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  • #22

Closed
Open
Opened Feb 04, 2016 by Martí Boleda@marti-boleda

bug in unfold

It happens on a Poaceae genome a bit more complex than is usual

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'
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Reference: org-asm/org-asm#22