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
