ORG.Asm issues
https://git.metabarcoding.org/org-asm/org-asm/-/issues
2017-09-20T20:43:47Z
https://git.metabarcoding.org/org-asm/org-asm/-/issues/50
Error when unfolding low quality data
2017-09-20T20:43:47Z
Eric Coissac
Error when unfolding low quality data
dataset : /Users/coissac/travail/__MOI__/ORG.Asm_paper/dataset/Fungi/Aspergillus
```
Traceback (most recent call last):
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/bin/oa", line 64, in <module>
config[root_config_name]['module'].run(config)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/commands/unfold.py", line 186, in run
paths=buildPath(asm, cg, back, minlink, config)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/commands/unfold.py", line 106, in buildPath
back=int(back),minlink=minlink)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/tango.py", line 1523, in pathConstraints
constraints = mergeConstraints(constraints,minisatDoubleConstraints(self,cg))
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/tango.py", line 1390, in minisatDoubleConstraints
r1 = round(middleFcov/float(inputcov))
ZeroDivisionError: float division by zero
```
dataset : /Users/coissac/travail/__MOI__/ORG.Asm_paper/dataset/Fungi/Aspergillus
```
Traceback (most recent call last):
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/bin/oa", line 64, in <module>
config[root_config_name]['module'].run(config)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/commands/unfold.py", line 186, in run
paths=buildPath(asm, cg, back, minlink, config)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/commands/unfold.py", line 106, in buildPath
back=int(back),minlink=minlink)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/tango.py", line 1523, in pathConstraints
constraints = mergeConstraints(constraints,minisatDoubleConstraints(self,cg))
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha5/lib/python3.5/site-packages/orgasm/tango.py", line 1390, in minisatDoubleConstraints
r1 = round(middleFcov/float(inputcov))
ZeroDivisionError: float division by zero
```
Eric Coissac
Eric Coissac
https://git.metabarcoding.org/org-asm/org-asm/-/issues/47
Error during buildgraph cleaning step
2017-09-20T20:43:47Z
Eric Coissac
Error during buildgraph cleaning step
With plant dataset SRR4996200
```
Traceback (most recent call last):
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/bin/oa", line 64, in <module>
config[root_config_name]['module'].run(config)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/commands/buildgraph.py", line 563, in run
nodeLimit=assmax)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/tango.py", line 608, in fillGaps
exi = [getPairedRead(self,assgraph,i,back,end=False) for i in eiid]
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/tango.py", line 608, in <listcomp>
exi = [getPairedRead(self,assgraph,i,back,end=False) for i in eiid]
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/tango.py", line 848, in getPairedRead
path=assgraph.getEdgeAttr(*stem)['path'][-back:]
UnboundLocalError: local variable 'stem' referenced before assignment
```
With plant dataset SRR4996200
```
Traceback (most recent call last):
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/bin/oa", line 64, in <module>
config[root_config_name]['module'].run(config)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/commands/buildgraph.py", line 563, in run
nodeLimit=assmax)
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/tango.py", line 608, in fillGaps
exi = [getPairedRead(self,assgraph,i,back,end=False) for i in eiid]
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/tango.py", line 608, in <listcomp>
exi = [getPairedRead(self,assgraph,i,back,end=False) for i in eiid]
File "/Users/coissac/git/org-asm/ORG.asm-1.0.00-alpha2/lib/python3.5/site-packages/orgasm/tango.py", line 848, in getPairedRead
path=assgraph.getEdgeAttr(*stem)['path'][-back:]
UnboundLocalError: local variable 'stem' referenced before assignment
```
Eric Coissac
Eric Coissac
https://git.metabarcoding.org/org-asm/org-asm/-/issues/46
Circle are not convert to fasta as circular secquences
2017-09-20T20:43:48Z
Eric Coissac
Circle are not convert to fasta as circular secquences
Circles in the assembling graph are no more output in fasta files as circular sequences
Circles in the assembling graph are no more output in fasta files as circular sequences
Eric Coissac
Eric Coissac
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/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/33
Bug in unfoldrrna
2017-09-20T20:43:54Z
Eric Coissac
Bug in unfoldrrna
While unfolding the species Abutilon_theophrasti_Medik/RSZAXPI000683-37
The graph is just constituted by a single circular edge
```
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/unfoldrdna.py", line 113, in run
path = unfoldmarker(cg,seeds=seeds)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.2.03/lib/python3.5/site-packages/orgasm/tango.py", line 1582, in unfoldmarker
p = set(assgraph.parentIterator(maxp[0]))
IndexError: list index out of range
```
While unfolding the species Abutilon_theophrasti_Medik/RSZAXPI000683-37
The graph is just constituted by a single circular edge
```
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/unfoldrdna.py", line 113, in run
path = unfoldmarker(cg,seeds=seeds)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.2.03/lib/python3.5/site-packages/orgasm/tango.py", line 1582, in unfoldmarker
p = set(assgraph.parentIterator(maxp[0]))
IndexError: list index out of range
```
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/25
Bug in unfold in force mode
2017-09-20T20:43:55Z
Eric Coissac
Bug in unfold in force mode
```
2016-02-20 21:03:14,095 [INFO ] Both segments -5 and -3 are connected (paired-end=185 frg length=425.827027 sd=119.743249)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.12/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.12/lib/python3.5/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.12/lib/python3.5/site-packages/orgasm/tango.py", line 1472, in path2fasta
s1 = alledges[path[-1]]
KeyError: 0
```
```
2016-02-20 21:03:14,095 [INFO ] Both segments -5 and -3 are connected (paired-end=185 frg length=425.827027 sd=119.743249)
Traceback (most recent call last):
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.12/export/bin/oa", line 232, in <module>
config['orgasm']['module'].run(config)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.12/lib/python3.5/site-packages/orgasm/command/unfold.py", line 115, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.12/lib/python3.5/site-packages/orgasm/tango.py", line 1472, in path2fasta
s1 = alledges[path[-1]]
KeyError: 0
```
https://git.metabarcoding.org/org-asm/org-asm/-/issues/24
Some nodes should be deleted several times during branch cleaning
2023-04-25T19:40:00Z
Eric Coissac
Some nodes should be deleted several times during branch cleaning
```
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'2849968',)
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'2849968',)
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'630467',)
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'630467',)
```
```
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'2849968',)
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'2849968',)
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'630467',)
Exception ignored in: 'orgasm.assembler._assembler.weight'
Traceback (most recent call last):
File "python/orgasm/assembler/_asmbgraph.pyx", line 168, in orgasm.assembler._asmbgraph.AsmbGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c:3944)
File "python/orgasm/graph/_graph.pyx", line 203, in orgasm.graph._graph.DiGraph.getNodeAttr (build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c:4687)
KeyError: (b'630467',)
```
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'
--------------
}
https://git.metabarcoding.org/org-asm/org-asm/-/issues/16
bug on unfold
2018-11-09T16:38:29Z
Martí Boleda
bug on unfold
The unfolded path on Fumana_thymifolia/RS is different for both IR regarding the number of times it passes through the repeated regions.
[RS.chloroplast.path.gml](https://git.metabarcoding.org/org-asm/org-asm/uploads/28345ffef47114f53420672c95f3d075/RS.chloroplast.path.gml)
The unfolded path on Fumana_thymifolia/RS is different for both IR regarding the number of times it passes through the repeated regions.
[RS.chloroplast.path.gml](https://git.metabarcoding.org/org-asm/org-asm/uploads/28345ffef47114f53420672c95f3d075/RS.chloroplast.path.gml)
https://git.metabarcoding.org/org-asm/org-asm/-/issues/11
Error in the --help of the fillgaps command
2018-11-09T16:38:29Z
Eric Coissac
Error in the --help of the fillgaps command
the `--help` prints the following message:
```
--snp desactivate the SNP clearing mode
```
instead of *activate*
the `--help` prints the following message:
```
--snp desactivate the SNP clearing mode
```
instead of *activate*
https://git.metabarcoding.org/org-asm/org-asm/-/issues/8
Typo: De Bruinj Graph
2018-11-09T16:38:30Z
Peter Cock
Typo: De Bruinj Graph
```
$ oa buildgraph --seeds protChloroArabidopsis example_index example_protChloroArabidopsis > example_protChloroArabidopsis_stdout.log
2015-08-24 16:36:20,570 [INFO ] Building De Bruinj Graph
2015-08-24 16:36:20,570 [INFO ] Minimum overlap between read: 50
...
```
Should be De Bruijn Graph, correction needed in ``python/orgasm/command/buildgraph.py``
From searching the source code you also need to fix:
* ``doc/sphinx/source/mitochondrion.rst``
* ``doc/sphinx/source/commands/buildgraph.rst``
```
$ oa buildgraph --seeds protChloroArabidopsis example_index example_protChloroArabidopsis > example_protChloroArabidopsis_stdout.log
2015-08-24 16:36:20,570 [INFO ] Building De Bruinj Graph
2015-08-24 16:36:20,570 [INFO ] Minimum overlap between read: 50
...
```
Should be De Bruijn Graph, correction needed in ``python/orgasm/command/buildgraph.py``
From searching the source code you also need to fix:
* ``doc/sphinx/source/mitochondrion.rst``
* ``doc/sphinx/source/commands/buildgraph.rst``
https://git.metabarcoding.org/org-asm/org-asm/-/issues/4
oa command does not report the version
2018-11-09T16:38:30Z
Peter Cock
oa command does not report the version
The current usage text does not report the tool version:
```
$ oa -h
usage: oa [-h] [--no-log] [--no-progress]
{list,index,buildgraph,seeds,compact,fasta,path,cutlow,graphstats,unfoldrdna,unfold,fillgaps}
...
optional arguments:
-h, --help show this help message and exit
--no-log Do not create a logfile for the assembling
--no-progress Do not print the progress bar during assembling
subcommands:
valid subcommands
{list,index,buildgraph,seeds,compact,fasta,path,cutlow,graphstats,unfoldrdna,unfold,fillgaps}
additional help
list List information about a read index
index Index a set of reads
buildgraph Build the initial assembling graph
seeds Build the set of seed reads
compact Recompact the assembling graph
fasta Build a fasta file from the assembling graph
path Build a fasta file from a path across the assembling
graph
cutlow Cut low coverage edge in an assembling graph
graphstats Print some statistics about the assembling graph
unfoldrdna Assembling graph unfolder for the nuclear rDNA complex
unfold Universal assembling graph unfolder
fillgaps Fill gaps of a partially assembled graph
```
Furthermore I would have expected ``oa -v`` and/or ``oa --version`` to report the version only, and immediately exit. e.g.
```
$ os -v
ORG.asm version 0.1.0b3
```
The current usage text does not report the tool version:
```
$ oa -h
usage: oa [-h] [--no-log] [--no-progress]
{list,index,buildgraph,seeds,compact,fasta,path,cutlow,graphstats,unfoldrdna,unfold,fillgaps}
...
optional arguments:
-h, --help show this help message and exit
--no-log Do not create a logfile for the assembling
--no-progress Do not print the progress bar during assembling
subcommands:
valid subcommands
{list,index,buildgraph,seeds,compact,fasta,path,cutlow,graphstats,unfoldrdna,unfold,fillgaps}
additional help
list List information about a read index
index Index a set of reads
buildgraph Build the initial assembling graph
seeds Build the set of seed reads
compact Recompact the assembling graph
fasta Build a fasta file from the assembling graph
path Build a fasta file from a path across the assembling
graph
cutlow Cut low coverage edge in an assembling graph
graphstats Print some statistics about the assembling graph
unfoldrdna Assembling graph unfolder for the nuclear rDNA complex
unfold Universal assembling graph unfolder
fillgaps Fill gaps of a partially assembled graph
```
Furthermore I would have expected ``oa -v`` and/or ``oa --version`` to report the version only, and immediately exit. e.g.
```
$ os -v
ORG.asm version 0.1.0b3
```
https://git.metabarcoding.org/org-asm/org-asm/-/issues/2
oa index fails with bytes vs string problem
2023-04-25T19:30:24Z
Peter Cock
oa index fails with bytes vs string problem
Using 0.1.0b2 (compiled from source with Python 3.4.3 on Linux), specifically this commit:
https://git.metabarcoding.org/org-asm/org-asm/commit/40c859a5b4ed9d8a6f0d0523136dd8afdb877a7d
Attempting to follow the example but with local data:
http://pythonhosted.org/ORG.asm/mitochondrion.html
The first command fails on uncompressed FASTQ files:
```
$ oa index --estimate-length=0.9 example_index example_R1.fastq example_R2.fastq
2015-08-21 12:14:43,042 [INFO ] Computing read length statistics for the forward file
Traceback (most recent call last):
File "/home/pc40583/bin/oa", line 206, in <module>
config['orgasm']['module'].run(config)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 448, in run
stats,cforward = lengthStats(acgtCut(cforward))
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 282, in lengthStats
stats = Counter(reader())
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 475, in __init__
self.update(*args, **kwds)
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 562, in update
_count_elements(self, iterable)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 279, in reader
store.append((s[0],zlib.compress(s[1])))
TypeError: 'str' does not support the buffer interface
```
I thought this might be due to opening the FASTQ file in text mode (giving strings) versus bytes from gzipped FASTQ files, but that breaks too:
```
$ oa index --estimate-length=0.9 example_index example_R1.fastq.gz example_R2.fastq.gz
2015-08-21 12:21:22,733 [INFO ] Forward file compressed by gzip
2015-08-21 12:21:22,739 [INFO ] Reverse file compressed by gzip
2015-08-21 12:21:22,742 [INFO ] Computing read length statistics for the forward file
Traceback (most recent call last):
File "/home/pc40583/bin/oa", line 206, in <module>
config['orgasm']['module'].run(config)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 448, in run
stats,cforward = lengthStats(acgtCut(cforward))
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 282, in lengthStats
stats = Counter(reader())
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 475, in __init__
self.update(*args, **kwds)
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 562, in update
_count_elements(self, iterable)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 279, in reader
store.append((s[0],zlib.compress(s[1])))
TypeError: 'str' does not support the buffer interface
Deleting tmp file : /tmp/tmp954emhqb/unziped-_gzr7ybi
Deleting tmp file : /tmp/tmp954emhqb/unziped-ed89l2i_
Deleting tmp directory : /tmp/tmp954emhqb
```
Using 0.1.0b2 (compiled from source with Python 3.4.3 on Linux), specifically this commit:
https://git.metabarcoding.org/org-asm/org-asm/commit/40c859a5b4ed9d8a6f0d0523136dd8afdb877a7d
Attempting to follow the example but with local data:
http://pythonhosted.org/ORG.asm/mitochondrion.html
The first command fails on uncompressed FASTQ files:
```
$ oa index --estimate-length=0.9 example_index example_R1.fastq example_R2.fastq
2015-08-21 12:14:43,042 [INFO ] Computing read length statistics for the forward file
Traceback (most recent call last):
File "/home/pc40583/bin/oa", line 206, in <module>
config['orgasm']['module'].run(config)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 448, in run
stats,cforward = lengthStats(acgtCut(cforward))
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 282, in lengthStats
stats = Counter(reader())
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 475, in __init__
self.update(*args, **kwds)
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 562, in update
_count_elements(self, iterable)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 279, in reader
store.append((s[0],zlib.compress(s[1])))
TypeError: 'str' does not support the buffer interface
```
I thought this might be due to opening the FASTQ file in text mode (giving strings) versus bytes from gzipped FASTQ files, but that breaks too:
```
$ oa index --estimate-length=0.9 example_index example_R1.fastq.gz example_R2.fastq.gz
2015-08-21 12:21:22,733 [INFO ] Forward file compressed by gzip
2015-08-21 12:21:22,739 [INFO ] Reverse file compressed by gzip
2015-08-21 12:21:22,742 [INFO ] Computing read length statistics for the forward file
Traceback (most recent call last):
File "/home/pc40583/bin/oa", line 206, in <module>
config['orgasm']['module'].run(config)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 448, in run
stats,cforward = lengthStats(acgtCut(cforward))
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 282, in lengthStats
stats = Counter(reader())
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 475, in __init__
self.update(*args, **kwds)
File "/home/pc40583/lib/python3.4/collections/__init__.py", line 562, in update
_count_elements(self, iterable)
File "/home/pc40583/lib/python3.4/site-packages/orgasm/command/index.py", line 279, in reader
store.append((s[0],zlib.compress(s[1])))
TypeError: 'str' does not support the buffer interface
Deleting tmp file : /tmp/tmp954emhqb/unziped-_gzr7ybi
Deleting tmp file : /tmp/tmp954emhqb/unziped-ed89l2i_
Deleting tmp directory : /tmp/tmp954emhqb
```
Eric Coissac
Eric Coissac