bug
martiboleda@luke21:~/assembly/comments/Vicia_sylvatica/BSM$ oa path --path -40 5 44 5 43 42 18 42 18 42 19 -37 0 -35 -35 12 38 -31 -25 24 39 21 39 21 39 -32 -34 -33 -34 -33 -34 -23 25 -- BSM chloroplast/BSM.chloroplast
Loading global data...
Done.
Reading indexed sequence reads...
7985938 sequences read
Reading indexed pair data...
Done.
Loading reverse index...
Done.
Indexing reverse complement sequences ...
Fast indexing forward reads...
Fast indexing reverse reads...
Done.
2016-02-22 12:40:07,766 [INFO ] Load matches from previous run : 1 probe sets restored
2016-02-22 12:40:07,766 [INFO ] ==> A total of : 16691
2016-02-22 12:40:07,766 [INFO ] Match list :
2016-02-22 12:40:07,769 [INFO ] petG : 247 (211.4x)
2016-02-22 12:40:07,770 [INFO ] psbM : 215 (200.2x)
2016-02-22 12:40:07,770 [INFO ] psbZ : 360 (183.9x)
2016-02-22 12:40:07,770 [INFO ] psbE : 476 (181.6x)
2016-02-22 12:40:07,770 [INFO ] psbI : 206 (181.2x)
2016-02-22 12:40:07,770 [INFO ] psaC : 386 (150.9x)
2016-02-22 12:40:07,770 [INFO ] psbJ : 180 (142.5x)
2016-02-22 12:40:07,770 [INFO ] atpH : 364 (142.3x)
2016-02-22 12:40:07,770 [INFO ] psbL : 162 (135.0x)
2016-02-22 12:40:07,770 [INFO ] rbcL : 2016 (133.3x)
2016-02-22 12:40:07,771 [INFO ] psbA : 1298 (116.4x)
2016-02-22 12:40:07,771 [INFO ] psbF : 140 (113.7x)
2016-02-22 12:40:07,771 [INFO ] psbN : 138 (101.6x)
2016-02-22 12:40:07,771 [INFO ] rpl36 : 112 ( 95.9x)
2016-02-22 12:40:07,771 [INFO ] rps2 : 708 ( 95.0x)
2016-02-22 12:40:07,771 [INFO ] psbB : 1505 ( 93.8x)
2016-02-22 12:40:07,771 [INFO ] atpA : 1469 ( 91.8x)
2016-02-22 12:40:07,771 [INFO ] psbC : 1331 ( 89.1x)
2016-02-22 12:40:07,771 [INFO ] psbD : 988 ( 88.6x)
2016-02-22 12:40:07,772 [INFO ] rps12 : 675 ( 86.9x)
2016-02-22 12:40:07,772 [INFO ] psaB : 1881 ( 81.2x)
2016-02-22 12:40:07,772 [INFO ] atpE : 333 ( 79.9x)
2016-02-22 12:40:07,772 [INFO ] psaA : 1888 ( 79.7x)
2016-02-22 12:40:07,772 [INFO ] psbT : 83 ( 79.6x)
2016-02-22 12:40:07,772 [INFO ] rps4 : 494 ( 77.8x)
2016-02-22 12:40:07,772 [INFO ] petA : 783 ( 77.5x)
2016-02-22 12:40:07,772 [INFO ] rps7 : 717 ( 73.2x)
2016-02-22 12:40:07,772 [INFO ] atpB : 1006 ( 64.0x)
2016-02-22 12:40:07,773 [INFO ] rpl14 : 230 ( 59.7x)
2016-02-22 12:40:07,773 [INFO ] rps18 : 177 ( 55.5x)
2016-02-22 12:40:07,773 [INFO ] rpl23 : 301 ( 51.2x)
2016-02-22 12:40:07,773 [INFO ] psbH : 116 ( 50.3x)
2016-02-22 12:40:07,773 [INFO ] rpl16 : 200 ( 46.9x)
2016-02-22 12:40:07,773 [INFO ] rpoC1 : 914 ( 42.6x)
2016-02-22 12:40:07,773 [INFO ] psbK : 57 ( 29.6x)
2016-02-22 12:40:07,773 [INFO ] rpoA : 302 ( 29.1x)
2016-02-22 12:40:07,773 [INFO ] ndhA : 315 ( 27.7x)
2016-02-22 12:40:07,773 [INFO ] rpoB : 854 ( 25.2x)
2016-02-22 12:40:07,774 [INFO ] cemA : 108 ( 14.9x)
2016-02-22 12:40:07,774 [INFO ] ccsA : 135 ( 13.0x)
2016-02-22 12:40:07,774 [INFO ] rpoC2 : 436 ( 10.0x)
2016-02-22 12:40:07,774 [INFO ] accD : 139 ( 9.0x)
2016-02-22 12:40:07,774 [INFO ] rps8 : 7 ( 1.7x)
2016-02-22 12:40:07,774 [INFO ] clpP : 4 ( 0.6x)
2016-02-22 12:40:07,774 [INFO ] ycf1 : 26 ( 0.4x)
2016-02-22 12:40:11,964 [INFO ] Evaluate fragment length
Compacting graph 100.0 % |##################################################-] remain : 00:00:00
Minimum stem coverage = 100
2016-02-22 12:40:15,211 [INFO ] Fragment length estimated : 425.830817 pb (sd: 184.224292)
Compacting graph 100.0 % |##################################################-] remain : 00:00:00
Minimum stem coverage = 100
-14 -> 4 scaffolded by 284 pair ended links
-4 -> 14 scaffolded by 284 pair ended links
2016-02-22 12:40:17,446 [INFO ] Print the result as a fasta file
2016-02-22 12:40:17,446 [INFO ] Built path : [-40, 5, 44, 5, 43, 42, 18, 42, 18, 42, 19, -37, 0, -35, -35, 12, 38, -31, -25, 24, 39, 21, 39, 21, 39, -32, -34, -33, -34, -33, -34, -23, 25]
Compacting graph 100.0 % |##################################################-] remain : 00:00:00
Minimum stem coverage = 100
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/path.py", line 92, in run
logger=logger)
File "/nfs_scratch/LECA_ENVIRONEMENT/softs/ORG.asm-0.1.12/lib/python3.5/site-packages/orgasm/tango.py", line 1357, in path2fasta
stem = alledges[stemid]
KeyError: -40
