problem with Newbler2SAM

[acpatel]

I have a set of transcriptome SFF files that I've aligned to the mouse reference genome mm9 using gsMapper (aka Newbler) -- the latest 2.5.3 version.  When I try to take the 454PairAlign.txt file from that mapping, and turn it into a SAM, something bad happens.

Using Fedora 12, and the glu-1.0b2-prerelease-Linux_x86-64.tgz, I get a strange error:

[acpatel@sevenswords mapping]$ glu -v seq.Newbler2SAM ./454PairAlign.txt ~/mysff/*.sff -o rebalb2.sam

GLU (unknown) module: seq.Newbler2SAM

Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.

Loading SFF index for /home/acpatel/mysff/FV70H5K01.sff

Loading SFF index for /home/acpatel/mysff/FV70H5K02.sff

Loading SFF index for /home/acpatel/mysff/FWKYPDT01.sff

Loading SFF index for /home/acpatel/mysff/FWKYPDT02.sff

Loading SFF index for /home/acpatel/mysff/FWKZMOX01.sff

Loading SFF index for /home/acpatel/mysff/FWKZMOX02.sff

Loading SFF index for /home/acpatel/mysff/FWV0HRM01.sff

Loading SFF index for /home/acpatel/mysff/FWV0HRM02.sff

Generating alignment from ./454PairAlign.txt to rebalb2.sam

Well, that could have gone better.

Execution aborted due to a problem with the program input, parameters

supplied, an error in the program.  Please examine the following failure

trace for clues as to what may have gone wrong.  When in doubt, please send

this message and a complete description of the analysis you are attempting

to perform to the software developers.

Error: substring not found

Command line:

  glu seq.Newbler2SAM ./454PairAlign.txt /home/acpatel/mysff/FV70H5K01.sff /home/acpatel/mysff/FV70H5K02.sff /home/acpatel/mysff/FWKYPDT01.sff /home/acpatel/mysff/FWKYPDT02.sff /home/acpatel/mysff/FWKZMOX01.sff /home/acpatel/mysff/FWKZMOX02.sff /home/acpatel/mysff/FWV0HRM01.sff /home/acpatel/mysff/FWV0HRM02.sff -o rebalb2.sam

Well, this is embarrassing.

Traceback:  Traceback (most recent call last):

    File "glu/lib/glu_launcher.py", line 212, in main

    File "glu/modules/seq/Newbler2SAM.py", line 459, in main

    File "glu/modules/seq/Newbler2SAM.py", line 280, in handle_unaligned

    File "glu/modules/seq/Newbler2SAM.py", line 219, in handle_maligned

    File "glu/modules/seq/Newbler2SAM.py", line 156, in pair_align_records

  ValueError: substring not found

  

[Wed May  4 11:56:03 2011] Execution aborted due to a fatal error

I have no idea what the problem is -- both the sff files and the txt file are perfectly working in other tools.

Thanks,

Anand

[Jacobs, Kevin (NIH/NCI) [C]]

Hi Anand,

 

I may be making some undue DNAseq assumptions about the SFF files.  Could you send me a small portion of your 454PairAlign.txt file to test?  Hopefully enough of it to exhibit the error below.  I do not need any of the SFF files, at least at this stage.

 

Thanks for the bug report,

-Kevin

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