAGTTATAATTATTTTTCAAAAAATTAATATAAAATATAGATTAATTTGAGTAATTATTA
GATTATTAGGGGGTTTATATATTAGATTAAATTGTTTTTGCCAAGTTGACATGAAATCAT
TAATTGCTTATTCATCTGTAGCTCATATAAGATTGGTAATTTGTGGGATTATAACTATAA
ATTATTGAGGTTATTTAGGTTCATATGTAATAATAATTGGACATGGGTTATGTTCTTCAG
GGATATTTTGTTTGGCAAATATTAATTACGAACGATTACATAGTCGTAGATTATTTATAA
ATAAGGGGATGATAAATTTTATGCCTTCAATAAGTTTATGGTGATTTTTAATTATATCAT
CAAATATAGCAGCTCCTCCATCTATGAATTTAATAGGGGAAATTAGATTAATTAATAGAG
TTATTAGATGATCTTATTTAACAATAATTATTCTTATTATGATTTCATTTTTTAGAGCTG
GTTATAGATTATACTTATATTCTTATACACAACATGGGAAATATAATATAAGAATTTATA
GATTTTATACTGGAGTATCTCGTGAATATTTAATATTAATATTACATTGATTACCATTAA
ATTTATTAATTTTAAAAATTGATTTTTTTATAATTTGATTTTAATTTAAATAATTTAAGT
AAAAATATTGATTTGTGGAATCAAAAATATGAGGTTTCATTTAAAATAAAAAATTTTTCA
ATTTGTTTTATTAGTTTTTTTTTTTTATTTTTTTTTAGAATAATAAATTTTTTTTTTATG
ATTTATTTTATTATGGAAAATGTATTTTTTTTTTTAGAGTGAGAAATTATTTCTTTTAAT
TCTATAAAAATTGTAATATCTATTTTATTGGATTGAATATCATTATTATTTATAATATTT
GTAACTATGATTTCATCTTCAGTAATTTATTATAGAAAAAGATATATATCTTCAGAATTA
AACTTAAATCGTTTTATTATTTTAGTGTTATTGTTTGTATTTTCTATAATTTTATTAATT
ATTAGACCTAATATAATTAGAATTTTTTTAGGTTGAGATGGATTGGGCTTAGTTTCTTAT
TGTTTAGTTATTTATTATCAAAATATTAAGTCTTATAATGCTGGTATATTAACTGCTTTA
TCAAATCGAATTGGAGATGTAATAATTTTAATAGTATTTTCTTGAATAATAAATTATGGG
AGATGAAATTATATTTTTTTTTTAAATTTTATAAATAATGATTTTATAATAAAAATTATT
AGTTTTTTATTAATTATTGCTGCTATAACTAAAAGAGCTCAAATTCCTTTTAGATCGTGA
TTACCTGCTGCTATAGCAGCTCCTACTCCTGTTTCAGCTTTAGTTCATTCTTCAACGCTA
GTAACTGCGGGAGTTTATTTATTAATTCGATTTAATATAATATTAGTAGATATAATTTTT
TTAAAGTTTTTGTTGTTATTATCGGGTTTAACAATGTTTATAGCGGGAATTTCCGCTAAT
TATGAGTTTGATTTAAAGAAAATTATTGCTTTATCAACATTAAGACAATTAGGTTTGATA
ATAAGAATTTTAAGAATAGGAATACCAGATTTAGCTTTTTTTCATTTATTAACTCATGCT
ATATTTAAGGCTTTATTATTTATATGTGCTGGAGTAGTAATTCATATAATGAATGATATT
CAAGATATTCGATATATAGGGGGAATTAGATTTTATATTCCTTTAACAAGTTTATGTTTA
AATATTTCAAATTTAGCTTTATGTGGTATTCCATTTTTAGCTGGGTTTTATTCAAAGGAC
ATAATTTTAGAAATAGTAAGAATAAGAAATTTAAATTTAATAATTTTTTTTTTATATTAT
TTTTCAACAGGATTAACTATATTTTATACTGTTCGTTTATTATTTTATTTAATAGTAAAT
GATTATAATTTAATAGTTGTTTATAATTTATATGATGAAGATTATGTAATATTAAAAAGA
ATATTTATGTTATTATTTATAAGTTTAGTTGTAGGTAGATTTTTAAGTTGAATAATTTTT
AATTATCCTTATATAATTTATTTACCTATTAATATAAAAATAATAGTTATTTATGTAATA
TTAATGGGTTTATTTTTAGGGTATTTAATTAGAAATATAAAAATTTATTCAATTAATAAG
TTTTTAATGACTTATAATTTAAGAAATTTTCTGTGTTTAATATGATTTATACCAAATCTC
TCTACTTATGGATTAAATATTTATTTTTTAAAAATAGGGCAAAGTTTATTAAAGAATATT
GATATAGGATGAAGAGAATTATATAGAGGACAAGGTATATTTAATATTATCAAAAATTAT
TCTGTTTTTTATAATTTTTATCAAATAAATAATTTTAAAATTTATTTATTTAGATTTTTT
TTTTGATTAATAATTTTTTATTTAATATTATTATTATTATAAAATTTAAATAGCTTATAA
TTAGAGCATAATATTGAAGATATTAAGGAGATTGTTAAATCTTTAAATATTTATAAAAAA
AATTCTTTTTATTTTTACAATGAAAATGTAATGTTTTAAATAAACTATATAAATAGAAAT
ATTAATAGATATTTTCTACTATATTTTAAGTTAGAAGCTTAATTTTTATATTTCTTTAAT
TGGAATAAAAATTCATTAATATCATTAACAGTGATATACCTCTATTTGGTTTCAATTAAT
AAATATGGAGTAAAATACTCTTTCTTTTAAGTCGAAATTAAATGCATGATATTGCTTCAT
ATTTAAGATAAATTGATTTCAATATTTTTTGAATGCAAATCAAATGTTTTAAATAAACTA
TAATCCTAATTTGTTCAATTTAATATATTTTGATTTCATTCATGGTAAAGTCCAATTAAA
AGTATAATTAAAAAAAAAAATCTAATTTTTATTAATGAATAAAAGTTTACTAAATTAAAA
GAATAAATTATTGGGAAAATTAAGGCAATTTCTACATCAAAAATTAAAAAAATTACTGTA
ATTAAAAAAAAATGCAATGAAAATGGAATTCGTGCTGAAGATTTAGGGTCGAATCCACAT
TCAAATGGGGAATTTTTTTCTCGGTCTATAAATGATTTCTTAGATAAGATAATTGTTAAA
AATATAATAATATTAGAAATTAAAATAATTAAAATTGAAATAATAAATAAGAAAATAATT
ATTTATATTAATTTAAATTAAACTTTTTGATTGGAAATCAAATATACTAAATATATTATA
TAAATAAATTAATTACCTCATCAGTAAATAGAAATATAAAGGAATAATCAAACTACATCT
ACAAAATGTCAATATCATGCTGCTGCTTCAAATCCAAAGTGATGTTTATTAGAAAAATGT
GCTGATAAATGACGTAAAAAACAAATAAATAAAAAAATTGTTCCAATAATTACATGAAGT
CCGTGGAATCCAGTAGCTATAAAAAAAGTTGATCCATAAATTGAATCGGCAATAGTAAAT
GGAGCTTCAATGTATTCATAAGCTTGAAGAATAGTAAAATAAATTCCTAAGATAATAGTA
ATAAATAATCCTTGGGTAGTTTGGGAGAAATTATTTTCTATAATTGCATGATGAGCTCAA
GTTACTGAAACTCCTGATGTAATTAGAATAATAGTATTTAGAAGGGGAATTTGAAAGGGG
TTAAAAGGAATAATTCTAGAAGGAGGTCATATAGCTCCAATATCAATATTAGGGGATAAA
CTTCTATGAAAAAAAGCTCAAAAAAAAGAAATAAAAAAAAAAATTTCAGAGATAATAAAT
AAAATTATTCCTCATCGTAATCCTTTCGAAACTAAAATAGTATGACTACCTTGATATGTT
CCTTCTCGACAAATATCTCGTCATCATTGATATATAGTTAATAAAATAATTATATAACCT
AAAATTATTAAATTTATGTTAAATTCATGAAATCATTTAATTATTCCTGTAACTAATGTT
ATTACACCAATTGCTCCAGTTAATGGTCAAGGACTATAATCTACTAAGTGAAAAGGGTGG
TTGTTATTTATTGACATTAGTTATTAATTAACTTCTCTAGAATATAGTGTTCTTAAAATA
GAAATTACATAGGCTTGAATAACTGCAACTGCTGATTCTAAAATTAATAATAAAATTTGT
ATAAAAATTAAAATAAATAATAAATAAAATGATAAACTATTACTAGTTCTTCTTAGAAGA
GTTAATAATAAATGACCGGCAATTATATTAGCAGATAGACGAACAGCTAATGTTCCAGGA
CGAATAATATTTCTAATTGTTTCAATTATTACTATAAAAGGCATTAAAATTGAAGGAGTT
CCTTGCGGGATTATATGGATAAATATATGTTGATAGTTATTAATTCAACCATATAATATA
AATCTTAATCATAAAGAAAGAGAAATAGATAAAGAGATAGTAAGATGTCTAGTTCTTGTA
AAAATATAGGGAAATAATCCTAAAAAATTATTAAATAAGATAAAAGAAAATAAGGAGATA
AAAATAAAAGTTGATCCTTTATTAAGTTTATTATTTCCTAATAATATTTTAAATTCATTG
TGAAGTTTGTTAAGAATAAAATTTCAAAAAATAAATTGTCGATTTGGAATAAGTCAAAAA
GAGTAAGGAATAAATAATAATCCAATAAATGTTCTAATTCAATTTAACGATAAGTTAAAA
ATATTAGTAGAAGGATCAAAAATAGAAAATAAATTATTTATCATTTTCAATTTAAATTGT
TAAAATTTTTATTAATGAATTTATTATTTAATATATTATTATTATTATTAATAAAAATAT
AATAGTTTATAATATTAAAAATAATAAAAATTACAATAAATAAAATAAAAGAAAGAATTC
AGTTAATTGGTATTATTTGAGGGATAAAAGAATATTACTAGAGTAATAATTTAAATTTGA
CATATTTATGTTATATTTTAACTAATTCTTTCATTAGAAGTAATTGCTAATTTACTATAA
AATGGTTTAAGAGACCAGTACTTGCTTTCAGTCATCTAATGAGGAATAATTATTAATTCA
ATTAATAAAATTTTTAATTGAAATTCTTTCAATTATAATAGGCATAAATCTGTGATTAGC
CCCACAAATTTCTGAACATTGACCAAAAAAAATACCTGGTCGATTAATAAATAAATTAGT
TTGATTTAATCGACCAGGATTAGCGTCAATTTTAACCCCTAAAGAGGGGATGGTTCATGA
ATGAATAACATCTGTAGCGGTAACTATAATTCGAATTTGATTATTTATAGGTAAAATAAT
TCGATTATCAACATCTAATAATCGAAAATTATTAATATTAGAATTATCATAATTAATTAT
ATAAGAATCGAATTCTACATTATTAAAATCAGAATATTCATAACTTCAATATCATTGATG
ACCAATTGATTTTAGTGTAATTAAAGGATTATTTAGTTCATCTAATAAATATAATAAGCG
TAATGAAGGAAGAGCAATAAAAATTAAAGTAATAGTAGGAATAATAGTTCAAATTAATTC
AATTATTTGTCCTTCTAGTAAAAAACGATTAATATATTTGTTAAAAAATAAATTAATTAT
TAAGTAACCTACTAAAATAGTAATTATAATTAAAATAATTAAAGTATGGTCATGAAAAAA
AATAATTTGTTCTATTAAAGGAGAAGCTCTATTTTGAAGATTAAAATTAGATCAAGTAGC
CATTTCTAAAAAAAGGATAAACCTTTATTGATGGGGTTTAAATCCATTACATATAATCTG
TCATATTAGAAGTTTCTTAAAATAGGAAGTTCATTATATGAATGTTCAGCAGGTGGTAAA
TTTTGTAATCATTCAATAGAAGAAGGTATATTAAGAGAAAATAAAATAATTCGTTGATTA
ATAAATGATTCTCAAATAATTATTATTATTATTATAAAAGATAATAAAGAAATATATGAT
CCAAAAGAAGATAAAATATTTCAAGATATATAATTATCTGGGTAATCAGAATAACGACGA
GGTATACCTGCTAACCCTAAAAAATGTTGAGGGAAAAAAGTTAAATTAACTCCAATAAAT
ATAGTAAAAAATTGGATTTTTAAATAATATGAATTTAATGAAAGTCCAGTAAATAAAGGA
TATCAATGAATAAATCTTCCTATAATAGCAAATACAGCTCCTATAGATAAAACATAATGA
AAGTGAGCTACTACATAATAAGTATCATGTAATGTTACATCAATAGATGAATTAGCAAGA
ATTACACCAGTTAATCCTCCTACTGTAAAAAGAAAAACAAATCCTAATCTTCATAGAATT
GATGGACTGTAATTGATTTGTGTTCCATGGAAAGTAGCTAATCAACTAAAAATTTTAATA
CCTGTAGGAACTGCAATAATTATTGTTGCTGAAGTAAAATAAGCTCGAGTATCCGTATCT
ATTCCTACAGTAAATATATGATGAGCTCAAACAATAAATCCTAATAAACCAATTGCTATT
ATTGCATAAATTATTCCTAAACATCCAAATGTTTCTTTTTTCCCTCTTTCTTGGGAAATA
ATATGAGAAATTATTCCAAATCCAGGTAAAATTAAAATGTAAACTTCTGGGTGCCCAAAA
AATCAAAATAAATGTTGGTATAAAATAGGATCTCCTCCCCCAGCAGGATCAAAAAAAGAA
GTATTTAAATTTCGATCTGTTAATAATATAGTAATAGCTCCAGCTAAAACTGGTAAGGAA
AGAAGTAATAATAAAGCTGTAATTCCAACAGCTCAAACAAATAAAGGTATTTGATCAAAT
GATATATTATTAATACGTATATTAATAATTGTTGTGATGAAATTAATTGCTCCTAAAATT
GATGAGATACCTGCTAAATGTAAAGAAAAAATAACTAAATCTACTGATCTTCTTCCATGT
GCAATGTTAGAAGAGAGAGGGGGGTAAACAGTTCAACCAGTTCCAGCTCCATTTTCTACA
ATTATTCTTGAAATTAAAAGAGTTAATGAAGGAGGTAATAATCAAAATCTTATATTATTT
ATTCGGGGGAAAGCTATGTCAGGGGCTCCCAATATTAAAGGAATTAATCAATTTCCAAAT
CCTCCAATTATAATAGGTATAACTATAAAAAAAATTATAATAAAAGCGTGAGCTGTAACA
ATAGTATTATAAATTTGATCATCTCCAATTAATGAACCTGGTGTTCCTAATTCAGTTCGA
ATTAATAAACTAAGAGAAGTTCCTAATATACTTGCTCAAATACCAAAAATAAAATATAAT
GTTCCAATATCTTTATGATTTGTTGAATAAAGTCATTTTCGCTAATAAAATGGCTGAATT
ATAAGCGATAAATTGTAAATTTATTTATGAGAAAAATCTCTTTTATTAAGCTTTATAGTC
AATTATGATATAAAATTGCAAATTTTAAGGAGTATAATAATAAATTACTAAGGCTTAAAG
AATTTCTTTTTTTATAATTTTGAAGATTATTAGTTTATTATAACTTAAAACCTTATAGAT
AGACAAAAGTTCTAATAATTATACCTAATAATGAAATTATTCTAGAAAAATTAATAATTA
ATATTGAATTATTTTTTAAATAAAATTTAAATCATTTTAATTTTAAATAATTAAATGTAA
TTGAAGAATAAATAATTCGAATATATAAAAATAATATAATTAATCTTATTATAATAAAAA
TAAATGTAATTATAAAAAAATTATTTGTGATTAAAAAATTAATAGTAATTCATTTAGGAA
AAAATCCTAAGAATGGAGGTAATCCTCCTAATGATAAAAAATTAATTAATAAAGAAATTT
TAATAATAGGATTTATATTAATGATAAATAATTGATTTAAAAAATAAGTATTTATTAAAT
TGAATATAAAACATATAATTCTAATTAAAAAGGAATATATAATTAAATAAAATATTCATA
AATTTTCTCTAATTATTAAAGCAGCTAATATTCAACCTAAATTATTAATTGAAGAAAAAG
ATATTAATTTACGTAAAGAAGTTTGATTAATACCCCCTAGAACACCAATAATAACATTAA
TAATTATAATTATTATTAAAAAATTATTATTTATATAATAGGAAAGTAAAATTATAGGGG
AAATTTTTTGTCAAGTTATTAATATAAAACAATTAATTCAGGATAAACCTTCAACAATAT
TGGGGAATCAAAAGTGAAATGGGGCAGATCCTATTTTTATTAATAATGAAGAATCAATTA
TAATTGAAATTAAATTATTAATTTCAAAATTTTTTAATAAAATTATTTTAATTAGAATAG
AAAACAAAAAATTAATAGAAGCAATAGCTTGTGTTAAAAAATATTTTAGTGCTGCTTCAG
AAGATAAAAGATTTTTATACCTAGAAATTAGGGGGATAAATCTAAGTAAATTAATTTCAA
GTCCAATCCAACACCCTAATCAAGAATTAGAAGAAATTGAAATTAAAGTTCTAAAAATTA
AAATAAAATAAAAAAATATTTTATTTGAATTAATATTTAAAAAAATTTAAAATGGGGGAA
TTAAATTAAATTAAAAATTTAATATAATTTATTTATATTTATATATTTTAGTGTAGGGGC
ACAATAATTTTTGATATTATTAGATATAGTTAAATTCTATAAAATATAATAAAGGTAGAA
TTCTACTTAATTTATCCTATCAGAATAATCCTTTAATCAGGCACTTTATTTTTAAAAAAA
AGGGATTTCCTTTATATTTGGGGTATGAACCCAAAAGCTTATTTTAGCTTATTTTTAATT
TTATTTTTTTTTATTTATATAAATATTTATATGGAATGGTTTAGTAAAAAAATAAAAATA
TTATATAAATTATTAATAGTAAAAAAAAAATTAAGGTTTTTAAATTTTTTTAGTAATATA
TATATATATATATTAAAAATTTAATATATTAATATATTTAATAATATAATAAAAATATTT
AATTTATTAATATATAAATTAATATATTATAATTTTTTAGTTTTTAAAATTTTATATAGC
AATTTAGGTATTTAATATTTATTATGAAAAAAAAAAAAAAAAAAATTATTTAAGGGTTTA
ATAAGGGCCTAATAAAAAATTTTATAAAAGGGGATTTTTTTAAAAATTAAAAAATTTAAA
AAAC
(ORG.asm-0.2.07) ls -l
total 4704
-rwxr-xr-x@ 1 jeankeller staff 1201837 6 sep 14:52 papi_R1.fastq.gz
-rwxr-xr-x@ 1 jeankeller staff 1202027 6 sep 14:52 papi_R2.fastq.gz
drwxr-xr-x 9 jeankeller staff 306 15 sep 08:05 test.mito.oas
drwxr-xr-x 7 jeankeller staff 238 15 sep 08:02 test.odx
(ORG.asm-0.2.07)
(ORG.asm-0.2.07) cd test.mito.oas/
(ORG.asm-0.2.07) ls -l
total 4784
-rw-r--r-- 1 jeankeller staff 423740 15 sep 08:03 assembling.gml
-rw-r--r-- 1 jeankeller staff 423740 15 sep 08:03 assembling.intermediate.gml
-rw-r--r-- 1 jeankeller staff 417567 15 sep 08:03 assembling.intermediate.oax
-rw-r--r-- 1 jeankeller staff 417567 15 sep 08:03 assembling.oax
-rw-r--r-- 1 jeankeller staff 328285 15 sep 08:02 assembling.omx
-rw-r--r-- 1 jeankeller staff 5 15 sep 08:05 assembling.path
-rw-r--r-- 1 jeankeller staff 423878 15 sep 08:05 assembling.path.gml
(ORG.asm-0.2.07)
(ORG.asm-0.2.07) cd ../test.odx/
(ORG.asm-0.2.07) ls -l
total 6680
-rw-r--r-- 1 jeankeller staff 2652776 15 sep 08:01 index.ofx
-rw-r--r-- 1 jeankeller staff 112 15 sep 08:01 index.ogx
-rw-r--r-- 1 jeankeller staff 378968 15 sep 08:01 index.opx
-rw-r--r-- 1 jeankeller staff 378968 15 sep 08:01 index.orx
drwxr-xr-x 2 jeankeller staff 68 15 sep 08:02 test.mito.oas
(ORG.asm-0.2.07) cd test.mito.oas/
(ORG.asm-0.2.07) ls -l
(ORG.asm-0.2.07)
Hello,
After running ORG.asm following the tutorial on the sample data, two scaffolds are printed in the terminal but no fasta output is generated. I tried on other datasets but I experienced the same trouble.
Moreover, on all my data set, when i used the -estimate-length=0.9 option, ORG.asm output strange stats : Counter({100: 5663614, 77: 1997, 76: 1102, 91: 557, 74: 527, 30: 419, 87: 349, 90: 245, 35: 231, 39: 223, 43: 218, 19: 174, 47: 153, 54: 150, 38: 108, 78: 97, 14: 94, 73: 93, 17: 78, 55: 69, 42: 59, 53: 50, 20: 49, 34: 49, 13: 40, 33: 38, 45: 37, 15: 35, 28: 35, 50: 35, 89: 32, 18: 31, 56: 25, 16: 18, 48: 17, 61: 16, 32: 13, 75: 13, 26: 9, 29: 9, 37: 9, 21: 6, 31: 6, 57: 5, 25: 4, 58: 4, 12: 3, 27: 2, 9: 1, 23: 1, 59: 1}) but I checked with the FASTQC software and all my reads are 100 bp longer. After indexing, ORG.asm is blocked at 290000 indexed reads (for days). In contrast, indexing reads works well when i don't use the --estimate-length parameter
(ORG.asm-0.2.07) oa unfold test test.mito
Loading global data...
Done.
Reading indexed sequence reads...
94742 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-09-15 08:05:03,155 [INFO ] No new probe set specified
2016-09-15 08:05:03,155 [INFO ] No new probe set specified
2016-09-15 08:05:03,160 [INFO ] Load matches from previous run : 1 probe sets restored
2016-09-15 08:05:03,160 [INFO ] ==> A total of : 10724
2016-09-15 08:05:03,160 [INFO ] Match list :
2016-09-15 08:05:03,163 [INFO ] nd3 : 1497 (422.2x)
2016-09-15 08:05:03,163 [INFO ] nd4L : 981 (337.2x)
2016-09-15 08:05:03,163 [INFO ] atp6 : 1765 (257.7x)
2016-09-15 08:05:03,163 [INFO ] cox3 : 1615 (203.4x)
2016-09-15 08:05:03,163 [INFO ] nd1 : 1679 (177.6x)
2016-09-15 08:05:03,163 [INFO ] cytB : 1772 (153.1x)
2016-09-15 08:05:03,163 [INFO ] nd6 : 714 (133.1x)
2016-09-15 08:05:03,163 [INFO ] cox1 : 1586 (102.6x)
2016-09-15 08:05:03,163 [INFO ] nd4 : 731 ( 54.1x)
2016-09-15 08:05:03,163 [INFO ] cox2 : 222 ( 32.3x)
2016-09-15 08:05:03,163 [INFO ] atp8 : 5 ( 3.0x)
2016-09-15 08:05:03,163 [INFO ] nd5 : 39 ( 2.2x)
2016-09-15 08:05:03,163 [INFO ] nd2 : 2 ( 0.2x)
2016-09-15 08:05:03,491 [INFO ] Evaluate fragment length
2016-09-15 08:05:03,704 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:03,704 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:03,845 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:03,847 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:03,856 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:03,996 [INFO ] Fragment length estimated : 100.000000 pb (sd: 0.000000)
2016-09-15 08:05:03,996 [INFO ] Evaluate pair-end constraints
2016-09-15 08:05:04,205 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:04,205 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:04,351 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:04,352 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:04,362 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:04,393 [INFO ] Select the good connected components
2016-09-15 08:05:04,393 [INFO ] Print the result as a fasta file
Coverage 1x = 396
2016-09-15 08:05:04,641 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:04,642 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:04,786 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:04,788 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:04,798 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:04,940 [INFO ] Path is circular
>test.mito_1 seq_length=15184; coverage=393.0; circular=True; 1 : ATAAT->(15184)->TTTTT [393].{connection: 1}
ATAATAAATATTAAATACCTAAATTGCTATATAAAATTTTAAAAACTAAAAAATTATAAT
ATATTAATTTATATATTAATAAATTAAATATTTTTATTATATTATTAAATATATTAATAT
ATTAAATTTTTAATATATATATATATATATTACTAAAAAAATTTAAAAACCTTAATTTTT
TTTTTACTATTAATAATTTATATAATATTTTTATTTTTTTACTAAACCATTCCATATAAA
TATTTATATAAATAAAAAAAAATAAAATTAAAAATAAGCTAAAATAAGCTTTTGGGTTCA
TACCCCAAATATAAAGGAAATCCCTTTTTTTTAAAAATAAAGTGCCTGATTAAAGGATTA
TTCTGATAGGATAAATTAAGTAGAATTCTACCTTTATTATATTTTATAGAATTTAACTAT
ATCTAATAATATCAAAAATTATTGTGCCCCTACACTAAAATATATAAATATAAATAAATT
ATATTAAATTTTTAATTTAATTTAATTCCCCCATTTTAAATTTTTTTAAATATTAATTCA
AATAAAATATTTTTTTATTTTATTTTAATTTTTAGAACTTTAATTTCAATTTCTTCTAAT
TCTTGATTAGGGTGTTGGATTGGACTTGAAATTAATTTACTTAGATTTATCCCCCTAATT
TCTAGGTATAAAAATCTTTTATCTTCTGAAGCAGCACTAAAATATTTTTTAACACAAGCT
ATTGCTTCTATTAATTTTTTGTTTTCTATTCTAATTAAAATAATTTTATTAAAAAATTTT
GAAATTAATAATTTAATTTCAATTATAATTGATTCTTCATTATTAATAAAAATAGGATCT
GCCCCATTTCACTTTTGATTCCCCAATATTGTTGAAGGTTTATCCTGAATTAATTGTTTT
ATATTAATAACTTGACAAAAAATTTCCCCTATAATTTTACTTTCCTATTATATAAATAAT
AATTTTTTAATAATAATTATAATTATTAATGTTATTATTGGTGTTCTAGGGGGTATTAAT
CAAACTTCTTTACGTAAATTAATATCTTTTTCTTCAATTAATAATTTAGGTTGAATATTA
GCTGCTTTAATAATTAGAGAAAATTTATGAATATTTTATTTAATTATATATTCCTTTTTA
ATTAGAATTATATGTTTTATATTCAATTTAATAAATACTTATTTTTTAAATCAATTATTT
ATCATTAATATAAATCCTATTATTAAAATTTCTTTATTAATTAATTTTTTATCATTAGGA
GGATTACCTCCATTCTTAGGATTTTTTCCTAAATGAATTACTATTAATTTTTTAATCACA
AATAATTTTTTTATAATTACATTTATTTTTATTATAATAAGATTAATTATATTATTTTTA
TATATTCGAATTATTTATTCTTCAATTACATTTAATTATTTAAAATTAAAATGATTTAAA
TTTTATTTAAAAAATAATTCAATATTAATTATTAATTTTTCTAGAATAATTTCATTATTA
GGTATAATTATTAGAACTTTTGTCTATCTATAAGGTTTTAAGTTATAATAAACTAATAAT
CTTCAAAATTATAAAAAAAGAAATTCTTTAAGCCTTAGTAATTTATTATTATACTCCTTA
AAATTTGCAATTTTATATCATAATTGACTATAAAGCTTAATAAAAGAGATTTTTCTCATA
AATAAATTTACAATTTATCGCTTATAATTCAGCCATTTTATTAGCGAAAATGACTTTATT
CAACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGTATTTGAGCAAGTATAT
TAGGAACTTCTCTTAGTTTATTAATTCGAACTGAATTAGGAACACCAGGTTCATTAATTG
GAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCTTTTATTATAATTTTTTTTA
TAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAATTCCTTTAATATTGGGAG
CCCCTGACATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCTCCTTCAT
TAACTCTTTTAATTTCAAGAATAATTGTAGAAAATGGAGCTGGAACTGGTTGAACTGTTT
ACCCCCCTCTCTCTTCTAACATTGCACATGGAAGAAGATCAGTAGATTTAGTTATTTTTT
CTTTACATTTAGCAGGTATCTCATCAATTTTAGGAGCAATTAATTTCATCACAACAATTA
TTAATATACGTATTAATAATATATCATTTGATCAAATACCTTTATTTGTTTGAGCTGTTG
GAATTACAGCTTTATTATTACTTCTTTCCTTACCAGTTTTAGCTGGAGCTATTACTATAT
TATTAACAGATCGAAATTTAAATACTTCTTTTTTTGATCCTGCTGGGGGAGGAGATCCTA
TTTTATACCAACATTTATTTTGATTTTTTGGGCACCCAGAAGTTTACATTTTAATTTTAC
CTGGATTTGGAATAATTTCTCATATTATTTCCCAAGAAAGAGGGAAAAAAGAAACATTTG
GATGTTTAGGAATAATTTATGCAATAATAGCAATTGGTTTATTAGGATTTATTGTTTGAG
CTCATCATATATTTACTGTAGGAATAGATACGGATACTCGAGCTTATTTTACTTCAGCAA
CAATAATTATTGCAGTTCCTACAGGTATTAAAATTTTTAGTTGATTAGCTACTTTCCATG
GAACACAAATCAATTACAGTCCATCAATTCTATGAAGATTAGGATTTGTTTTTCTTTTTA
CAGTAGGAGGATTAACTGGTGTAATTCTTGCTAATTCATCTATTGATGTAACATTACATG
ATACTTATTATGTAGTAGCTCACTTTCATTATGTTTTATCTATAGGAGCTGTATTTGCTA
TTATAGGAAGATTTATTCATTGATATCCTTTATTTACTGGACTTTCATTAAATTCATATT
ATTTAAAAATCCAATTTTTTACTATATTTATTGGAGTTAATTTAACTTTTTTCCCTCAAC
ATTTTTTAGGGTTAGCAGGTATACCTCGTCGTTATTCTGATTACCCAGATAATTATATAT
CTTGAAATATTTTATCTTCTTTTGGATCATATATTTCTTTATTATCTTTTATAATAATAA
TAATAATTATTTGAGAATCATTTATTAATCAACGAATTATTTTATTTTCTCTTAATATAC
CTTCTTCTATTGAATGATTACAAAATTTACCACCTGCTGAACATTCATATAATGAACTTC
CTATTTTAAGAAACTTCTAATATGACAGATTATATGTAATGGATTTAAACCCCATCAATA
AAGGTTTATCCTTTTTTTAGAAATGGCTACTTGATCTAATTTTAATCTTCAAAATAGAGC
TTCTCCTTTAATAGAACAAATTATTTTTTTTCATGACCATACTTTAATTATTTTAATTAT
AATTACTATTTTAGTAGGTTACTTAATAATTAATTTATTTTTTAACAAATATATTAATCG
TTTTTTACTAGAAGGACAAATAATTGAATTAATTTGAACTATTATTCCTACTATTACTTT
AATTTTTATTGCTCTTCCTTCATTACGCTTATTATATTTATTAGATGAACTAAATAATCC
TTTAATTACACTAAAATCAATTGGTCATCAATGATATTGAAGTTATGAATATTCTGATTT
TAATAATGTAGAATTCGATTCTTATATAATTAATTATGATAATTCTAATATTAATAATTT
TCGATTATTAGATGTTGATAATCGAATTATTTTACCTATAAATAATCAAATTCGAATTAT
AGTTACCGCTACAGATGTTATTCATTCATGAACCATCCCCTCTTTAGGGGTTAAAATTGA
CGCTAATCCTGGTCGATTAAATCAAACTAATTTATTTATTAATCGACCAGGTATTTTTTT
TGGTCAATGTTCAGAAATTTGTGGGGCTAATCACAGATTTATGCCTATTATAATTGAAAG
AATTTCAATTAAAAATTTTATTAATTGAATTAATAATTATTCCTCATTAGATGACTGAAA
GCAAGTACTGGTCTCTTAAACCATTTTATAGTAAATTAGCAATTACTTCTAATGAAAGAA
TTAGTTAAAATATAACATAAATATGTCAAATTTAAATTATTACTCTAGTAATATTCTTTT
ATCCCTCAAATAATACCAATTAACTGAATTCTTTCTTTTATTTTATTTATTGTAATTTTT
ATTATTTTTAATATTATAAACTATTATATTTTTATTAATAATAATAATAATATATTAAAT
AATAAATTCATTAATAAAAATTTTAACAATTTAAATTGAAAATGATAAATAATTTATTTT
CTATTTTTGATCCTTCTACTAATATTTTTAACTTATCGTTAAATTGAATTAGAACATTTA
TTGGATTATTATTTATTCCTTACTCTTTTTGACTTATTCCAAATCGACAATTTATTTTTT
GAAATTTTATTCTTAACAAACTTCACAATGAATTTAAAATATTATTAGGAAATAATAAAC
TTAATAAAGGATCAACTTTTATTTTTATCTCCTTATTTTCTTTTATCTTATTTAATAATT
TTTTAGGATTATTTCCCTATATTTTTACAAGAACTAGACATCTTACTATCTCTTTATCTA
TTTCTCTTTCTTTATGATTAAGATTTATATTATATGGTTGAATTAATAACTATCAACATA
TATTTATCCATATAATCCCGCAAGGAACTCCTTCAATTTTAATGCCTTTTATAGTAATAA
TTGAAACAATTAGAAATATTATTCGTCCTGGAACATTAGCTGTTCGTCTATCTGCTAATA
TAATTGCCGGTCATTTATTATTAACTCTTCTAAGAAGAACTAGTAATAGTTTATCATTTT
ATTTATTATTTATTTTAATTTTTATACAAATTTTATTATTAATTTTAGAATCAGCAGTTG
CAGTTATTCAAGCCTATGTAATTTCTATTTTAAGAACACTATATTCTAGAGAAGTTAATT
AATAACTAATGTCAATAAATAACAACCACCCTTTTCACTTAGTAGATTATAGTCCTTGAC
CATTAACTGGAGCAATTGGTGTAATAACATTAGTTACAGGAATAATTAAATGATTTCATG
AATTTAACATAAATTTAATAATTTTAGGTTATATAATTATTTTATTAACTATATATCAAT
GATGACGAGATATTTGTCGAGAAGGAACATATCAAGGTAGTCATACTATTTTAGTTTCGA
AAGGATTACGATGAGGAATAATTTTATTTATTATCTCTGAAATTTTTTTTTTTATTTCTT
TTTTTTGAGCTTTTTTTCATAGAAGTTTATCCCCTAATATTGATATTGGAGCTATATGAC
CTCCTTCTAGAATTATTCCTTTTAACCCCTTTCAAATTCCCCTTCTAAATACTATTATTC
TAATTACATCAGGAGTTTCAGTAACTTGAGCTCATCATGCAATTATAGAAAATAATTTCT
CCCAAACTACCCAAGGATTATTTATTACTATTATCTTAGGAATTTATTTTACTATTCTTC
AAGCTTATGAATACATTGAAGCTCCATTTACTATTGCCGATTCAATTTATGGATCAACTT
TTTTTATAGCTACTGGATTCCACGGACTTCATGTAATTATTGGAACAATTTTTTTATTTA
TTTGTTTTTTACGTCATTTATCAGCACATTTTTCTAATAAACATCACTTTGGATTTGAAG
CAGCAGCATGATATTGACATTTTGTAGATGTAGTTTGATTATTCCTTTATATTTCTATTT
ACTGATGAGGTAATTAATTTATTTATATAATATATTTAGTATATTTGATTTCCAATCAAA
AAGTTTAATTTAAATTAATATAAATAATTATTTTCTTATTTATTATTTCAATTTTAATTA
TTTTAATTTCTAATATTATTATATTTTTAACAATTATCTTATCTAAGAAATCATTTATAG
ACCGAGAAAAAAATTCCCCATTTGAATGTGGATTCGACCCTAAATCTTCAGCACGAATTC
CATTTTCATTGCATTTTTTTTTAATTACAGTAATTTTTTTAATTTTTGATGTAGAAATTG
CCTTAATTTTCCCAATAATTTATTCTTTTAATTTAGTAAACTTTTATTCATTAATAAAAA
TTAGATTTTTTTTTTTAATTATACTTTTAATTGGACTTTACCATGAATGAAATCAAAATA
TATTAAATTGAACAAATTAGGATTATAGTTTATTTAAAACATTTGATTTGCATTCAAAAA
ATATTGAAATCAATTTATCTTAAATATGAAGCAATATCATGCATTTAATTTCGACTTAAA
AGAAAGAGTATTTTACTCCATATTTATTAATTGAAACCAAATAGAGGTATATCACTGTTA
ATGATATTAATGAATTTTTATTCCAATTAAAGAAATATAAAAATTAAGCTTCTAACTTAA
AATATAGTAGAAAATATCTATTAATATTTCTATTTATATAGTTTATTTAAAACATTACAT
TTTCATTGTAAAAATAAAAAGAATTTTTTTTATAAATATTTAAAGATTTAACAATCTCCT
TAATATCTTCAATATTATGCTCTAATTATAAGCTATTTAAATTTTATAATAATAATAATA
TTAAATAAAAAATTATTAATCAAAAAAAAAATCTAAATAAATAAATTTTAAAATTATTTA
TTTGATAAAAATTATAAAAAACAGAATAATTTTTGATAATATTAAATATACCTTGTCCTC
TATATAATTCTCTTCATCCTATATCAATATTCTTTAATAAACTTTGCCCTATTTTTAAAA
AATAAATATTTAATCCATAAGTAGAGAGATTTGGTATAAATCATATTAAACACAGAAAAT
TTCTTAAATTATAAGTCATTAAAAACTTATTAATTGAATAAATTTTTATATTTCTAATTA
AATACCCTAAAAATAAACCCATTAATATTACATAAATAACTATTATTTTTATATTAATAG
GTAAATAAATTATATAAGGATAATTAAAAATTATTCAACTTAAAAATCTACCTACAACTA
AACTTATAAATAATAACATAAATATTCTTTTTAATATTACATAATCTTCATCATATAAAT
TATAAACAACTATTAAATTATAATCATTTACTATTAAATAAAATAATAAACGAACAGTAT
AAAATATAGTTAATCCTGTTGAAAAATAATATAAAAAAAAAATTATTAAATTTAAATTTC
TTATTCTTACTATTTCTAAAATTATGTCCTTTGAATAAAACCCAGCTAAAAATGGAATAC
CACATAAAGCTAAATTTGAAATATTTAAACATAAACTTGTTAAAGGAATATAAAATCTAA
TTCCCCCTATATATCGAATATCTTGAATATCATTCATTATATGAATTACTACTCCAGCAC
ATATAAATAATAAAGCCTTAAATATAGCATGAGTTAATAAATGAAAAAAAGCTAAATCTG
GTATTCCTATTCTTAAAATTCTTATTATCAAACCTAATTGTCTTAATGTTGATAAAGCAA
TAATTTTCTTTAAATCAAACTCATAATTAGCGGAAATTCCCGCTATAAACATTGTTAAAC
CCGATAATAACAACAAAAACTTTAAAAAAATTATATCTACTAATATTATATTAAATCGAA
TTAATAAATAAACTCCCGCAGTTACTAGCGTTGAAGAATGAACTAAAGCTGAAACAGGAG
TAGGAGCTGCTATAGCAGCAGGTAATCACGATCTAAAAGGAATTTGAGCTCTTTTAGTTA
TAGCAGCAATAATTAATAAAAAACTAATAATTTTTATTATAAAATCATTATTTATAAAAT
TTAAAAAAAAAATATAATTTCATCTCCCATAATTTATTATTCAAGAAAATACTATTAAAA
TTATTACATCTCCAATTCGATTTGATAAAGCAGTTAATATACCAGCATTATAAGACTTAA
TATTTTGATAATAAATAACTAAACAATAAGAAACTAAGCCCAATCCATCTCAACCTAAAA
AAATTCTAATTATATTAGGTCTAATAATTAATAAAATTATAGAAAATACAAACAATAACA
CTAAAATAATAAAACGATTTAAGTTTAATTCTGAAGATATATATCTTTTTCTATAATAAA
TTACTGAAGATGAAATCATAGTTACAAATATTATAAATAATAATGATATTCAATCCAATA
AAATAGATATTACAATTTTTATAGAATTAAAAGAAATAATTTCTCACTCTAAAAAAAAAA
ATACATTTTCCATAATAAAATAAATCATAAAAAAAAAATTTATTATTCTAAAAAAAAATA
AAAAAAAAAAACTAATAAAACAAATTGAAAAATTTTTTATTTTAAATGAAACCTCATATT
TTTGATTCCACAAATCAATATTTTTACTTAAATTATTTAAATTAAAATCAAATTATAAAA
AAATCAATTTTTAAAATTAATAAATTTAATGGTAATCAATGTAATATTAATATTAAATAT
TCACGAGATACTCCAGTATAAAATCTATAAATTCTTATATTATATTTCCCATGTTGTGTA
TAAGAATATAAGTATAATCTATAACCAGCTCTAAAAAATGAAATCATAATAAGAATAATT
ATTGTTAAATAAGATCATCTAATAACTCTATTAATTAATCTAATTTCCCCTATTAAATTC
ATAGATGGAGGAGCTGCTATATTTGATGATATAATTAAAAATCACCATAAACTTATTGAA
GGCATAAAATTTATCATCCCCTTATTTATAAATAATCTACGACTATGTAATCGTTCGTAA
TTAATATTTGCCAAACAAAATATCCCTGAAGAACATAACCCATGTCCAATTATTATTACA
TATGAACCTAAATAACCTCAATAATTTATAGTTATAATCCCACAAATTACCAATCTTATA
TGAGCTACAGATGAATAAGCAATTAATGATTTCATGTCAACTTGGCAAAAACAATTTAAT
CTAATATATAAACCCCCTAATAATCTAATAATTACTCAAATTAATCTATATTTTATATTA
ATTTTTTGAAAAATAATTATAACTCGAAAAAGTCCATAACCACCTAATTTCAATATAATT
CCAGCTAAAATTATTGACCCTGAAACAGGAGCCTCCACATGAGCTTTTGGTAATCATAAA
TGAACAAAATATATAGGTATTTTAACTAAAAAAGCTAAAATTATTGATAAATATAATAAA
AAAAAATTCATATTATAAAACTTAAAAAAATATATAATCATACAATTATAATTATAAAAA
ATAAAAAAAATTCCTATTAATATTGGTAAAGAAGCAAATAAAGTATAAAATAATAAATAT
ATTCCTGCTTGAATTCGTTCTGGTTGATATCCTCACCCAATAATTAATATTAACGTAGGA
ATTAAACTCCCCTCAAAAAATAAATAAAACATAAATAAATTTAATACTCTAAAAGTTAAG
TATAACATAATTAATAAAATAATAATATTAAATATAAAAAAATTAATATAAAAATTTATC
TTATTTAAATTTTCTCTTGCTATAATTATCAATAAACAAATTCAAATTCTTAATAAAATT
AAGCCATAAGAAATTATATCACATCCTATCATATATGAAAGATTACAAAAATTTATAATA
TTTATATTTATATTTATAAATATAAATATTAATAATAATAAAAATATTTGAACCATTCAA
AATATATTATTTAAAAAACATAAAGGAATTATAAAAATTATCATTATTAAAAATTTTATC
ATTATAATATATTAAATCTTTGAAAATAATCATTTCCATGTGTCCGAATTATAGAAACTA
AAATTGATAAACCTAAAGCTCCTTCACAAACAGAAAATAATAAAAAAATTATTAATATAT
ATATGTCATATTCAATATAATTTAAATAAATAAGTATTAAAAAAAAAATTCTTAAAACAA
TAAATTCTAATCTTAATAAAACAATTAATAAATGTTTATGCTTAGAAATAAAAATTACAT
TACCAATAATAAATATTATAATAATAATTAATCATATATTTAATATTATCATTAGTTTTT
ATAGTTTAAATAAAACATTGGTCTTGTAAATCAAAAATAAGATTTTTCTTTAAAAACTTC
AAAGAAAAAGAACTTCTTTATCTATAATCTCCAAAATTATTATTTTTTATAAACTATTCT
TTGAAATAATAAAAATATTTCTTTCTTTATTAATTATTATATTTTCTATTATTATATTAT
TTTTAAATCATCCTTTATCTATAGGATTAATAATTTTAATTCAAACTCTTGTTATTTGTC
TTTTATCAGGAATATTAATTAACTCTTATTGATTTTCTTATATTTTATTCTTAGTATTTT
TAGGAGGCTTATTAGTTTTATTTATTTACGTTTCTAGAGTAGCCTCTAATGAATTATTTA
ATATAAATTTTTCTCTAAAAAATATTATATTTTTTCTTTTAATTATATCATTATTTTTAA
GATTTAACTATATAAATAATTTAAATTGACTAAATTTTTCATTTAACTACGAAATAAAAA
ACATAATAAATTTTTTTATTTTTTTTAATAATGAAAATAAAATTAATTTATCTAAATTAT
ATAATAATCAAAATTATATATTAATAATAATATTAATTACCTATTTATTTATTACTTTAG
TAGCTATTGTAAAAATTACAAATATTTTTTATGGTCCTATTCGATCTATCAATTACTAAT
TACTAATGATAAATAAATTTCCCCCATTACGAAAAACTCACCCATTATTTAAAATTATTA
ATAACTCATTAATTGATTTACCTTCTCCGTCTAATATTTCAGCTTGATGAAATTTTGGCT
CTCTTTTAGCATTATGTTTAATTATTCAAATTATTACAGGATTATTTTTAACTATATATT
ATACAGCTAATATTGAATTAGCTTTTTACAGAGTTAATTATATTTGTCGTAATGTTAATT
ACGGCTGATTAATTCGTACTCTTCATGCAAATGGAGCTTCTTTTTTCTTTATTTGTATTT
ACCTTCATATTGGACGAGGAATTTATTATGAATCCTTTAATCTAAAATATACATGAATAG
TAGGAATTATTATTTTATTTATTTTAATAGCAACAGCTTTTATAGGTTATGTCTTACCTT
GAGGACAAATATCTTTTTGAGGGGCTACAGTAATTACTAATTTACTTTCAGCTATTCCTT
ATTTAGGATCTATACTAGTTAATTGAATTTGAGGGGGATTTGCTATTGATAATGCAACCT
TAACACGATTTTATTCTTTCCATTTTCTATTCCCCTTTATTATTATAATATTAACTATAA
TTCATTTATTATTTTTACACCAAACTGGTTCTAATAACCCATTAGGATTAAATAGAAATT
TAGATAAAATTCCATTTCATCCTTTTTTTACTTTTAAGGACTTAATTGGATTTATTTTTT
TATTATTTTTTTTAAGATTATTAACTTTAACTAATCCTTATTTATTGGGAGATCCTGATA
ATTTTATACCTGCCAATCCTTTAGTTACTCCCATTCATATTCAACCTGAATGATATTTTT
TATTTGCATATGCTATTCTACGATCAATTCCTAATAAACTAGGAGGAGTTATTGCTTTAG
TTATATCTATTTTAATTTTAATTATTTTACCTTTAACTTTTAATAAAAAAATTCAAGGAA
TCCAATTCTATCCATTAAATCAATTTTTATTTTGATCTATAGTTACTACTATTATTCTTC
TTACTTGAGCCGGAGCCCGACCAGTAGAAGAACCTTATATTTTTACTAGCCAACTATTAA
CTTTATTATATTTCTCTTATTTTATTATTAACCCAATTATTAATAAATACTGAGATAATT
TAATTTTTAAATAATTATTAATTAATGAGCTTGTTAAAGCATTTGTTTTGAAAACTTAAG
AAAGAATCTTATATTCTATTAATTTATACTAAAAATATTAACTATTTAAAAAAAATTTTT
AATCCTAAAAAAAATAATAAAAAATTTAAAGAAACTGGTAAATATCTCTTTCAAGATAAA
TATATTAATTTATCGTAACGATAACGAGGTAAAGTCCCTCGAATTCAAACAAATATAAAA
GAAATAAATGATAATTTTAAATAAAAAATTAATCTTAGTCTATATCCTCCCATATATAAT
AAAATAAATAGTATACTTATAAAAAGAATTCTAGAATATTCAGATAAAAAAATTAAAGTA
AATCCCCCTCTTCTATACTCAACATTAAATCCTGAAACTAACTCTCTTTCCCCCTCAGCA
AAATCAAAAGGTGTTCGATTAGTTTCTGCCAATCTTGAAGATAATCAACACAATCTTAAA
GGTATTATTAAAAAAAAAAATCAAATAATTTCTTGATAAAAAAAAAAATCAATTATATTA
AAACTCATAATTATAATAATTCTTGATAATATAATTAAAGATAATCTAACTTCATATGAA
ATCGTTTGAGCTACAGCTCGTAATCCCCCTAATAAAGCATAATTTGAATTTGAAGACCAT
CCTGCAATTATTACTGTAAATACCCCAATTCTTGTACAACATAAAAAAAATAAAACTCCT
AAATTAAATCTAATTATATTAAAATAATAAGGAATTAATAATCAAGTTATTAAAGTAACG
ACTAATCTTACGACTGGAGAAAAATAATAAGCTATATAATTTGAATAATTAGGGAAAGTT
TGTTCTTTGACAAATAATTTAATAACATCAGCAAATGGTTGTAAAATTCCTATATATCCA
ACTTTATTAGGACCTTTTCGAATTTGAATATAACCTAAAGCTTGACGCTCTAATAAAGTT
AAAAAAGCAACCCCCACTATTACCCCAATAACCATAATTAACACTCCAATAATATATATA
TAAATATCATTTAATATCATTTACTATATATATAATAAATTATATATTTATGACTTCTAA
AATCATTACATTTTTCTGCCAAAATAGTTTTATAAATATTATTAATAATATTCATTTTTA
TAAAATTATTTTTAATATTTGATCCTTTCGTACTAAAATATTATTTTTATTTAAAGATAG
AAACCAACCTGGCTCACACCGGTTTGAACTCAGATCATGTAAGATTTTAATGATCGAACA
GATCAAAATTTTAAACTTTTGCATTTAAATTTTATTTTAATCCAACATCGAGGTCGCAAA
CTTTTTTTCCTATTTGAACTAAAAAAAAAAATTACGCTGTTATCCCTAAGGTAATTTTTT
CTTTTAATCAATATTAATGGATCATTTATTCATAAATTAATGTTAATTATTTAAAAAAGT
TAATTTAATTTTTCTGTCACCCCAACAAAATAATTTATTTAATTTTAATTTTAAAATTTA
CATATTAAAAAGAACCAAATAAATTATAAAACTCTTTAGGGTCTTCCCGTCTTTTAAAAT
TATTTAAGCTTTTTTACTAAAAAATTAGATTTTAAAAATTAATTACAGACAGTTTATATT
TCATCCAATCTTTCATACAGGTCCCCAATTAAAAGACAAAGGATGATGCTACCTTTGTAC
AGCCAAAATACTGCAGCCCTTTAAAATATTTATCAGGGGGCAGATTAAACTTTAAATTAT
TTCCAAAAAGACATGTTTTTGATAAACAAGTGAATATATAATTTTGCCGAATTCCTTTAA
TTAATTTTTAATAAATCATTATTTTTATAATTTTTATATACTAATTTTATCATTATATTT
AATTTTATCTTATTAAAATATATTTTTTTATAAAAATTTAAATTTTATATTAAATTTTAA
TTAAAATTAAATTATTTGTAAAAAATTATAATTTATTTAACAATTTAAATTTTAAAATTT
TAATTTTTTTTATTATTATTAATTATAAAAATTTATTTTAAAGCTTATCCCTTAAAATAT
TTAATATTAATTATTAAAATTTTTATTAATAAAATTTTAAAATATAATATTTAAAATTAA
ATTTTTTTCTAAAAAAACTAGATATTTTTAAAAACGATTAACATTTCATTTCTAATTAAT
TATTAAAAATAATTATTCTACATTAACTTTTATAATTAATTAACTCTTTTAAATTCGAGA
AATTTATATTTAGAAAATTTTATTAATAAACTCTGATACACAAGATACAATAAATTAAAT
TTACTTTTTTATAATTTTTATACTTATTTCAAAATTCTCTTACAATACTATTTCACTATA
AATTTTAAAATTTTTCCTATATATATACTCTAACCCCCATTAAAATATACCTTAAAAATT
TTTTTATTATTTTTTTTTTATTAATTTTTCCCCTCAAATTAATTAAATTTAATATCTTTT
CAATGTAAATGAAATACTTATTCAAGCTCTAATTTGTTCTTTCTAGAAACACTTTCCAGT
ACTTCTACTTTGTTACGACTTATTCCAATTTATAAATGAAAGCGACGGGCAATATGTACA
TATTTCAATTTTTAATCATTTTATCAAATTAAATAAAATTACATTTAAATCCACCTTCAA
ATATATATTAAAATATATTATTCATTTAATCATTTCTTATTGTAATCCATTATATTCTTA
ATTATAATCTGCATCTTGATCTGAATTAATTTAATTTTAAAATTTTTAAATATTATTTTT
ATTAAAAAATATTTTTTTAACAACGATATACAAAATATATAAATTAAGTAAATTTATTCG
TGGATTATCAATTATTAAACAGATTCCTCTAAATGAACTAAAATACCGCCAAATTATTTA
AGTTTCTATAAATAATTATATACTATTTTAGTATTTTTTATTTAATTTTTAATAATAGAG
TATCTAATTCTAGTTTTTTATAAAATTTAATAAATCATATTATTTATTAAAATTTTAATT
AAATTAAAATTTCACCTAATAATTTAATATTTAATTTAATCTATTAATATTTATTATTTA
CTAATAAAATTTATTTAAATGAAATTTATTAACTTTTTTATCTTTAAAAGATTTTTTTTT
TTGAGAATTTTCTCTGAGGGTGTTTTTTTAAATTTTAAAAAATATTTTTTTTTTAAAAAT
TATATAAATAGTGGAAAAAAATATAAATGTTTTTTGGTGTTGATAGGTTTAGTAAAATTT
TATTTATTCTGGGAAATTTTCGGGTGGTTTTTTAAATTTTTTAATTTTTAAAAAAATCCC
CTTTTATAAAATTTTTTATTAGGCCCTTATTAAACCCTTAAATAATTTTTTTTTTTTTTT
TTTT
Coverage 1x = 396
2016-09-15 08:05:05,201 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 50.0 % |########################/ ] remain : 00:00:00
2016-09-15 08:05:05,202 [INFO ] Compacting graph 50.0 % remain : 00:00:00
2016-09-15 08:05:05,344 [INFO ] Circle : 15184 bp coverage : 393x
Compacting graph 100.0 % |#################################################- ] remain : 00:00:00
2016-09-15 08:05:05,346 [INFO ] Compacting graph 100.0 % remain : 00:00:00
2016-09-15 08:05:05,356 [INFO ] Minimum stem coverage = 393
2016-09-15 08:05:05,496 [INFO ] Path is circular
>test.mito_2 seq_length=15184; coverage=393.0; circular=True; -1 : ACCCG->(15184)->AAAAC [393].{connection: 1}
ACCCGAAAATTTCCCAGAATAAATAAAATTTTACTAAACCTATCAACACCAAAAAACATT
TATATTTTTTTCCACTATTTATATAATTTTTAAAAAAAAAATATTTTTTAAAATTTAAAA
AAACACCCTCAGAGAAAATTCTCAAAAAAAAAAATCTTTTAAAGATAAAAAAGTTAATAA
ATTTCATTTAAATAAATTTTATTAGTAAATAATAAATATTAATAGATTAAATTAAATATT
AAATTATTAGGTGAAATTTTAATTTAATTAAAATTTTAATAAATAATATGATTTATTAAA
TTTTATAAAAAACTAGAATTAGATACTCTATTATTAAAAATTAAATAAAAAATACTAAAA
TAGTATATAATTATTTATAGAAACTTAAATAATTTGGCGGTATTTTAGTTCATTTAGAGG
AATCTGTTTAATAATTGATAATCCACGAATAAATTTACTTAATTTATATATTTTGTATAT
CGTTGTTAAAAAAATATTTTTTAATAAAAATAATATTTAAAAATTTTAAAATTAAATTAA
TTCAGATCAAGATGCAGATTATAATTAAGAATATAATGGATTACAATAAGAAATGATTAA
ATGAATAATATATTTTAATATATATTTGAAGGTGGATTTAAATGTAATTTTATTTAATTT
GATAAAATGATTAAAAATTGAAATATGTACATATTGCCCGTCGCTTTCATTTATAAATTG
GAATAAGTCGTAACAAAGTAGAAGTACTGGAAAGTGTTTCTAGAAAGAACAAATTAGAGC
TTGAATAAGTATTTCATTTACATTGAAAAGATATTAAATTTAATTAATTTGAGGGGAAAA
ATTAATAAAAAAAAAATAATAAAAAAATTTTTAAGGTATATTTTAATGGGGGTTAGAGTA
TATATATAGGAAAAATTTTAAAATTTATAGTGAAATAGTATTGTAAGAGAATTTTGAAAT
AAGTATAAAAATTATAAAAAAGTAAATTTAATTTATTGTATCTTGTGTATCAGAGTTTAT
TAATAAAATTTTCTAAATATAAATTTCTCGAATTTAAAAGAGTTAATTAATTATAAAAGT
TAATGTAGAATAATTATTTTTAATAATTAATTAGAAATGAAATGTTAATCGTTTTTAAAA
ATATCTAGTTTTTTTAGAAAAAAATTTAATTTTAAATATTATATTTTAAAATTTTATTAA
TAAAAATTTTAATAATTAATATTAAATATTTTAAGGGATAAGCTTTAAAATAAATTTTTA
TAATTAATAATAATAAAAAAAATTAAAATTTTAAAATTTAAATTGTTAAATAAATTATAA
TTTTTTACAAATAATTTAATTTTAATTAAAATTTAATATAAAATTTAAATTTTTATAAAA
AAATATATTTTAATAAGATAAAATTAAATATAATGATAAAATTAGTATATAAAAATTATA
AAAATAATGATTTATTAAAAATTAATTAAAGGAATTCGGCAAAATTATATATTCACTTGT
TTATCAAAAACATGTCTTTTTGGAAATAATTTAAAGTTTAATCTGCCCCCTGATAAATAT
TTTAAAGGGCTGCAGTATTTTGGCTGTACAAAGGTAGCATCATCCTTTGTCTTTTAATTG
GGGACCTGTATGAAAGATTGGATGAAATATAAACTGTCTGTAATTAATTTTTAAAATCTA
ATTTTTTAGTAAAAAAGCTTAAATAATTTTAAAAGACGGGAAGACCCTAAAGAGTTTTAT
AATTTATTTGGTTCTTTTTAATATGTAAATTTTAAAATTAAAATTAAATAAATTATTTTG
TTGGGGTGACAGAAAAATTAAATTAACTTTTTTAAATAATTAACATTAATTTATGAATAA
ATGATCCATTAATATTGATTAAAAGAAAAAATTACCTTAGGGATAACAGCGTAATTTTTT
TTTTTAGTTCAAATAGGAAAAAAAGTTTGCGACCTCGATGTTGGATTAAAATAAAATTTA
AATGCAAAAGTTTAAAATTTTGATCTGTTCGATCATTAAAATCTTACATGATCTGAGTTC
AAACCGGTGTGAGCCAGGTTGGTTTCTATCTTTAAATAAAAATAATATTTTAGTACGAAA
GGATCAAATATTAAAAATAATTTTATAAAAATGAATATTATTAATAATATTTATAAAACT
ATTTTGGCAGAAAAATGTAATGATTTTAGAAGTCATAAATATATAATTTATTATATATAT
AGTAAATGATATTAAATGATATTTATATATATATTATTGGAGTGTTAATTATGGTTATTG
GGGTAATAGTGGGGGTTGCTTTTTTAACTTTATTAGAGCGTCAAGCTTTAGGTTATATTC
AAATTCGAAAAGGTCCTAATAAAGTTGGATATATAGGAATTTTACAACCATTTGCTGATG
TTATTAAATTATTTGTCAAAGAACAAACTTTCCCTAATTATTCAAATTATATAGCTTATT
ATTTTTCTCCAGTCGTAAGATTAGTCGTTACTTTAATAACTTGATTATTAATTCCTTATT
ATTTTAATATAATTAGATTTAATTTAGGAGTTTTATTTTTTTTATGTTGTACAAGAATTG
GGGTATTTACAGTAATAATTGCAGGATGGTCTTCAAATTCAAATTATGCTTTATTAGGGG
GATTACGAGCTGTAGCTCAAACGATTTCATATGAAGTTAGATTATCTTTAATTATATTAT
CAAGAATTATTATAATTATGAGTTTTAATATAATTGATTTTTTTTTTTATCAAGAAATTA
TTTGATTTTTTTTTTTAATAATACCTTTAAGATTGTGTTGATTATCTTCAAGATTGGCAG
AAACTAATCGAACACCTTTTGATTTTGCTGAGGGGGAAAGAGAGTTAGTTTCAGGATTTA
ATGTTGAGTATAGAAGAGGGGGATTTACTTTAATTTTTTTATCTGAATATTCTAGAATTC
TTTTTATAAGTATACTATTTATTTTATTATATATGGGAGGATATAGACTAAGATTAATTT
TTTATTTAAAATTATCATTTATTTCTTTTATATTTGTTTGAATTCGAGGGACTTTACCTC
GTTATCGTTACGATAAATTAATATATTTATCTTGAAAGAGATATTTACCAGTTTCTTTAA
ATTTTTTATTATTTTTTTTAGGATTAAAAATTTTTTTTAAATAGTTAATATTTTTAGTAT
AAATTAATAGAATATAAGATTCTTTCTTAAGTTTTCAAAACAAATGCTTTAACAAGCTCA
TTAATTAATAATTATTTAAAAATTAAATTATCTCAGTATTTATTAATAATTGGGTTAATA
ATAAAATAAGAGAAATATAATAAAGTTAATAGTTGGCTAGTAAAAATATAAGGTTCTTCT
ACTGGTCGGGCTCCGGCTCAAGTAAGAAGAATAATAGTAGTAACTATAGATCAAAATAAA
AATTGATTTAATGGATAGAATTGGATTCCTTGAATTTTTTTATTAAAAGTTAAAGGTAAA
ATAATTAAAATTAAAATAGATATAACTAAAGCAATAACTCCTCCTAGTTTATTAGGAATT
GATCGTAGAATAGCATATGCAAATAAAAAATATCATTCAGGTTGAATATGAATGGGAGTA
ACTAAAGGATTGGCAGGTATAAAATTATCAGGATCTCCCAATAAATAAGGATTAGTTAAA
GTTAATAATCTTAAAAAAAATAATAAAAAAATAAATCCAATTAAGTCCTTAAAAGTAAAA
AAAGGATGAAATGGAATTTTATCTAAATTTCTATTTAATCCTAATGGGTTATTAGAACCA
GTTTGGTGTAAAAATAATAAATGAATTATAGTTAATATTATAATAATAAAGGGGAATAGA
AAATGGAAAGAATAAAATCGTGTTAAGGTTGCATTATCAATAGCAAATCCCCCTCAAATT
CAATTAACTAGTATAGATCCTAAATAAGGAATAGCTGAAAGTAAATTAGTAATTACTGTA
GCCCCTCAAAAAGATATTTGTCCTCAAGGTAAGACATAACCTATAAAAGCTGTTGCTATT
AAAATAAATAAAATAATAATTCCTACTATTCATGTATATTTTAGATTAAAGGATTCATAA
TAAATTCCTCGTCCAATATGAAGGTAAATACAAATAAAGAAAAAAGAAGCTCCATTTGCA
TGAAGAGTACGAATTAATCAGCCGTAATTAACATTACGACAAATATAATTAACTCTGTAA
AAAGCTAATTCAATATTAGCTGTATAATATATAGTTAAAAATAATCCTGTAATAATTTGA
ATAATTAAACATAATGCTAAAAGAGAGCCAAAATTTCATCAAGCTGAAATATTAGACGGA
GAAGGTAAATCAATTAATGAGTTATTAATAATTTTAAATAATGGGTGAGTTTTTCGTAAT
GGGGGAAATTTATTTATCATTAGTAATTAGTAATTGATAGATCGAATAGGACCATAAAAA
ATATTTGTAATTTTTACAATAGCTACTAAAGTAATAAATAAATAGGTAATTAATATTATT
ATTAATATATAATTTTGATTATTATATAATTTAGATAAATTAATTTTATTTTCATTATTA
AAAAAAATAAAAAAATTTATTATGTTTTTTATTTCGTAGTTAAATGAAAAATTTAGTCAA
TTTAAATTATTTATATAGTTAAATCTTAAAAATAATGATATAATTAAAAGAAAAAATATA
ATATTTTTTAGAGAAAAATTTATATTAAATAATTCATTAGAGGCTACTCTAGAAACGTAA
ATAAATAAAACTAATAAGCCTCCTAAAAATACTAAGAATAAAATATAAGAAAATCAATAA
GAGTTAATTAATATTCCTGATAAAAGACAAATAACAAGAGTTTGAATTAAAATTATTAAT
CCTATAGATAAAGGATGATTTAAAAATAATATAATAATAGAAAATATAATAATTAATAAA
GAAAGAAATATTTTTATTATTTCAAAGAATAGTTTATAAAAAATAATAATTTTGGAGATT
ATAGATAAAGAAGTTCTTTTTCTTTGAAGTTTTTAAAGAAAAATCTTATTTTTGATTTAC
AAGACCAATGTTTTATTTAAACTATAAAAACTAATGATAATATTAAATATATGATTAATT
ATTATTATAATATTTATTATTGGTAATGTAATTTTTATTTCTAAGCATAAACATTTATTA
ATTGTTTTATTAAGATTAGAATTTATTGTTTTAAGAATTTTTTTTTTAATACTTATTTAT
TTAAATTATATTGAATATGACATATATATATTAATAATTTTTTTATTATTTTCTGTTTGT
GAAGGAGCTTTAGGTTTATCAATTTTAGTTTCTATAATTCGGACACATGGAAATGATTAT
TTTCAAAGATTTAATATATTATAATGATAAAATTTTTAATAATGATAATTTTTATAATTC
CTTTATGTTTTTTAAATAATATATTTTGAATGGTTCAAATATTTTTATTATTATTAATAT
TTATATTTATAAATATAAATATAAATATTATAAATTTTTGTAATCTTTCATATATGATAG
GATGTGATATAATTTCTTATGGCTTAATTTTATTAAGAATTTGAATTTGTTTATTGATAA
TTATAGCAAGAGAAAATTTAAATAAGATAAATTTTTATATTAATTTTTTTATATTTAATA
TTATTATTTTATTAATTATGTTATACTTAACTTTTAGAGTATTAAATTTATTTATGTTTT
ATTTATTTTTTGAGGGGAGTTTAATTCCTACGTTAATATTAATTATTGGGTGAGGATATC
AACCAGAACGAATTCAAGCAGGAATATATTTATTATTTTATACTTTATTTGCTTCTTTAC
CAATATTAATAGGAATTTTTTTTATTTTTTATAATTATAATTGTATGATTATATATTTTT
TTAAGTTTTATAATATGAATTTTTTTTTATTATATTTATCAATAATTTTAGCTTTTTTAG
TTAAAATACCTATATATTTTGTTCATTTATGATTACCAAAAGCTCATGTGGAGGCTCCTG
TTTCAGGGTCAATAATTTTAGCTGGAATTATATTGAAATTAGGTGGTTATGGACTTTTTC
GAGTTATAATTATTTTTCAAAAAATTAATATAAAATATAGATTAATTTGAGTAATTATTA
GATTATTAGGGGGTTTATATATTAGATTAAATTGTTTTTGCCAAGTTGACATGAAATCAT
TAATTGCTTATTCATCTGTAGCTCATATAAGATTGGTAATTTGTGGGATTATAACTATAA
ATTATTGAGGTTATTTAGGTTCATATGTAATAATAATTGGACATGGGTTATGTTCTTCAG
GGATATTTTGTTTGGCAAATATTAATTACGAACGATTACATAGTCGTAGATTATTTATAA
ATAAGGGGATGATAAATTTTATGCCTTCAATAAGTTTATGGTGATTTTTAATTATATCAT
CAAATATAGCAGCTCCTCCATCTATGAATTTAATAGGGGAAATTAGATTAATTAATAGAG
TTATTAGATGATCTTATTTAACAATAATTATTCTTATTATGATTTCATTTTTTAGAGCTG
GTTATAGATTATACTTATATTCTTATACACAACATGGGAAATATAATATAAGAATTTATA
GATTTTATACTGGAGTATCTCGTGAATATTTAATATTAATATTACATTGATTACCATTAA
ATTTATTAATTTTAAAAATTGATTTTTTTATAATTTGATTTTAATTTAAATAATTTAAGT
AAAAATATTGATTTGTGGAATCAAAAATATGAGGTTTCATTTAAAATAAAAAATTTTTCA
ATTTGTTTTATTAGTTTTTTTTTTTTATTTTTTTTTAGAATAATAAATTTTTTTTTTATG
ATTTATTTTATTATGGAAAATGTATTTTTTTTTTTAGAGTGAGAAATTATTTCTTTTAAT
TCTATAAAAATTGTAATATCTATTTTATTGGATTGAATATCATTATTATTTATAATATTT
GTAACTATGATTTCATCTTCAGTAATTTATTATAGAAAAAGATATATATCTTCAGAATTA
AACTTAAATCGTTTTATTATTTTAGTGTTATTGTTTGTATTTTCTATAATTTTATTAATT
ATTAGACCTAATATAATTAGAATTTTTTTAGGTTGAGATGGATTGGGCTTAGTTTCTTAT
TGTTTAGTTATTTATTATCAAAATATTAAGTCTTATAATGCTGGTATATTAACTGCTTTA
TCAAATCGAATTGGAGATGTAATAATTTTAATAGTATTTTCTTGAATAATAAATTATGGG
AGATGAAATTATATTTTTTTTTTAAATTTTATAAATAATGATTTTATAATAAAAATTATT
AGTTTTTTATTAATTATTGCTGCTATAACTAAAAGAGCTCAAATTCCTTTTAGATCGTGA
TTACCTGCTGCTATAGCAGCTCCTACTCCTGTTTCAGCTTTAGTTCATTCTTCAACGCTA
GTAACTGCGGGAGTTTATTTATTAATTCGATTTAATATAATATTAGTAGATATAATTTTT
TTAAAGTTTTTGTTGTTATTATCGGGTTTAACAATGTTTATAGCGGGAATTTCCGCTAAT
TATGAGTTTGATTTAAAGAAAATTATTGCTTTATCAACATTAAGACAATTAGGTTTGATA
ATAAGAATTTTAAGAATAGGAATACCAGATTTAGCTTTTTTTCATTTATTAACTCATGCT
ATATTTAAGGCTTTATTATTTATATGTGCTGGAGTAGTAATTCATATAATGAATGATATT
CAAGATATTCGATATATAGGGGGAATTAGATTTTATATTCCTTTAACAAGTTTATGTTTA
AATATTTCAAATTTAGCTTTATGTGGTATTCCATTTTTAGCTGGGTTTTATTCAAAGGAC
ATAATTTTAGAAATAGTAAGAATAAGAAATTTAAATTTAATAATTTTTTTTTTATATTAT
TTTTCAACAGGATTAACTATATTTTATACTGTTCGTTTATTATTTTATTTAATAGTAAAT
GATTATAATTTAATAGTTGTTTATAATTTATATGATGAAGATTATGTAATATTAAAAAGA
ATATTTATGTTATTATTTATAAGTTTAGTTGTAGGTAGATTTTTAAGTTGAATAATTTTT
AATTATCCTTATATAATTTATTTACCTATTAATATAAAAATAATAGTTATTTATGTAATA
TTAATGGGTTTATTTTTAGGGTATTTAATTAGAAATATAAAAATTTATTCAATTAATAAG
TTTTTAATGACTTATAATTTAAGAAATTTTCTGTGTTTAATATGATTTATACCAAATCTC
TCTACTTATGGATTAAATATTTATTTTTTAAAAATAGGGCAAAGTTTATTAAAGAATATT
GATATAGGATGAAGAGAATTATATAGAGGACAAGGTATATTTAATATTATCAAAAATTAT
TCTGTTTTTTATAATTTTTATCAAATAAATAATTTTAAAATTTATTTATTTAGATTTTTT
TTTTGATTAATAATTTTTTATTTAATATTATTATTATTATAAAATTTAAATAGCTTATAA
TTAGAGCATAATATTGAAGATATTAAGGAGATTGTTAAATCTTTAAATATTTATAAAAAA
AATTCTTTTTATTTTTACAATGAAAATGTAATGTTTTAAATAAACTATATAAATAGAAAT
ATTAATAGATATTTTCTACTATATTTTAAGTTAGAAGCTTAATTTTTATATTTCTTTAAT
TGGAATAAAAATTCATTAATATCATTAACAGTGATATACCTCTATTTGGTTTCAATTAAT
AAATATGGAGTAAAATACTCTTTCTTTTAAGTCGAAATTAAATGCATGATATTGCTTCAT
ATTTAAGATAAATTGATTTCAATATTTTTTGAATGCAAATCAAATGTTTTAAATAAACTA
TAATCCTAATTTGTTCAATTTAATATATTTTGATTTCATTCATGGTAAAGTCCAATTAAA
AGTATAATTAAAAAAAAAAATCTAATTTTTATTAATGAATAAAAGTTTACTAAATTAAAA
GAATAAATTATTGGGAAAATTAAGGCAATTTCTACATCAAAAATTAAAAAAATTACTGTA
ATTAAAAAAAAATGCAATGAAAATGGAATTCGTGCTGAAGATTTAGGGTCGAATCCACAT
TCAAATGGGGAATTTTTTTCTCGGTCTATAAATGATTTCTTAGATAAGATAATTGTTAAA
AATATAATAATATTAGAAATTAAAATAATTAAAATTGAAATAATAAATAAGAAAATAATT
ATTTATATTAATTTAAATTAAACTTTTTGATTGGAAATCAAATATACTAAATATATTATA
TAAATAAATTAATTACCTCATCAGTAAATAGAAATATAAAGGAATAATCAAACTACATCT
ACAAAATGTCAATATCATGCTGCTGCTTCAAATCCAAAGTGATGTTTATTAGAAAAATGT
GCTGATAAATGACGTAAAAAACAAATAAATAAAAAAATTGTTCCAATAATTACATGAAGT
CCGTGGAATCCAGTAGCTATAAAAAAAGTTGATCCATAAATTGAATCGGCAATAGTAAAT
GGAGCTTCAATGTATTCATAAGCTTGAAGAATAGTAAAATAAATTCCTAAGATAATAGTA
ATAAATAATCCTTGGGTAGTTTGGGAGAAATTATTTTCTATAATTGCATGATGAGCTCAA
GTTACTGAAACTCCTGATGTAATTAGAATAATAGTATTTAGAAGGGGAATTTGAAAGGGG
TTAAAAGGAATAATTCTAGAAGGAGGTCATATAGCTCCAATATCAATATTAGGGGATAAA
CTTCTATGAAAAAAAGCTCAAAAAAAAGAAATAAAAAAAAAAATTTCAGAGATAATAAAT
AAAATTATTCCTCATCGTAATCCTTTCGAAACTAAAATAGTATGACTACCTTGATATGTT
CCTTCTCGACAAATATCTCGTCATCATTGATATATAGTTAATAAAATAATTATATAACCT
AAAATTATTAAATTTATGTTAAATTCATGAAATCATTTAATTATTCCTGTAACTAATGTT
ATTACACCAATTGCTCCAGTTAATGGTCAAGGACTATAATCTACTAAGTGAAAAGGGTGG
TTGTTATTTATTGACATTAGTTATTAATTAACTTCTCTAGAATATAGTGTTCTTAAAATA
GAAATTACATAGGCTTGAATAACTGCAACTGCTGATTCTAAAATTAATAATAAAATTTGT
ATAAAAATTAAAATAAATAATAAATAAAATGATAAACTATTACTAGTTCTTCTTAGAAGA
GTTAATAATAAATGACCGGCAATTATATTAGCAGATAGACGAACAGCTAATGTTCCAGGA
CGAATAATATTTCTAATTGTTTCAATTATTACTATAAAAGGCATTAAAATTGAAGGAGTT
CCTTGCGGGATTATATGGATAAATATATGTTGATAGTTATTAATTCAACCATATAATATA
AATCTTAATCATAAAGAAAGAGAAATAGATAAAGAGATAGTAAGATGTCTAGTTCTTGTA
AAAATATAGGGAAATAATCCTAAAAAATTATTAAATAAGATAAAAGAAAATAAGGAGATA
AAAATAAAAGTTGATCCTTTATTAAGTTTATTATTTCCTAATAATATTTTAAATTCATTG
TGAAGTTTGTTAAGAATAAAATTTCAAAAAATAAATTGTCGATTTGGAATAAGTCAAAAA
GAGTAAGGAATAAATAATAATCCAATAAATGTTCTAATTCAATTTAACGATAAGTTAAAA
ATATTAGTAGAAGGATCAAAAATAGAAAATAAATTATTTATCATTTTCAATTTAAATTGT
TAAAATTTTTATTAATGAATTTATTATTTAATATATTATTATTATTATTAATAAAAATAT
AATAGTTTATAATATTAAAAATAATAAAAATTACAATAAATAAAATAAAAGAAAGAATTC
AGTTAATTGGTATTATTTGAGGGATAAAAGAATATTACTAGAGTAATAATTTAAATTTGA
CATATTTATGTTATATTTTAACTAATTCTTTCATTAGAAGTAATTGCTAATTTACTATAA
AATGGTTTAAGAGACCAGTACTTGCTTTCAGTCATCTAATGAGGAATAATTATTAATTCA
ATTAATAAAATTTTTAATTGAAATTCTTTCAATTATAATAGGCATAAATCTGTGATTAGC
CCCACAAATTTCTGAACATTGACCAAAAAAAATACCTGGTCGATTAATAAATAAATTAGT
TTGATTTAATCGACCAGGATTAGCGTCAATTTTAACCCCTAAAGAGGGGATGGTTCATGA
ATGAATAACATCTGTAGCGGTAACTATAATTCGAATTTGATTATTTATAGGTAAAATAAT
TCGATTATCAACATCTAATAATCGAAAATTATTAATATTAGAATTATCATAATTAATTAT
ATAAGAATCGAATTCTACATTATTAAAATCAGAATATTCATAACTTCAATATCATTGATG
ACCAATTGATTTTAGTGTAATTAAAGGATTATTTAGTTCATCTAATAAATATAATAAGCG
TAATGAAGGAAGAGCAATAAAAATTAAAGTAATAGTAGGAATAATAGTTCAAATTAATTC
AATTATTTGTCCTTCTAGTAAAAAACGATTAATATATTTGTTAAAAAATAAATTAATTAT
TAAGTAACCTACTAAAATAGTAATTATAATTAAAATAATTAAAGTATGGTCATGAAAAAA
AATAATTTGTTCTATTAAAGGAGAAGCTCTATTTTGAAGATTAAAATTAGATCAAGTAGC
CATTTCTAAAAAAAGGATAAACCTTTATTGATGGGGTTTAAATCCATTACATATAATCTG
TCATATTAGAAGTTTCTTAAAATAGGAAGTTCATTATATGAATGTTCAGCAGGTGGTAAA
TTTTGTAATCATTCAATAGAAGAAGGTATATTAAGAGAAAATAAAATAATTCGTTGATTA
ATAAATGATTCTCAAATAATTATTATTATTATTATAAAAGATAATAAAGAAATATATGAT
CCAAAAGAAGATAAAATATTTCAAGATATATAATTATCTGGGTAATCAGAATAACGACGA
GGTATACCTGCTAACCCTAAAAAATGTTGAGGGAAAAAAGTTAAATTAACTCCAATAAAT
ATAGTAAAAAATTGGATTTTTAAATAATATGAATTTAATGAAAGTCCAGTAAATAAAGGA
TATCAATGAATAAATCTTCCTATAATAGCAAATACAGCTCCTATAGATAAAACATAATGA
AAGTGAGCTACTACATAATAAGTATCATGTAATGTTACATCAATAGATGAATTAGCAAGA
ATTACACCAGTTAATCCTCCTACTGTAAAAAGAAAAACAAATCCTAATCTTCATAGAATT
GATGGACTGTAATTGATTTGTGTTCCATGGAAAGTAGCTAATCAACTAAAAATTTTAATA
CCTGTAGGAACTGCAATAATTATTGTTGCTGAAGTAAAATAAGCTCGAGTATCCGTATCT
ATTCCTACAGTAAATATATGATGAGCTCAAACAATAAATCCTAATAAACCAATTGCTATT
ATTGCATAAATTATTCCTAAACATCCAAATGTTTCTTTTTTCCCTCTTTCTTGGGAAATA
ATATGAGAAATTATTCCAAATCCAGGTAAAATTAAAATGTAAACTTCTGGGTGCCCAAAA
AATCAAAATAAATGTTGGTATAAAATAGGATCTCCTCCCCCAGCAGGATCAAAAAAAGAA
GTATTTAAATTTCGATCTGTTAATAATATAGTAATAGCTCCAGCTAAAACTGGTAAGGAA
AGAAGTAATAATAAAGCTGTAATTCCAACAGCTCAAACAAATAAAGGTATTTGATCAAAT
GATATATTATTAATACGTATATTAATAATTGTTGTGATGAAATTAATTGCTCCTAAAATT
GATGAGATACCTGCTAAATGTAAAGAAAAAATAACTAAATCTACTGATCTTCTTCCATGT
GCAATGTTAGAAGAGAGAGGGGGGTAAACAGTTCAACCAGTTCCAGCTCCATTTTCTACA
ATTATTCTTGAAATTAAAAGAGTTAATGAAGGAGGTAATAATCAAAATCTTATATTATTT
ATTCGGGGGAAAGCTATGTCAGGGGCTCCCAATATTAAAGGAATTAATCAATTTCCAAAT
CCTCCAATTATAATAGGTATAACTATAAAAAAAATTATAATAAAAGCGTGAGCTGTAACA
ATAGTATTATAAATTTGATCATCTCCAATTAATGAACCTGGTGTTCCTAATTCAGTTCGA
ATTAATAAACTAAGAGAAGTTCCTAATATACTTGCTCAAATACCAAAAATAAAATATAAT
GTTCCAATATCTTTATGATTTGTTGAATAAAGTCATTTTCGCTAATAAAATGGCTGAATT
ATAAGCGATAAATTGTAAATTTATTTATGAGAAAAATCTCTTTTATTAAGCTTTATAGTC
AATTATGATATAAAATTGCAAATTTTAAGGAGTATAATAATAAATTACTAAGGCTTAAAG
AATTTCTTTTTTTATAATTTTGAAGATTATTAGTTTATTATAACTTAAAACCTTATAGAT
AGACAAAAGTTCTAATAATTATACCTAATAATGAAATTATTCTAGAAAAATTAATAATTA
ATATTGAATTATTTTTTAAATAAAATTTAAATCATTTTAATTTTAAATAATTAAATGTAA
TTGAAGAATAAATAATTCGAATATATAAAAATAATATAATTAATCTTATTATAATAAAAA
TAAATGTAATTATAAAAAAATTATTTGTGATTAAAAAATTAATAGTAATTCATTTAGGAA
AAAATCCTAAGAATGGAGGTAATCCTCCTAATGATAAAAAATTAATTAATAAAGAAATTT
TAATAATAGGATTTATATTAATGATAAATAATTGATTTAAAAAATAAGTATTTATTAAAT
TGAATATAAAACATATAATTCTAATTAAAAAGGAATATATAATTAAATAAAATATTCATA
AATTTTCTCTAATTATTAAAGCAGCTAATATTCAACCTAAATTATTAATTGAAGAAAAAG
ATATTAATTTACGTAAAGAAGTTTGATTAATACCCCCTAGAACACCAATAATAACATTAA
TAATTATAATTATTATTAAAAAATTATTATTTATATAATAGGAAAGTAAAATTATAGGGG
AAATTTTTTGTCAAGTTATTAATATAAAACAATTAATTCAGGATAAACCTTCAACAATAT
TGGGGAATCAAAAGTGAAATGGGGCAGATCCTATTTTTATTAATAATGAAGAATCAATTA
TAATTGAAATTAAATTATTAATTTCAAAATTTTTTAATAAAATTATTTTAATTAGAATAG
AAAACAAAAAATTAATAGAAGCAATAGCTTGTGTTAAAAAATATTTTAGTGCTGCTTCAG
AAGATAAAAGATTTTTATACCTAGAAATTAGGGGGATAAATCTAAGTAAATTAATTTCAA
GTCCAATCCAACACCCTAATCAAGAATTAGAAGAAATTGAAATTAAAGTTCTAAAAATTA
AAATAAAATAAAAAAATATTTTATTTGAATTAATATTTAAAAAAATTTAAAATGGGGGAA
TTAAATTAAATTAAAAATTTAATATAATTTATTTATATTTATATATTTTAGTGTAGGGGC
ACAATAATTTTTGATATTATTAGATATAGTTAAATTCTATAAAATATAATAAAGGTAGAA
TTCTACTTAATTTATCCTATCAGAATAATCCTTTAATCAGGCACTTTATTTTTAAAAAAA
AGGGATTTCCTTTATATTTGGGGTATGAACCCAAAAGCTTATTTTAGCTTATTTTTAATT
TTATTTTTTTTTATTTATATAAATATTTATATGGAATGGTTTAGTAAAAAAATAAAAATA
TTATATAAATTATTAATAGTAAAAAAAAAATTAAGGTTTTTAAATTTTTTTAGTAATATA
TATATATATATATTAAAAATTTAATATATTAATATATTTAATAATATAATAAAAATATTT
AATTTATTAATATATAAATTAATATATTATAATTTTTTAGTTTTTAAAATTTTATATAGC
AATTTAGGTATTTAATATTTATTATGAAAAAAAAAAAAAAAAAAATTATTTAAGGGTTTA
ATAAGGGCCTAATAAAAAATTTTATAAAAGGGGATTTTTTTAAAAATTAAAAAATTTAAA
AAAC
(ORG.asm-0.2.07) ls -l
total 4704
-rwxr-xr-x@ 1 jeankeller staff 1201837 6 sep 14:52 papi_R1.fastq.gz
-rwxr-xr-x@ 1 jeankeller staff 1202027 6 sep 14:52 papi_R2.fastq.gz
drwxr-xr-x 9 jeankeller staff 306 15 sep 08:05 test.mito.oas
drwxr-xr-x 7 jeankeller staff 238 15 sep 08:02 test.odx
(ORG.asm-0.2.07)
(ORG.asm-0.2.07) cd test.mito.oas/
(ORG.asm-0.2.07) ls -l
total 4784
-rw-r--r-- 1 jeankeller staff 423740 15 sep 08:03 assembling.gml
-rw-r--r-- 1 jeankeller staff 423740 15 sep 08:03 assembling.intermediate.gml
-rw-r--r-- 1 jeankeller staff 417567 15 sep 08:03 assembling.intermediate.oax
-rw-r--r-- 1 jeankeller staff 417567 15 sep 08:03 assembling.oax
-rw-r--r-- 1 jeankeller staff 328285 15 sep 08:02 assembling.omx
-rw-r--r-- 1 jeankeller staff 5 15 sep 08:05 assembling.path
-rw-r--r-- 1 jeankeller staff 423878 15 sep 08:05 assembling.path.gml
(ORG.asm-0.2.07)
(ORG.asm-0.2.07) cd ../test.odx/
(ORG.asm-0.2.07) ls -l
total 6680
-rw-r--r-- 1 jeankeller staff 2652776 15 sep 08:01 index.ofx
-rw-r--r-- 1 jeankeller staff 112 15 sep 08:01 index.ogx
-rw-r--r-- 1 jeankeller staff 378968 15 sep 08:01 index.opx
-rw-r--r-- 1 jeankeller staff 378968 15 sep 08:01 index.orx
drwxr-xr-x 2 jeankeller staff 68 15 sep 08:02 test.mito.oas
(ORG.asm-0.2.07) cd test.mito.oas/
(ORG.asm-0.2.07) ls -l
(ORG.asm-0.2.07)
https://git.metabarcoding.org/org-asm/org-asm/-/issues/40
indexing reads problems
2017-09-20T20:43:59Z
Xiao Zhong
indexing reads problems
./oa index test papi_R1.fastq.gz papi_R2.fastq.gz
2016-05-17 10:36:10,321 [INFO ] Forward file compressed by gzip
2016-05-17 10:36:10,340 [INFO ] Reverse file compressed by gzip
2016-05-17 10:36:10,355 [INFO ] orgasmi -o test.odx/index /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-dvu88jkj /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-h5n8japu
2016-05-17 10:36:10,355 [INFO ] Starting indexing...
2016-05-17 10:36:10,355 [INFO ] orgasmi -o test.odx/index /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-dvu88jkj /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-h5n8japu
sh: orgasmi: command not found
[src/load.c:40] ERROR : Cannot open file test.odx/index.ogx
./oa index test papi_R1.fastq.gz papi_R2.fastq.gz
2016-05-17 10:36:10,321 [INFO ] Forward file compressed by gzip
2016-05-17 10:36:10,340 [INFO ] Reverse file compressed by gzip
2016-05-17 10:36:10,355 [INFO ] orgasmi -o test.odx/index /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-dvu88jkj /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-h5n8japu
2016-05-17 10:36:10,355 [INFO ] Starting indexing...
2016-05-17 10:36:10,355 [INFO ] orgasmi -o test.odx/index /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-dvu88jkj /scratchfs/xzhong/tmpdir/tmpinozjhdf/unziped-h5n8japu
sh: orgasmi: command not found
[src/load.c:40] ERROR : Cannot open file test.odx/index.ogx
https://git.metabarcoding.org/org-asm/org-asm/-/issues/37
oa index issue
2017-09-20T20:43:59Z
Rob Ness
oa index issue
For some reason when I run oa index with the parameter estimate-length I get an error that it can not open files in[INDEX].odx/index.* -- I don't remember in an older version of the program that these commands (index, seeds, buildgraph) created new folders but the version I have now seems to do this. Oddly when I exclude the --estimate-length option it works fine despite that it has to create the same [INDEX].odx/* files
eg. Here are the errors
oa index --estimate-length 0.9 sample1 $fwd $rev
...
[src/buildindex.c:50] ERROR : Cannot open file sample1.odx/index.ofx
2016-04-28 14:55:46,578 [INFO ] Done.
[src/load.c:40] ERROR : Cannot open file sample1.odx/index.ogx
For some reason when I run oa index with the parameter estimate-length I get an error that it can not open files in[INDEX].odx/index.* -- I don't remember in an older version of the program that these commands (index, seeds, buildgraph) created new folders but the version I have now seems to do this. Oddly when I exclude the --estimate-length option it works fine despite that it has to create the same [INDEX].odx/* files
eg. Here are the errors
oa index --estimate-length 0.9 sample1 $fwd $rev
...
[src/buildindex.c:50] ERROR : Cannot open file sample1.odx/index.ofx
2016-04-28 14:55:46,578 [INFO ] Done.
[src/load.c:40] ERROR : Cannot open file sample1.odx/index.ogx
https://git.metabarcoding.org/org-asm/org-asm/-/issues/35
oa clone crash when the destination directory already existe
2017-09-20T20:43:59Z
Eric Coissac
oa clone crash when the destination directory already existe
```
oa clone AV.chloroplast AV.chloroplast.save
2016-04-22 17:06:21,962 [INFO ] Copying the assembly AV.chloroplast to AV.chloroplast.save
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.2.03/export/bin/oa", line 62, in <module>
config[root_config_name]['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.2.03/lib/python3.5/site-packages/orgasm/commands/clone.py", line 46, in run
"%s.oas" % config['clone']['dest'])
File "/applis/ciment/v2/stow/x86_64/gcc_4.6.2/python_3.5.0/lib/python3.5/shutil.py", line 309, in copytree
os.makedirs(dst)
File "/applis/ciment/v2/stow/x86_64/gcc_4.6.2/python_3.5.0/lib/python3.5/os.py", line 241, in makedirs
mkdir(name, mode)
FileExistsError: [Errno 17] File exists: 'AV.chloroplast.save.oas'
```
```
oa clone AV.chloroplast AV.chloroplast.save
2016-04-22 17:06:21,962 [INFO ] Copying the assembly AV.chloroplast to AV.chloroplast.save
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.2.03/export/bin/oa", line 62, in <module>
config[root_config_name]['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.2.03/lib/python3.5/site-packages/orgasm/commands/clone.py", line 46, in run
"%s.oas" % config['clone']['dest'])
File "/applis/ciment/v2/stow/x86_64/gcc_4.6.2/python_3.5.0/lib/python3.5/shutil.py", line 309, in copytree
os.makedirs(dst)
File "/applis/ciment/v2/stow/x86_64/gcc_4.6.2/python_3.5.0/lib/python3.5/os.py", line 241, in makedirs
mkdir(name, mode)
FileExistsError: [Errno 17] File exists: 'AV.chloroplast.save.oas'
```
https://git.metabarcoding.org/org-asm/org-asm/-/issues/32
Move the seed file in the oas directory
2017-09-20T20:43:59Z
Eric Coissac
Move the seed file in the oas directory
The omx file is still stored outside of the oas directory
The omx file is still stored outside of the oas directory
Eric Coissac
Eric Coissac
https://git.metabarcoding.org/org-asm/org-asm/-/issues/31
Store seed matches in a new way
2017-09-20T20:43:59Z
Eric Coissac
Store seed matches in a new way
With the restructuration of the *organelle assemble* files (#28) we can create an `.omx` file per seed set.
With the restructuration of the *organelle assemble* files (#28) we can create an `.omx` file per seed set.
https://git.metabarcoding.org/org-asm/org-asm/-/issues/30
A new way for managing seeds with the --seeds option in buildgraph
2017-09-20T20:43:59Z
Eric Coissac
A new way for managing seeds with the --seeds option in buildgraph
In relation with issue #27, the `--seeds` option have to change its behavior.
If the `--seeds <SEEDNAME>` option is added to the `buildgraph` command, the new seed set is added to the seed set collection and put the new seeds in the stack for the first graph extension step.
if the `--seeds <SEEDNAME>` is used in conjunction with the `--clean` option (#27) , all the previous seed sets are erased
In relation with issue #27, the `--seeds` option have to change its behavior.
If the `--seeds <SEEDNAME>` option is added to the `buildgraph` command, the new seed set is added to the seed set collection and put the new seeds in the stack for the first graph extension step.
if the `--seeds <SEEDNAME>` is used in conjunction with the `--clean` option (#27) , all the previous seed sets are erased
A new buildgraph command
https://git.metabarcoding.org/org-asm/org-asm/-/issues/29
Add a command 'clone' to copy an already built assembly graph
2017-09-20T20:43:59Z
Frédéric Boyer
Add a command 'clone' to copy an already built assembly graph
https://git.metabarcoding.org/org-asm/org-asm/-/issues/28
Group files for index or assembly under a directory
2017-09-20T20:43:59Z
Frédéric Boyer
Group files for index or assembly under a directory
Eric Coissac
Eric Coissac
https://git.metabarcoding.org/org-asm/org-asm/-/issues/27
Merge the buildgraph and fillgaps commands
2017-09-20T20:44:00Z
Eric Coissac
Merge the buildgraph and fillgaps commands
`buildgraph` and `fillgaps` do actually almost the same thing except that `fillgaps` runs on an already existing graph.
We propose to merge both the commands and to add a `--clean` option to `buildgraph` for reseting an eventually existing graph an restart an assembling from scratch
`buildgraph` and `fillgaps` do actually almost the same thing except that `fillgaps` runs on an already existing graph.
We propose to merge both the commands and to add a `--clean` option to `buildgraph` for reseting an eventually existing graph an restart an assembling from scratch
A new buildgraph command
https://git.metabarcoding.org/org-asm/org-asm/-/issues/23
bug in path
2017-09-20T20:44:00Z
Martí Boleda
bug in path
```{shell}
martiboleda@luke21:~/assembly/Alchemilla_incisa/DTV$ oa path --path -2 0 1 4 -3 -4 -- DTV chloroplast/DTV.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
7530152 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-10 17:04:35,538 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-10 17:04:35,539 [INFO ] ==> A total of : 23473
2016-02-10 17:04:35,539 [INFO ] Match list :
2016-02-10 17:04:35,543 [INFO ] rpl23 : 1758 (293.0x)
2016-02-10 17:04:35,543 [INFO ] rps7 : 2566 (256.6x)
2016-02-10 17:04:35,544 [INFO ] rpl14 : 1007 (255.9x)
2016-02-10 17:04:35,544 [INFO ] psbE : 641 (239.4x)
2016-02-10 17:04:35,544 [INFO ] psaC : 605 (231.5x)
2016-02-10 17:04:35,544 [INFO ] psbF : 269 (213.8x)
2016-02-10 17:04:35,544 [INFO ] atpH : 551 (210.9x)
2016-02-10 17:04:35,544 [INFO ] psbN : 292 (210.5x)
2016-02-10 17:04:35,544 [INFO ] rpl36 : 233 (195.2x)
2016-02-10 17:04:35,544 [INFO ] psbT : 201 (188.8x)
2016-02-10 17:04:35,544 [INFO ] rps12 : 1497 (188.6x)
2016-02-10 17:04:35,545 [INFO ] psbL : 231 (188.4x)
2016-02-10 17:04:35,545 [INFO ] psbM : 187 (170.5x)
2016-02-10 17:04:35,545 [INFO ] psbI : 194 (167.1x)
2016-02-10 17:04:35,545 [INFO ] rps2 : 1227 (161.2x)
2016-02-10 17:04:35,545 [INFO ] petG : 191 (160.0x)
2016-02-10 17:04:35,545 [INFO ] rbcL : 2433 (157.5x)
2016-02-10 17:04:35,545 [INFO ] psbC : 2223 (145.7x)
2016-02-10 17:04:35,545 [INFO ] rpl16 : 608 (139.6x)
2016-02-10 17:04:35,545 [INFO ] rps4 : 895 (138.0x)
2016-02-10 17:04:35,546 [INFO ] psbD : 1545 (135.7x)
2016-02-10 17:04:35,546 [INFO ] atpA : 2177 (133.1x)
2016-02-10 17:04:35,546 [INFO ] psbB : 2044 (124.7x)
2016-02-10 17:04:35,546 [INFO ] atpE : 523 (122.8x)
2016-02-10 17:04:35,546 [INFO ] psbZ : 236 (118.0x)
2016-02-10 17:04:35,546 [INFO ] atpB : 1824 (113.5x)
2016-02-10 17:04:35,546 [INFO ] rpoC1 : 2391 (109.0x)
2016-02-10 17:04:35,546 [INFO ] psaB : 2514 (106.2x)
2016-02-10 17:04:35,546 [INFO ] psbH : 249 (105.7x)
2016-02-10 17:04:35,546 [INFO ] psaA : 2472 (102.2x)
2016-02-10 17:04:35,547 [INFO ] psbK : 201 (102.1x)
2016-02-10 17:04:35,547 [INFO ] psbA : 1155 (101.4x)
2016-02-10 17:04:35,547 [INFO ] petA : 1032 (100.0x)
2016-02-10 17:04:35,547 [INFO ] ndhA : 898 ( 77.3x)
2016-02-10 17:04:35,547 [INFO ] rps18 : 246 ( 75.5x)
2016-02-10 17:04:35,547 [INFO ] clpP : 476 ( 75.3x)
2016-02-10 17:04:35,547 [INFO ] psbJ : 87 ( 67.4x)
2016-02-10 17:04:35,547 [INFO ] rpoB : 1886 ( 54.5x)
2016-02-10 17:04:35,547 [INFO ] rpoA : 507 ( 47.8x)
2016-02-10 17:04:35,548 [INFO ] rpl32 : 41 ( 24.4x)
2016-02-10 17:04:35,548 [INFO ] rps8 : 100 ( 23.1x)
2016-02-10 17:04:35,548 [INFO ] matK : 279 ( 17.2x)
2016-02-10 17:04:35,548 [INFO ] ccsA : 172 ( 16.3x)
2016-02-10 17:04:35,548 [INFO ] rpoC2 : 590 ( 13.3x)
2016-02-10 17:04:35,548 [INFO ] cemA : 89 ( 12.0x)
2016-02-10 17:04:35,548 [INFO ] accD : 127 ( 8.1x)
2016-02-10 17:04:35,548 [INFO ] ycf1 : 431 ( 6.3x)
2016-02-10 17:04:39,601 [INFO ] Evaluate fragment length
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-10 17:04:43,342 [INFO ] Fragment length estimated : 387.422754 pb (sd: 206.620446)
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-10 17:04:45,668 [INFO ] Print the result as a fasta file
2016-02-10 17:04:45,668 [INFO ] Built path : [-2, 0, 1, 4, -3, -4]
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-10 17:04:49,459 [INFO ] Both segments -2 and 1 are disconnected
2016-02-10 17:04:49,460 [INFO ] Connection is forced with only 2 pair ended links (gap length=101.000000 sd=0.000000)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.11/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.11/lib/python3.5/site-packages/orgasm/command/path.py", line 92, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.11/lib/python3.5/site-packages/orgasm/tango.py", line 1430, in path2fasta
label.append('{F-connection: %d - Gap length: %d, sd: %d}' % (connected,int(glenth),int(sl)))
NameError: name 'glenth' is not defined
martiboleda@luke21:~/assembly/Alchemilla_incisa/DTV$
```{shell}
martiboleda@luke21:~/assembly/Alchemilla_incisa/DTV$ oa path --path -2 0 1 4 -3 -4 -- DTV chloroplast/DTV.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
7530152 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-10 17:04:35,538 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-10 17:04:35,539 [INFO ] ==> A total of : 23473
2016-02-10 17:04:35,539 [INFO ] Match list :
2016-02-10 17:04:35,543 [INFO ] rpl23 : 1758 (293.0x)
2016-02-10 17:04:35,543 [INFO ] rps7 : 2566 (256.6x)
2016-02-10 17:04:35,544 [INFO ] rpl14 : 1007 (255.9x)
2016-02-10 17:04:35,544 [INFO ] psbE : 641 (239.4x)
2016-02-10 17:04:35,544 [INFO ] psaC : 605 (231.5x)
2016-02-10 17:04:35,544 [INFO ] psbF : 269 (213.8x)
2016-02-10 17:04:35,544 [INFO ] atpH : 551 (210.9x)
2016-02-10 17:04:35,544 [INFO ] psbN : 292 (210.5x)
2016-02-10 17:04:35,544 [INFO ] rpl36 : 233 (195.2x)
2016-02-10 17:04:35,544 [INFO ] psbT : 201 (188.8x)
2016-02-10 17:04:35,544 [INFO ] rps12 : 1497 (188.6x)
2016-02-10 17:04:35,545 [INFO ] psbL : 231 (188.4x)
2016-02-10 17:04:35,545 [INFO ] psbM : 187 (170.5x)
2016-02-10 17:04:35,545 [INFO ] psbI : 194 (167.1x)
2016-02-10 17:04:35,545 [INFO ] rps2 : 1227 (161.2x)
2016-02-10 17:04:35,545 [INFO ] petG : 191 (160.0x)
2016-02-10 17:04:35,545 [INFO ] rbcL : 2433 (157.5x)
2016-02-10 17:04:35,545 [INFO ] psbC : 2223 (145.7x)
2016-02-10 17:04:35,545 [INFO ] rpl16 : 608 (139.6x)
2016-02-10 17:04:35,545 [INFO ] rps4 : 895 (138.0x)
2016-02-10 17:04:35,546 [INFO ] psbD : 1545 (135.7x)
2016-02-10 17:04:35,546 [INFO ] atpA : 2177 (133.1x)
2016-02-10 17:04:35,546 [INFO ] psbB : 2044 (124.7x)
2016-02-10 17:04:35,546 [INFO ] atpE : 523 (122.8x)
2016-02-10 17:04:35,546 [INFO ] psbZ : 236 (118.0x)
2016-02-10 17:04:35,546 [INFO ] atpB : 1824 (113.5x)
2016-02-10 17:04:35,546 [INFO ] rpoC1 : 2391 (109.0x)
2016-02-10 17:04:35,546 [INFO ] psaB : 2514 (106.2x)
2016-02-10 17:04:35,546 [INFO ] psbH : 249 (105.7x)
2016-02-10 17:04:35,546 [INFO ] psaA : 2472 (102.2x)
2016-02-10 17:04:35,547 [INFO ] psbK : 201 (102.1x)
2016-02-10 17:04:35,547 [INFO ] psbA : 1155 (101.4x)
2016-02-10 17:04:35,547 [INFO ] petA : 1032 (100.0x)
2016-02-10 17:04:35,547 [INFO ] ndhA : 898 ( 77.3x)
2016-02-10 17:04:35,547 [INFO ] rps18 : 246 ( 75.5x)
2016-02-10 17:04:35,547 [INFO ] clpP : 476 ( 75.3x)
2016-02-10 17:04:35,547 [INFO ] psbJ : 87 ( 67.4x)
2016-02-10 17:04:35,547 [INFO ] rpoB : 1886 ( 54.5x)
2016-02-10 17:04:35,547 [INFO ] rpoA : 507 ( 47.8x)
2016-02-10 17:04:35,548 [INFO ] rpl32 : 41 ( 24.4x)
2016-02-10 17:04:35,548 [INFO ] rps8 : 100 ( 23.1x)
2016-02-10 17:04:35,548 [INFO ] matK : 279 ( 17.2x)
2016-02-10 17:04:35,548 [INFO ] ccsA : 172 ( 16.3x)
2016-02-10 17:04:35,548 [INFO ] rpoC2 : 590 ( 13.3x)
2016-02-10 17:04:35,548 [INFO ] cemA : 89 ( 12.0x)
2016-02-10 17:04:35,548 [INFO ] accD : 127 ( 8.1x)
2016-02-10 17:04:35,548 [INFO ] ycf1 : 431 ( 6.3x)
2016-02-10 17:04:39,601 [INFO ] Evaluate fragment length
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-10 17:04:43,342 [INFO ] Fragment length estimated : 387.422754 pb (sd: 206.620446)
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-10 17:04:45,668 [INFO ] Print the result as a fasta file
2016-02-10 17:04:45,668 [INFO ] Built path : [-2, 0, 1, 4, -3, -4]
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-10 17:04:49,459 [INFO ] Both segments -2 and 1 are disconnected
2016-02-10 17:04:49,460 [INFO ] Connection is forced with only 2 pair ended links (gap length=101.000000 sd=0.000000)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.11/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.11/lib/python3.5/site-packages/orgasm/command/path.py", line 92, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.11/lib/python3.5/site-packages/orgasm/tango.py", line 1430, in path2fasta
label.append('{F-connection: %d - Gap length: %d, sd: %d}' % (connected,int(glenth),int(sl)))
NameError: name 'glenth' is not defined
martiboleda@luke21:~/assembly/Alchemilla_incisa/DTV$
https://git.metabarcoding.org/org-asm/org-asm/-/issues/22
bug in unfold
2017-09-20T20:44:00Z
Martí Boleda
bug in unfold
It happens on a Poaceae genome a bit more complex than is usual
```{shell}
martiboleda@luke21:~/assembly/Avena_fatua/EVH$ oa unfold EVH chloroplast/EVH.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
7402898 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-04 16:39:04,523 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-04 16:39:04,523 [INFO ] ==> A total of : 7817
2016-02-04 16:39:04,523 [INFO ] Match list :
2016-02-04 16:39:04,525 [INFO ] psbM : 92 ( 87.5x)
2016-02-04 16:39:04,525 [INFO ] psaC : 213 ( 85.0x)
2016-02-04 16:39:04,526 [INFO ] petG : 84 ( 73.4x)
2016-02-04 16:39:04,526 [INFO ] atpH : 179 ( 71.5x)
2016-02-04 16:39:04,526 [INFO ] psbE : 173 ( 67.4x)
2016-02-04 16:39:04,526 [INFO ] rpl23 : 386 ( 67.1x)
2016-02-04 16:39:04,526 [INFO ] psbT : 60 ( 58.8x)
2016-02-04 16:39:04,526 [INFO ] psbL : 67 ( 57.0x)
2016-02-04 16:39:04,526 [INFO ] psbN : 71 ( 53.4x)
2016-02-04 16:39:04,527 [INFO ] rps12 : 372 ( 48.9x)
2016-02-04 16:39:04,527 [INFO ] psbI : 52 ( 46.7x)
2016-02-04 16:39:04,527 [INFO ] rps7 : 446 ( 46.5x)
2016-02-04 16:39:04,527 [INFO ] atpA : 637 ( 40.6x)
2016-02-04 16:39:04,527 [INFO ] psbD : 417 ( 38.2x)
2016-02-04 16:39:04,527 [INFO ] psbA : 401 ( 36.7x)
2016-02-04 16:39:04,527 [INFO ] rpl16 : 150 ( 35.9x)
2016-02-04 16:39:04,527 [INFO ] psbF : 42 ( 34.8x)
2016-02-04 16:39:04,528 [INFO ] petA : 331 ( 33.4x)
2016-02-04 16:39:04,528 [INFO ] psbB : 512 ( 32.6x)
2016-02-04 16:39:04,528 [INFO ] rbcL : 469 ( 31.7x)
2016-02-04 16:39:04,528 [INFO ] psaA : 678 ( 29.2x)
2016-02-04 16:39:04,528 [INFO ] atpB : 433 ( 28.1x)
2016-02-04 16:39:04,528 [INFO ] psbC : 399 ( 27.3x)
2016-02-04 16:39:04,528 [INFO ] psaB : 602 ( 26.5x)
2016-02-04 16:39:04,528 [INFO ] psbZ : 48 ( 25.0x)
2016-02-04 16:39:04,529 [INFO ] rps18 : 69 ( 22.1x)
2016-02-04 16:39:04,529 [INFO ] rpl14 : 65 ( 17.2x)
2016-02-04 16:39:04,529 [INFO ] rpl36 : 19 ( 16.6x)
2016-02-04 16:39:04,529 [INFO ] rpoC1 : 290 ( 13.8x)
2016-02-04 16:39:04,529 [INFO ] rpoA : 79 ( 7.8x)
2016-02-04 16:39:04,529 [INFO ] ndhA : 82 ( 7.4x)
2016-02-04 16:39:04,529 [INFO ] psbK : 11 ( 5.8x)
2016-02-04 16:39:04,529 [INFO ] rps4 : 32 ( 5.1x)
2016-02-04 16:39:04,530 [INFO ] rpoB : 111 ( 3.3x)
2016-02-04 16:39:04,530 [INFO ] psbH : 2 ( 0.9x)
2016-02-04 16:39:04,530 [INFO ] rps8 : 2 ( 0.5x)
2016-02-04 16:39:04,530 [INFO ] rps2 : 3 ( 0.4x)
2016-02-04 16:39:04,530 [INFO ] atpE : 1 ( 0.2x)
2016-02-04 16:39:04,530 [INFO ] clpP : 1 ( 0.2x)
2016-02-04 16:39:04,530 [INFO ] accD : 2 ( 0.1x)
2016-02-04 16:39:04,530 [INFO ] ccsA : 1 ( 0.1x)
2016-02-04 16:39:04,531 [INFO ] ycf1 : 4 ( 0.1x)
2016-02-04 16:39:08,279 [INFO ] Evaluate fragment length
Compacting graph 100.0 % |##################################################\] remain : 00:00:00
Minimum stem coverage = 48
2016-02-04 16:39:10,499 [INFO ] Fragment length estimated : 382.999201 pb (sd: 145.165950)
2016-02-04 16:39:10,499 [INFO ] Evaluate pair-end constraints
Compacting graph 100.0 % |##################################################-] remain : 00:00:00
Minimum stem coverage = 48
2016-02-04 16:39:12,220 [INFO ] Select the good connected componantes
2016-02-04 16:39:12,221 [INFO ] Print the result as a fasta file
Coverage 1x = 76
Compacting graph 100.0 % |##################################################-] remain : 00:00:00
Minimum stem coverage = 48
2016-02-04 16:39:14,815 [INFO ] Both segments 9 and 8 are connected (paired-end=164 frg length=429.993902 sd=124.444448)
2016-02-04 16:39:14,818 [INFO ] Both segments 8 and -4 are connected (paired-end=65 frg length=357.307692 sd=115.441217)
2016-02-04 16:39:14,819 [INFO ] Both segments -4 and -7 are connected (paired-end=9 frg length=191.222222 sd=26.690730)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/tango.py", line 1370, in path2fasta
logger.info("Both segments %d and %d are connected (paired-end=%d frg length=%f sd=%f)" % (oldid,stemid,connected,float(ml),float(sl)))
TypeError: float() argument must be a string or a number, not 'NoneType'
It happens on a Poaceae genome a bit more complex than is usual
```{shell}
martiboleda@luke21:~/assembly/Avena_fatua/EVH$ oa unfold EVH chloroplast/EVH.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
7402898 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-04 16:39:04,523 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-04 16:39:04,523 [INFO ] ==> A total of : 7817
2016-02-04 16:39:04,523 [INFO ] Match list :
2016-02-04 16:39:04,525 [INFO ] psbM : 92 ( 87.5x)
2016-02-04 16:39:04,525 [INFO ] psaC : 213 ( 85.0x)
2016-02-04 16:39:04,526 [INFO ] petG : 84 ( 73.4x)
2016-02-04 16:39:04,526 [INFO ] atpH : 179 ( 71.5x)
2016-02-04 16:39:04,526 [INFO ] psbE : 173 ( 67.4x)
2016-02-04 16:39:04,526 [INFO ] rpl23 : 386 ( 67.1x)
2016-02-04 16:39:04,526 [INFO ] psbT : 60 ( 58.8x)
2016-02-04 16:39:04,526 [INFO ] psbL : 67 ( 57.0x)
2016-02-04 16:39:04,526 [INFO ] psbN : 71 ( 53.4x)
2016-02-04 16:39:04,527 [INFO ] rps12 : 372 ( 48.9x)
2016-02-04 16:39:04,527 [INFO ] psbI : 52 ( 46.7x)
2016-02-04 16:39:04,527 [INFO ] rps7 : 446 ( 46.5x)
2016-02-04 16:39:04,527 [INFO ] atpA : 637 ( 40.6x)
2016-02-04 16:39:04,527 [INFO ] psbD : 417 ( 38.2x)
2016-02-04 16:39:04,527 [INFO ] psbA : 401 ( 36.7x)
2016-02-04 16:39:04,527 [INFO ] rpl16 : 150 ( 35.9x)
2016-02-04 16:39:04,527 [INFO ] psbF : 42 ( 34.8x)
2016-02-04 16:39:04,528 [INFO ] petA : 331 ( 33.4x)
2016-02-04 16:39:04,528 [INFO ] psbB : 512 ( 32.6x)
2016-02-04 16:39:04,528 [INFO ] rbcL : 469 ( 31.7x)
2016-02-04 16:39:04,528 [INFO ] psaA : 678 ( 29.2x)
2016-02-04 16:39:04,528 [INFO ] atpB : 433 ( 28.1x)
2016-02-04 16:39:04,528 [INFO ] psbC : 399 ( 27.3x)
2016-02-04 16:39:04,528 [INFO ] psaB : 602 ( 26.5x)
2016-02-04 16:39:04,528 [INFO ] psbZ : 48 ( 25.0x)
2016-02-04 16:39:04,529 [INFO ] rps18 : 69 ( 22.1x)
2016-02-04 16:39:04,529 [INFO ] rpl14 : 65 ( 17.2x)
2016-02-04 16:39:04,529 [INFO ] rpl36 : 19 ( 16.6x)
2016-02-04 16:39:04,529 [INFO ] rpoC1 : 290 ( 13.8x)
2016-02-04 16:39:04,529 [INFO ] rpoA : 79 ( 7.8x)
2016-02-04 16:39:04,529 [INFO ] ndhA : 82 ( 7.4x)
2016-02-04 16:39:04,529 [INFO ] psbK : 11 ( 5.8x)
2016-02-04 16:39:04,529 [INFO ] rps4 : 32 ( 5.1x)
2016-02-04 16:39:04,530 [INFO ] rpoB : 111 ( 3.3x)
2016-02-04 16:39:04,530 [INFO ] psbH : 2 ( 0.9x)
2016-02-04 16:39:04,530 [INFO ] rps8 : 2 ( 0.5x)
2016-02-04 16:39:04,530 [INFO ] rps2 : 3 ( 0.4x)
2016-02-04 16:39:04,530 [INFO ] atpE : 1 ( 0.2x)
2016-02-04 16:39:04,530 [INFO ] clpP : 1 ( 0.2x)
2016-02-04 16:39:04,530 [INFO ] accD : 2 ( 0.1x)
2016-02-04 16:39:04,530 [INFO ] ccsA : 1 ( 0.1x)
2016-02-04 16:39:04,531 [INFO ] ycf1 : 4 ( 0.1x)
2016-02-04 16:39:08,279 [INFO ] Evaluate fragment length
Compacting graph 100.0 % |##################################################\] remain : 00:00:00
Minimum stem coverage = 48
2016-02-04 16:39:10,499 [INFO ] Fragment length estimated : 382.999201 pb (sd: 145.165950)
2016-02-04 16:39:10,499 [INFO ] Evaluate pair-end constraints
Compacting graph 100.0 % |##################################################-] remain : 00:00:00
Minimum stem coverage = 48
2016-02-04 16:39:12,220 [INFO ] Select the good connected componantes
2016-02-04 16:39:12,221 [INFO ] Print the result as a fasta file
Coverage 1x = 76
Compacting graph 100.0 % |##################################################-] remain : 00:00:00
Minimum stem coverage = 48
2016-02-04 16:39:14,815 [INFO ] Both segments 9 and 8 are connected (paired-end=164 frg length=429.993902 sd=124.444448)
2016-02-04 16:39:14,818 [INFO ] Both segments 8 and -4 are connected (paired-end=65 frg length=357.307692 sd=115.441217)
2016-02-04 16:39:14,819 [INFO ] Both segments -4 and -7 are connected (paired-end=9 frg length=191.222222 sd=26.690730)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/tango.py", line 1370, in path2fasta
logger.info("Both segments %d and %d are connected (paired-end=%d frg length=%f sd=%f)" % (oldid,stemid,connected,float(ml),float(sl)))
TypeError: float() argument must be a string or a number, not 'NoneType'
https://git.metabarcoding.org/org-asm/org-asm/-/issues/21
bug in cutlow
2017-09-20T20:44:00Z
Martí Boleda
bug in cutlow
```{shell}
martiboleda@luke21:~/assembly/Anagallis_tenella/NT$ oa cutlow --coverage 50 NT chloroplast/NT.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
11676910 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-04 15:37:14,558 [INFO ] Load matches from previous run : 46 probe sets restored
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/command/cutlow.py", line 55, in run
xxx,x = getSeeds(r,config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/__init__.py", line 122, in getSeeds
for m in probes[k][1].values():
AttributeError: 'tuple' object has no attribute 'values'
```
```{shell}
martiboleda@luke21:~/assembly/Anagallis_tenella/NT$ oa cutlow --coverage 50 NT chloroplast/NT.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
11676910 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-04 15:37:14,558 [INFO ] Load matches from previous run : 46 probe sets restored
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/command/cutlow.py", line 55, in run
xxx,x = getSeeds(r,config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/__init__.py", line 122, in getSeeds
for m in probes[k][1].values():
AttributeError: 'tuple' object has no attribute 'values'
```
https://git.metabarcoding.org/org-asm/org-asm/-/issues/20
bug in force
2017-09-20T20:44:01Z
Martí Boleda
bug in force
```{shell}
martiboleda@luke21:~/assembly/Alchemilla_incisa/DTV$ oa path --path 3 0 -4 2 1 -2 -- DTV chloroplast/DTV.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
7530152 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-04 15:18:53,773 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-04 15:18:53,773 [INFO ] ==> A total of : 23473
2016-02-04 15:18:53,773 [INFO ] Match list :
2016-02-04 15:18:53,778 [INFO ] rpl23 : 1758 (293.0x)
2016-02-04 15:18:53,778 [INFO ] rps7 : 2566 (256.6x)
2016-02-04 15:18:53,778 [INFO ] rpl14 : 1007 (255.9x)
2016-02-04 15:18:53,778 [INFO ] psbE : 641 (239.4x)
2016-02-04 15:18:53,779 [INFO ] psaC : 605 (231.5x)
2016-02-04 15:18:53,779 [INFO ] psbF : 269 (213.8x)
2016-02-04 15:18:53,779 [INFO ] atpH : 551 (210.9x)
2016-02-04 15:18:53,779 [INFO ] psbN : 292 (210.5x)
2016-02-04 15:18:53,779 [INFO ] rpl36 : 233 (195.2x)
2016-02-04 15:18:53,779 [INFO ] psbT : 201 (188.8x)
2016-02-04 15:18:53,779 [INFO ] rps12 : 1497 (188.6x)
2016-02-04 15:18:53,779 [INFO ] psbL : 231 (188.4x)
2016-02-04 15:18:53,780 [INFO ] psbM : 187 (170.5x)
2016-02-04 15:18:53,780 [INFO ] psbI : 194 (167.1x)
2016-02-04 15:18:53,780 [INFO ] rps2 : 1227 (161.2x)
2016-02-04 15:18:53,780 [INFO ] petG : 191 (160.0x)
2016-02-04 15:18:53,780 [INFO ] rbcL : 2433 (157.5x)
2016-02-04 15:18:53,780 [INFO ] psbC : 2223 (145.7x)
2016-02-04 15:18:53,780 [INFO ] rpl16 : 608 (139.6x)
2016-02-04 15:18:53,780 [INFO ] rps4 : 895 (138.0x)
2016-02-04 15:18:53,781 [INFO ] psbD : 1545 (135.7x)
2016-02-04 15:18:53,781 [INFO ] atpA : 2177 (133.1x)
2016-02-04 15:18:53,781 [INFO ] psbB : 2044 (124.7x)
2016-02-04 15:18:53,781 [INFO ] atpE : 523 (122.8x)
2016-02-04 15:18:53,781 [INFO ] psbZ : 236 (118.0x)
2016-02-04 15:18:53,781 [INFO ] atpB : 1824 (113.5x)
2016-02-04 15:18:53,781 [INFO ] rpoC1 : 2391 (109.0x)
2016-02-04 15:18:53,781 [INFO ] psaB : 2514 (106.2x)
2016-02-04 15:18:53,782 [INFO ] psbH : 249 (105.7x)
2016-02-04 15:18:53,782 [INFO ] psaA : 2472 (102.2x)
2016-02-04 15:18:53,782 [INFO ] psbK : 201 (102.1x)
2016-02-04 15:18:53,782 [INFO ] psbA : 1155 (101.4x)
2016-02-04 15:18:53,782 [INFO ] petA : 1032 (100.0x)
2016-02-04 15:18:53,782 [INFO ] ndhA : 898 ( 77.3x)
2016-02-04 15:18:53,782 [INFO ] rps18 : 246 ( 75.5x)
2016-02-04 15:18:53,782 [INFO ] clpP : 476 ( 75.3x)
2016-02-04 15:18:53,783 [INFO ] psbJ : 87 ( 67.4x)
2016-02-04 15:18:53,783 [INFO ] rpoB : 1886 ( 54.5x)
2016-02-04 15:18:53,783 [INFO ] rpoA : 507 ( 47.8x)
2016-02-04 15:18:53,783 [INFO ] rpl32 : 41 ( 24.4x)
2016-02-04 15:18:53,783 [INFO ] rps8 : 100 ( 23.1x)
2016-02-04 15:18:53,783 [INFO ] matK : 279 ( 17.2x)
2016-02-04 15:18:53,783 [INFO ] ccsA : 172 ( 16.3x)
2016-02-04 15:18:53,784 [INFO ] rpoC2 : 590 ( 13.3x)
2016-02-04 15:18:53,784 [INFO ] cemA : 89 ( 12.0x)
2016-02-04 15:18:53,784 [INFO ] accD : 127 ( 8.1x)
2016-02-04 15:18:53,784 [INFO ] ycf1 : 431 ( 6.3x)
2016-02-04 15:18:58,103 [INFO ] Evaluate fragment length
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-04 15:19:02,057 [INFO ] Fragment length estimated : 387.425123 pb (sd: 206.617607)
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-04 15:19:04,435 [INFO ] Print the result as a fasta file
2016-02-04 15:19:04,435 [INFO ] Built path : [3, 0, -4, 2, 1, -2]
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-04 15:19:08,393 [INFO ] Both segments 3 and -4 are disconnected
2016-02-04 15:19:08,393 [INFO ] Connection is forced with only 2 pair ended links (gap length=97.000000 sd=0.000000)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/command/path.py", line 92, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/tango.py", line 1421, in path2fasta
label.append('{F-connection: %d - Gap length: %d, sd: %d}' % (connected,int(glenth),int(sl)))
NameError: name 'glenth' is not defined
```
```{shell}
martiboleda@luke21:~/assembly/Alchemilla_incisa/DTV$ oa path --path 3 0 -4 2 1 -2 -- DTV chloroplast/DTV.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
7530152 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-04 15:18:53,773 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-04 15:18:53,773 [INFO ] ==> A total of : 23473
2016-02-04 15:18:53,773 [INFO ] Match list :
2016-02-04 15:18:53,778 [INFO ] rpl23 : 1758 (293.0x)
2016-02-04 15:18:53,778 [INFO ] rps7 : 2566 (256.6x)
2016-02-04 15:18:53,778 [INFO ] rpl14 : 1007 (255.9x)
2016-02-04 15:18:53,778 [INFO ] psbE : 641 (239.4x)
2016-02-04 15:18:53,779 [INFO ] psaC : 605 (231.5x)
2016-02-04 15:18:53,779 [INFO ] psbF : 269 (213.8x)
2016-02-04 15:18:53,779 [INFO ] atpH : 551 (210.9x)
2016-02-04 15:18:53,779 [INFO ] psbN : 292 (210.5x)
2016-02-04 15:18:53,779 [INFO ] rpl36 : 233 (195.2x)
2016-02-04 15:18:53,779 [INFO ] psbT : 201 (188.8x)
2016-02-04 15:18:53,779 [INFO ] rps12 : 1497 (188.6x)
2016-02-04 15:18:53,779 [INFO ] psbL : 231 (188.4x)
2016-02-04 15:18:53,780 [INFO ] psbM : 187 (170.5x)
2016-02-04 15:18:53,780 [INFO ] psbI : 194 (167.1x)
2016-02-04 15:18:53,780 [INFO ] rps2 : 1227 (161.2x)
2016-02-04 15:18:53,780 [INFO ] petG : 191 (160.0x)
2016-02-04 15:18:53,780 [INFO ] rbcL : 2433 (157.5x)
2016-02-04 15:18:53,780 [INFO ] psbC : 2223 (145.7x)
2016-02-04 15:18:53,780 [INFO ] rpl16 : 608 (139.6x)
2016-02-04 15:18:53,780 [INFO ] rps4 : 895 (138.0x)
2016-02-04 15:18:53,781 [INFO ] psbD : 1545 (135.7x)
2016-02-04 15:18:53,781 [INFO ] atpA : 2177 (133.1x)
2016-02-04 15:18:53,781 [INFO ] psbB : 2044 (124.7x)
2016-02-04 15:18:53,781 [INFO ] atpE : 523 (122.8x)
2016-02-04 15:18:53,781 [INFO ] psbZ : 236 (118.0x)
2016-02-04 15:18:53,781 [INFO ] atpB : 1824 (113.5x)
2016-02-04 15:18:53,781 [INFO ] rpoC1 : 2391 (109.0x)
2016-02-04 15:18:53,781 [INFO ] psaB : 2514 (106.2x)
2016-02-04 15:18:53,782 [INFO ] psbH : 249 (105.7x)
2016-02-04 15:18:53,782 [INFO ] psaA : 2472 (102.2x)
2016-02-04 15:18:53,782 [INFO ] psbK : 201 (102.1x)
2016-02-04 15:18:53,782 [INFO ] psbA : 1155 (101.4x)
2016-02-04 15:18:53,782 [INFO ] petA : 1032 (100.0x)
2016-02-04 15:18:53,782 [INFO ] ndhA : 898 ( 77.3x)
2016-02-04 15:18:53,782 [INFO ] rps18 : 246 ( 75.5x)
2016-02-04 15:18:53,782 [INFO ] clpP : 476 ( 75.3x)
2016-02-04 15:18:53,783 [INFO ] psbJ : 87 ( 67.4x)
2016-02-04 15:18:53,783 [INFO ] rpoB : 1886 ( 54.5x)
2016-02-04 15:18:53,783 [INFO ] rpoA : 507 ( 47.8x)
2016-02-04 15:18:53,783 [INFO ] rpl32 : 41 ( 24.4x)
2016-02-04 15:18:53,783 [INFO ] rps8 : 100 ( 23.1x)
2016-02-04 15:18:53,783 [INFO ] matK : 279 ( 17.2x)
2016-02-04 15:18:53,783 [INFO ] ccsA : 172 ( 16.3x)
2016-02-04 15:18:53,784 [INFO ] rpoC2 : 590 ( 13.3x)
2016-02-04 15:18:53,784 [INFO ] cemA : 89 ( 12.0x)
2016-02-04 15:18:53,784 [INFO ] accD : 127 ( 8.1x)
2016-02-04 15:18:53,784 [INFO ] ycf1 : 431 ( 6.3x)
2016-02-04 15:18:58,103 [INFO ] Evaluate fragment length
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-04 15:19:02,057 [INFO ] Fragment length estimated : 387.425123 pb (sd: 206.617607)
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-04 15:19:04,435 [INFO ] Print the result as a fasta file
2016-02-04 15:19:04,435 [INFO ] Built path : [3, 0, -4, 2, 1, -2]
Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 231
2016-02-04 15:19:08,393 [INFO ] Both segments 3 and -4 are disconnected
2016-02-04 15:19:08,393 [INFO ] Connection is forced with only 2 pair ended links (gap length=97.000000 sd=0.000000)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/command/path.py", line 92, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.10/lib/python3.5/site-packages/orgasm/tango.py", line 1421, in path2fasta
label.append('{F-connection: %d - Gap length: %d, sd: %d}' % (connected,int(glenth),int(sl)))
NameError: name 'glenth' is not defined
```
https://git.metabarcoding.org/org-asm/org-asm/-/issues/19
Bug in oa unfold second edition
2017-09-20T20:44:01Z
Eric Coissac
Bug in oa unfold second edition
```
Minimum stem coverage = 19
2016-02-02 01:00:33,796 [INFO ] Both segments -10 and -9 are connected (paired-end=132 frg length=358.909091 sd=135.568917)
2016-02-02 01:00:33,798 [INFO ] Both segments -9 and -12 are connected (paired-end=80 frg length=307.975000 sd=108.367543)
2016-02-02 01:00:33,800 [INFO ] Both segments -12 and -24 are connected (paired-end=38 frg length=258.684211 sd=47.346486)
2016-02-02 01:00:33,801 [INFO ] Both segments -24 and 16 are connected (paired-end=48 frg length=230.604167 sd=46.373367)
2016-02-02 01:00:33,803 [INFO ] Both segments 16 and 23 are connected (paired-end=72 frg length=301.500000 sd=109.416635)
2016-02-02 01:00:33,805 [INFO ] Both segments 23 and 19 are connected (paired-end=93 frg length=294.537634 sd=95.103516)
2016-02-02 01:00:33,807 [INFO ] Both segments 19 and 22 are connected (paired-end=43 frg length=214.651163 sd=33.242508)
2016-02-02 01:00:33,808 [INFO ] Both segments 22 and -5 are connected (paired-end=43 frg length=211.348837 sd=36.799825)
2016-02-02 01:00:33,808 [INFO ] Both segments -5 and -21 are connected (paired-end=2 frg length=200.000000 sd=0.000000)
Traceback (most recent call last):
File "/work/jchave/orgasm/ORG.asm-0.1.9/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/work/jchave/orgasm/ORG.asm-0.1.9/lib/python3.4/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/work/jchave/orgasm/ORG.asm-0.1.9/lib/python3.4/site-packages/orgasm/tango.py", line 1370, in path2fasta
logger.info("Both segments %d and %d are connected (paired-end=%d frg length=%f sd=%f)" % (oldid,stemid,connected,ml,sl))
TypeError: a float is required
(ORG.asm-0.1.9)
```
```
Minimum stem coverage = 19
2016-02-02 01:00:33,796 [INFO ] Both segments -10 and -9 are connected (paired-end=132 frg length=358.909091 sd=135.568917)
2016-02-02 01:00:33,798 [INFO ] Both segments -9 and -12 are connected (paired-end=80 frg length=307.975000 sd=108.367543)
2016-02-02 01:00:33,800 [INFO ] Both segments -12 and -24 are connected (paired-end=38 frg length=258.684211 sd=47.346486)
2016-02-02 01:00:33,801 [INFO ] Both segments -24 and 16 are connected (paired-end=48 frg length=230.604167 sd=46.373367)
2016-02-02 01:00:33,803 [INFO ] Both segments 16 and 23 are connected (paired-end=72 frg length=301.500000 sd=109.416635)
2016-02-02 01:00:33,805 [INFO ] Both segments 23 and 19 are connected (paired-end=93 frg length=294.537634 sd=95.103516)
2016-02-02 01:00:33,807 [INFO ] Both segments 19 and 22 are connected (paired-end=43 frg length=214.651163 sd=33.242508)
2016-02-02 01:00:33,808 [INFO ] Both segments 22 and -5 are connected (paired-end=43 frg length=211.348837 sd=36.799825)
2016-02-02 01:00:33,808 [INFO ] Both segments -5 and -21 are connected (paired-end=2 frg length=200.000000 sd=0.000000)
Traceback (most recent call last):
File "/work/jchave/orgasm/ORG.asm-0.1.9/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/work/jchave/orgasm/ORG.asm-0.1.9/lib/python3.4/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/work/jchave/orgasm/ORG.asm-0.1.9/lib/python3.4/site-packages/orgasm/tango.py", line 1370, in path2fasta
logger.info("Both segments %d and %d are connected (paired-end=%d frg length=%f sd=%f)" % (oldid,stemid,connected,ml,sl))
TypeError: a float is required
(ORG.asm-0.1.9)
```
https://git.metabarcoding.org/org-asm/org-asm/-/issues/18
Bug during unfolding of the assembling graph
2017-09-20T20:44:01Z
Eric Coissac
Bug during unfolding of the assembling graph
`oa unfold` exit with an error :
```
=========================================
You can now use ORG.asm
(ORG.asm-0.1.8) oa unfold caryocar caryocar.chloro
Loading global data...
Done.
Reading indexed sequence reads...
9509158 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-01 15:48:59,972 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-01 15:48:59,981 [INFO ] ==> A total of : 15297
2016-02-01 15:48:59,981 [INFO ] Match list :
2016-02-01 15:48:59,984 [INFO ] psaC : 306 (119.6x)
2016-02-01 15:48:59,984 [INFO ] rps7 : 1163 (118.8x)
2016-02-01 15:48:59,984 [INFO ] psbN : 157 (115.6x)
2016-02-01 15:48:59,984 [INFO ] petG : 135 (115.5x)
2016-02-01 15:48:59,984 [INFO ] rpl14 : 444 (115.2x)
2016-02-01 15:48:59,984 [INFO ] psbI : 131 (115.2x)
2016-02-01 15:48:59,984 [INFO ] rpl23 : 647 (110.2x)
2016-02-01 15:48:59,984 [INFO ] atpH : 280 (109.5x)
2016-02-01 15:48:59,985 [INFO ] psbE : 277 (105.7x)
2016-02-01 15:48:59,985 [INFO ] psbM : 109 (101.5x)
2016-02-01 15:48:59,986 [INFO ] rpl36 : 118 (101.0x)
2016-02-01 15:48:59,986 [INFO ] psbL : 115 ( 95.8x)
2016-02-01 15:48:59,986 [INFO ] psbT : 96 ( 92.1x)
2016-02-01 15:48:59,986 [INFO ] atpE : 371 ( 89.0x)
2016-02-01 15:48:59,986 [INFO ] rps12 : 672 ( 86.5x)
2016-02-01 15:48:59,986 [INFO ] psbF : 106 ( 86.1x)
2016-02-01 15:48:59,986 [INFO ] psbC : 1273 ( 85.2x)
2016-02-01 15:48:59,986 [INFO ] psbA : 926 ( 83.1x)
2016-02-01 15:48:59,986 [INFO ] atpA : 1284 ( 80.2x)
2016-02-01 15:48:59,986 [INFO ] psbH : 178 ( 77.2x)
2016-02-01 15:48:59,986 [INFO ] psbD : 859 ( 77.1x)
2016-02-01 15:48:59,987 [INFO ] rpl16 : 322 ( 75.5x)
2016-02-01 15:48:59,987 [INFO ] psbB : 1145 ( 71.4x)
2016-02-01 15:48:59,987 [INFO ] rps18 : 197 ( 61.8x)
2016-02-01 15:48:59,987 [INFO ] atpB : 963 ( 61.2x)
2016-02-01 15:48:59,987 [INFO ] psbJ : 77 ( 61.0x)
2016-02-01 15:48:59,987 [INFO ] rps2 : 445 ( 59.7x)
2016-02-01 15:48:59,988 [INFO ] psbK : 113 ( 58.7x)
2016-02-01 15:48:59,988 [INFO ] rbcL : 830 ( 54.9x)
2016-02-01 15:48:59,988 [INFO ] psaB : 1236 ( 53.3x)
2016-02-01 15:48:59,988 [INFO ] psbZ : 104 ( 53.1x)
2016-02-01 15:48:59,988 [INFO ] psaA : 1208 ( 51.0x)
2016-02-01 15:48:59,988 [INFO ] petA : 503 ( 49.8x)
2016-02-01 15:48:59,988 [INFO ] rps4 : 246 ( 38.8x)
2016-02-01 15:48:59,988 [INFO ] rpoB : 1163 ( 34.4x)
2016-02-01 15:48:59,988 [INFO ] rpoC1 : 661 ( 30.8x)
2016-02-01 15:48:59,988 [INFO ] ndhA : 319 ( 28.1x)
2016-02-01 15:48:59,988 [INFO ] clpP : 164 ( 26.5x)
2016-02-01 15:48:59,989 [INFO ] cemA : 183 ( 25.3x)
2016-02-01 15:48:59,995 [INFO ] rpoA : 251 ( 24.2x)
2016-02-01 15:48:59,996 [INFO ] rps8 : 43 ( 10.2x)
2016-02-01 15:48:59,996 [INFO ] ccsA : 95 ( 9.2x)
2016-02-01 15:48:59,996 [INFO ] rpoC2 : 280 ( 6.4x)
2016-02-01 15:48:59,996 [INFO ] ycf1 : 240 ( 3.6x)
2016-02-01 15:48:59,996 [INFO ] accD : 49 ( 3.2x)
2016-02-01 15:48:59,996 [INFO ] matK : 30 ( 1.9x)
2016-02-01 15:49:04,932 [INFO ] Evaluate fragment length
Compacting graph 0.0 % |/ ] remain : 00:0Compacting graph 0.6 % |- ] remain : 00:0Compacting graph 0.6 % |\ ] remain : 00:0Compacting graph 0.6 % || ] remain : 00:0Compacting graph 0.7 % |/ ] remain : 00:0Compacting graph 9.8 % |####- ] remain : 00:0Compacting graph 42.7 % |#####################\ ] remain : 00:0Compacting graph 74.4 % |#####################################| ] remain : 00:0Compacting graph 84.7 % |##########################################/ ] remain : 00:0Compacting graph 86.9 % |###########################################- ] remain : 00:0Compacting graph 89.9 % |############################################\ ] remain : 00:0Compacting graph 97.8 % |################################################| ] remain : 00:0Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 40
2016-02-01 15:49:08,411 [INFO ] Fragment length estimated : 275.029589 pb (sd: 131.561951)
2016-02-01 15:49:08,411 [INFO ] Evaluate pair-end constraints
Compacting graph 0.0 % |/ ] remain : 00:0Compacting graph 0.6 % |- ] remain : 00:0Compacting graph 0.6 % |\ ] remain : 00:0Compacting graph 0.6 % || ] remain : 00:0Compacting graph 0.7 % |/ ] remain : 00:0Compacting graph 9.8 % |####- ] remain : 00:0Compacting graph 42.7 % |#####################\ ] remain : 00:0Compacting graph 74.4 % |#####################################| ] remain : 00:0Compacting graph 84.7 % |##########################################/ ] remain : 00:0Compacting graph 86.9 % |###########################################- ] remain : 00:0Compacting graph 89.9 % |############################################\ ] remain : 00:0Compacting graph 97.8 % |################################################| ] remain : 00:0Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 40
-10 -> -3 scaffolded by 47 pair ended links
3 -> 10 scaffolded by 47 pair ended links
2016-02-01 15:49:11,005 [INFO ] Select the good connected componantes
2016-02-01 15:49:11,005 [INFO ] Print the result as a fasta file
Coverage 1x = 111
Compacting graph 0.0 % |/ ] remain : 00:0Compacting graph 0.6 % |- ] remain : 00:0Compacting graph 0.6 % |\ ] remain : 00:0Compacting graph 0.6 % || ] remain : 00:0Compacting graph 0.7 % |/ ] remain : 00:0Compacting graph 9.8 % |####- ] remain : 00:0Compacting graph 42.7 % |#####################\ ] remain : 00:0Compacting graph 74.4 % |#####################################| ] remain : 00:0Compacting graph 84.7 % |##########################################/ ] remain : 00:0Compacting graph 86.9 % |###########################################- ] remain : 00:0Compacting graph 89.9 % |############################################\ ] remain : 00:0Compacting graph 97.8 % |################################################| ] remain : 00:0Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 40
2016-02-01 15:49:15,014 [INFO ] Both segments 10 and 5 are connected (paired-end=69 frg length=308.347826 sd=120.379933)
2016-02-01 15:49:15,017 [INFO ] Both segments 5 and 2 are connected (paired-end=88 frg length=268.522727 sd=114.019334)
2016-02-01 15:49:15,031 [INFO ] Both segments 2 and 1 are connected (paired-end=158 frg length=411.215190 sd=144.536156)
2016-02-01 15:49:15,034 [INFO ] Both segments 1 and 9 are connected (paired-end=11 frg length=162.000000 sd=62.465991)
2016-02-01 15:49:15,036 [INFO ] Both segments 9 and 4 are connected (paired-end=10 frg length=198.400000 sd=97.411704)
2016-02-01 15:49:15,041 [INFO ] Both segments 4 and 7 are connected (paired-end=159 frg length=365.440252 sd=135.415066)
2016-02-01 15:49:15,043 [INFO ] Both segments 7 and -4 are connected (paired-end=112 frg length=360.767857 sd=160.839649)
2016-02-01 15:49:15,045 [INFO ] Both segments -4 and -9 are connected (paired-end=10 frg length=198.400000 sd=97.411704)
2016-02-01 15:49:15,047 [INFO ] Both segments -9 and -1 are connected (paired-end=11 frg length=162.000000 sd=62.465991)
2016-02-01 15:49:15,051 [INFO ] Both segments -1 and -8 are connected (paired-end=158 frg length=365.721519 sd=127.642592)
2016-02-01 15:49:15,068 [INFO ] Both segments -8 and 9 are connected (paired-end=1 frg length=283.000000 sd=0.000000)
2016-02-01 15:49:15,070 [INFO ] Both segments 9 and 3 are connected (paired-end=6 frg length=228.333333 sd=162.829836)
2016-02-01 15:49:15,073 [INFO ] Path is circular but disconnected
2016-02-01 15:49:15,073 [INFO ] Linked by 47 pair ended links (gap length=-171.587432 sd=140.191139)
Traceback (most recent call last):
File "/work/jchave/orgasm/ORG.asm-0.1.8/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/work/jchave/orgasm/ORG.asm-0.1.8/lib/python3.4/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/work/jchave/orgasm/ORG.asm-0.1.8/lib/python3.4/site-packages/orgasm/tango.py", line 1488, in path2fasta
seq.append(b'N'*glength)
TypeError: can't multiply sequence by non-int of type 'float'
(ORG.asm-0.1.8)
```
`oa unfold` exit with an error :
```
=========================================
You can now use ORG.asm
(ORG.asm-0.1.8) oa unfold caryocar caryocar.chloro
Loading global data...
Done.
Reading indexed sequence reads...
9509158 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-01 15:48:59,972 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-01 15:48:59,981 [INFO ] ==> A total of : 15297
2016-02-01 15:48:59,981 [INFO ] Match list :
2016-02-01 15:48:59,984 [INFO ] psaC : 306 (119.6x)
2016-02-01 15:48:59,984 [INFO ] rps7 : 1163 (118.8x)
2016-02-01 15:48:59,984 [INFO ] psbN : 157 (115.6x)
2016-02-01 15:48:59,984 [INFO ] petG : 135 (115.5x)
2016-02-01 15:48:59,984 [INFO ] rpl14 : 444 (115.2x)
2016-02-01 15:48:59,984 [INFO ] psbI : 131 (115.2x)
2016-02-01 15:48:59,984 [INFO ] rpl23 : 647 (110.2x)
2016-02-01 15:48:59,984 [INFO ] atpH : 280 (109.5x)
2016-02-01 15:48:59,985 [INFO ] psbE : 277 (105.7x)
2016-02-01 15:48:59,985 [INFO ] psbM : 109 (101.5x)
2016-02-01 15:48:59,986 [INFO ] rpl36 : 118 (101.0x)
2016-02-01 15:48:59,986 [INFO ] psbL : 115 ( 95.8x)
2016-02-01 15:48:59,986 [INFO ] psbT : 96 ( 92.1x)
2016-02-01 15:48:59,986 [INFO ] atpE : 371 ( 89.0x)
2016-02-01 15:48:59,986 [INFO ] rps12 : 672 ( 86.5x)
2016-02-01 15:48:59,986 [INFO ] psbF : 106 ( 86.1x)
2016-02-01 15:48:59,986 [INFO ] psbC : 1273 ( 85.2x)
2016-02-01 15:48:59,986 [INFO ] psbA : 926 ( 83.1x)
2016-02-01 15:48:59,986 [INFO ] atpA : 1284 ( 80.2x)
2016-02-01 15:48:59,986 [INFO ] psbH : 178 ( 77.2x)
2016-02-01 15:48:59,986 [INFO ] psbD : 859 ( 77.1x)
2016-02-01 15:48:59,987 [INFO ] rpl16 : 322 ( 75.5x)
2016-02-01 15:48:59,987 [INFO ] psbB : 1145 ( 71.4x)
2016-02-01 15:48:59,987 [INFO ] rps18 : 197 ( 61.8x)
2016-02-01 15:48:59,987 [INFO ] atpB : 963 ( 61.2x)
2016-02-01 15:48:59,987 [INFO ] psbJ : 77 ( 61.0x)
2016-02-01 15:48:59,987 [INFO ] rps2 : 445 ( 59.7x)
2016-02-01 15:48:59,988 [INFO ] psbK : 113 ( 58.7x)
2016-02-01 15:48:59,988 [INFO ] rbcL : 830 ( 54.9x)
2016-02-01 15:48:59,988 [INFO ] psaB : 1236 ( 53.3x)
2016-02-01 15:48:59,988 [INFO ] psbZ : 104 ( 53.1x)
2016-02-01 15:48:59,988 [INFO ] psaA : 1208 ( 51.0x)
2016-02-01 15:48:59,988 [INFO ] petA : 503 ( 49.8x)
2016-02-01 15:48:59,988 [INFO ] rps4 : 246 ( 38.8x)
2016-02-01 15:48:59,988 [INFO ] rpoB : 1163 ( 34.4x)
2016-02-01 15:48:59,988 [INFO ] rpoC1 : 661 ( 30.8x)
2016-02-01 15:48:59,988 [INFO ] ndhA : 319 ( 28.1x)
2016-02-01 15:48:59,988 [INFO ] clpP : 164 ( 26.5x)
2016-02-01 15:48:59,989 [INFO ] cemA : 183 ( 25.3x)
2016-02-01 15:48:59,995 [INFO ] rpoA : 251 ( 24.2x)
2016-02-01 15:48:59,996 [INFO ] rps8 : 43 ( 10.2x)
2016-02-01 15:48:59,996 [INFO ] ccsA : 95 ( 9.2x)
2016-02-01 15:48:59,996 [INFO ] rpoC2 : 280 ( 6.4x)
2016-02-01 15:48:59,996 [INFO ] ycf1 : 240 ( 3.6x)
2016-02-01 15:48:59,996 [INFO ] accD : 49 ( 3.2x)
2016-02-01 15:48:59,996 [INFO ] matK : 30 ( 1.9x)
2016-02-01 15:49:04,932 [INFO ] Evaluate fragment length
Compacting graph 0.0 % |/ ] remain : 00:0Compacting graph 0.6 % |- ] remain : 00:0Compacting graph 0.6 % |\ ] remain : 00:0Compacting graph 0.6 % || ] remain : 00:0Compacting graph 0.7 % |/ ] remain : 00:0Compacting graph 9.8 % |####- ] remain : 00:0Compacting graph 42.7 % |#####################\ ] remain : 00:0Compacting graph 74.4 % |#####################################| ] remain : 00:0Compacting graph 84.7 % |##########################################/ ] remain : 00:0Compacting graph 86.9 % |###########################################- ] remain : 00:0Compacting graph 89.9 % |############################################\ ] remain : 00:0Compacting graph 97.8 % |################################################| ] remain : 00:0Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 40
2016-02-01 15:49:08,411 [INFO ] Fragment length estimated : 275.029589 pb (sd: 131.561951)
2016-02-01 15:49:08,411 [INFO ] Evaluate pair-end constraints
Compacting graph 0.0 % |/ ] remain : 00:0Compacting graph 0.6 % |- ] remain : 00:0Compacting graph 0.6 % |\ ] remain : 00:0Compacting graph 0.6 % || ] remain : 00:0Compacting graph 0.7 % |/ ] remain : 00:0Compacting graph 9.8 % |####- ] remain : 00:0Compacting graph 42.7 % |#####################\ ] remain : 00:0Compacting graph 74.4 % |#####################################| ] remain : 00:0Compacting graph 84.7 % |##########################################/ ] remain : 00:0Compacting graph 86.9 % |###########################################- ] remain : 00:0Compacting graph 89.9 % |############################################\ ] remain : 00:0Compacting graph 97.8 % |################################################| ] remain : 00:0Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 40
-10 -> -3 scaffolded by 47 pair ended links
3 -> 10 scaffolded by 47 pair ended links
2016-02-01 15:49:11,005 [INFO ] Select the good connected componantes
2016-02-01 15:49:11,005 [INFO ] Print the result as a fasta file
Coverage 1x = 111
Compacting graph 0.0 % |/ ] remain : 00:0Compacting graph 0.6 % |- ] remain : 00:0Compacting graph 0.6 % |\ ] remain : 00:0Compacting graph 0.6 % || ] remain : 00:0Compacting graph 0.7 % |/ ] remain : 00:0Compacting graph 9.8 % |####- ] remain : 00:0Compacting graph 42.7 % |#####################\ ] remain : 00:0Compacting graph 74.4 % |#####################################| ] remain : 00:0Compacting graph 84.7 % |##########################################/ ] remain : 00:0Compacting graph 86.9 % |###########################################- ] remain : 00:0Compacting graph 89.9 % |############################################\ ] remain : 00:0Compacting graph 97.8 % |################################################| ] remain : 00:0Compacting graph 100.0 % |##################################################/] remain : 00:00:00
Minimum stem coverage = 40
2016-02-01 15:49:15,014 [INFO ] Both segments 10 and 5 are connected (paired-end=69 frg length=308.347826 sd=120.379933)
2016-02-01 15:49:15,017 [INFO ] Both segments 5 and 2 are connected (paired-end=88 frg length=268.522727 sd=114.019334)
2016-02-01 15:49:15,031 [INFO ] Both segments 2 and 1 are connected (paired-end=158 frg length=411.215190 sd=144.536156)
2016-02-01 15:49:15,034 [INFO ] Both segments 1 and 9 are connected (paired-end=11 frg length=162.000000 sd=62.465991)
2016-02-01 15:49:15,036 [INFO ] Both segments 9 and 4 are connected (paired-end=10 frg length=198.400000 sd=97.411704)
2016-02-01 15:49:15,041 [INFO ] Both segments 4 and 7 are connected (paired-end=159 frg length=365.440252 sd=135.415066)
2016-02-01 15:49:15,043 [INFO ] Both segments 7 and -4 are connected (paired-end=112 frg length=360.767857 sd=160.839649)
2016-02-01 15:49:15,045 [INFO ] Both segments -4 and -9 are connected (paired-end=10 frg length=198.400000 sd=97.411704)
2016-02-01 15:49:15,047 [INFO ] Both segments -9 and -1 are connected (paired-end=11 frg length=162.000000 sd=62.465991)
2016-02-01 15:49:15,051 [INFO ] Both segments -1 and -8 are connected (paired-end=158 frg length=365.721519 sd=127.642592)
2016-02-01 15:49:15,068 [INFO ] Both segments -8 and 9 are connected (paired-end=1 frg length=283.000000 sd=0.000000)
2016-02-01 15:49:15,070 [INFO ] Both segments 9 and 3 are connected (paired-end=6 frg length=228.333333 sd=162.829836)
2016-02-01 15:49:15,073 [INFO ] Path is circular but disconnected
2016-02-01 15:49:15,073 [INFO ] Linked by 47 pair ended links (gap length=-171.587432 sd=140.191139)
Traceback (most recent call last):
File "/work/jchave/orgasm/ORG.asm-0.1.8/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/work/jchave/orgasm/ORG.asm-0.1.8/lib/python3.4/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/work/jchave/orgasm/ORG.asm-0.1.8/lib/python3.4/site-packages/orgasm/tango.py", line 1488, in path2fasta
seq.append(b'N'*glength)
TypeError: can't multiply sequence by non-int of type 'float'
(ORG.asm-0.1.8)
```
https://git.metabarcoding.org/org-asm/org-asm/-/issues/17
Installation bug with Ubuntu LTS 14.04 and Python 3.4.3
2017-09-20T20:44:01Z
Eric Coissac
Installation bug with Ubuntu LTS 14.04 and Python 3.4.3
Pip has been updated to the latest version before the installation.
```{shell}
python3 get-orgasm.py
Unable to install ORG.asm on your system
Collecting ORG.asm
Downloading ORG.asm-0.1.3.tar.gz (234kB)
100% |████████████████████████████████| 237kB 17.9MB/s
Saved /tmp/tmpd7_11hgt/ORG.asm-0.1.3.tar.gz
Successfully downloaded ORG.asm
['/tmp/tmpd7_11hgt/ORG.asm-0.1.3', '/opt/src/orgasm',
'/usr/lib/python3.4', '/ usr/lib/python3.4/plat-x86_64-linux-gnu',
'/usr/lib/python3.4/lib-dynload', '/
usr/local/lib/python3.4/dist-packages', '/usr/lib/python3/dist-packages',
'/ tmp/tmpd7_11hgt/ORG.asm-0.1.3/distutils.ext',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/ python']
['/tmp/tmpd7_11hgt/ORG.asm-0.1.3', '/usr/lib/python3.4',
'/usr/lib/python3.4/ plat-x86_64-linux-gnu',
'/usr/lib/python3.4/lib-dynload', '/usr/local/lib/
python3.4/dist-packages', '/usr/lib/python3/dist-packages',
'/tmp/tmpd7_11hgt/ ORG.asm-0.1.3/distutils.ext',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/python'] Installing ORG.asm (0.1.3) in
serenity mode
You are running the good python
Restarting installation within the /opt/src/orgasm/ORG.asm-0.1.3
virtualenv
Install script restarting...
['/tmp/tmpd7_11hgt/ORG.asm-0.1.3', '/usr/lib/python3.4',
'/usr/lib/python3.4/ plat-x86_64-linux-gnu',
'/usr/lib/python3.4/lib-dynload', '/opt/src/orgasm/
ORG.asm-0.1.3/lib/python3.4/site-packages',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/ distutils.ext',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/python']
Traceback (most recent call last):
File "setup.py", line 42, in <module>
from obidistutils.serenity import serenity_mode
File "/tmp/tmpd7_11hgt/ORG.asm-0.1.3/distutils.ext/obidistutils/serenity/
__init__.py", line 32, in <module>
from obidistutils.serenity.checkpackage import install_requirements
File "/tmp/tmpd7_11hgt/ORG.asm-0.1.3/distutils.ext/obidistutils/serenity/
checkpackage.py", line 11, in <module>
from pip.utils import get_installed_distributions #
@UnresolvedImport
ImportError: No module named 'pip.utils'
--------------
}
Pip has been updated to the latest version before the installation.
```{shell}
python3 get-orgasm.py
Unable to install ORG.asm on your system
Collecting ORG.asm
Downloading ORG.asm-0.1.3.tar.gz (234kB)
100% |████████████████████████████████| 237kB 17.9MB/s
Saved /tmp/tmpd7_11hgt/ORG.asm-0.1.3.tar.gz
Successfully downloaded ORG.asm
['/tmp/tmpd7_11hgt/ORG.asm-0.1.3', '/opt/src/orgasm',
'/usr/lib/python3.4', '/ usr/lib/python3.4/plat-x86_64-linux-gnu',
'/usr/lib/python3.4/lib-dynload', '/
usr/local/lib/python3.4/dist-packages', '/usr/lib/python3/dist-packages',
'/ tmp/tmpd7_11hgt/ORG.asm-0.1.3/distutils.ext',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/ python']
['/tmp/tmpd7_11hgt/ORG.asm-0.1.3', '/usr/lib/python3.4',
'/usr/lib/python3.4/ plat-x86_64-linux-gnu',
'/usr/lib/python3.4/lib-dynload', '/usr/local/lib/
python3.4/dist-packages', '/usr/lib/python3/dist-packages',
'/tmp/tmpd7_11hgt/ ORG.asm-0.1.3/distutils.ext',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/python'] Installing ORG.asm (0.1.3) in
serenity mode
You are running the good python
Restarting installation within the /opt/src/orgasm/ORG.asm-0.1.3
virtualenv
Install script restarting...
['/tmp/tmpd7_11hgt/ORG.asm-0.1.3', '/usr/lib/python3.4',
'/usr/lib/python3.4/ plat-x86_64-linux-gnu',
'/usr/lib/python3.4/lib-dynload', '/opt/src/orgasm/
ORG.asm-0.1.3/lib/python3.4/site-packages',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/ distutils.ext',
'/tmp/tmpd7_11hgt/ORG.asm-0.1.3/python']
Traceback (most recent call last):
File "setup.py", line 42, in <module>
from obidistutils.serenity import serenity_mode
File "/tmp/tmpd7_11hgt/ORG.asm-0.1.3/distutils.ext/obidistutils/serenity/
__init__.py", line 32, in <module>
from obidistutils.serenity.checkpackage import install_requirements
File "/tmp/tmpd7_11hgt/ORG.asm-0.1.3/distutils.ext/obidistutils/serenity/
checkpackage.py", line 11, in <module>
from pip.utils import get_installed_distributions #
@UnresolvedImport
ImportError: No module named 'pip.utils'
--------------
}