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)