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glu usage: error? #6

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. type glu then enter
2.
3.

What is the expected output? What do you see instead?
expected is something like this, Usage: glu [glu options] module [module
options] [input file(s)] ...
What is presented is, usage: glu [options] [module] [args...]

What version of the product are you using? On what operating system?

Please provide any additional information below.

Original issue reported on code.google.com by mikegcul...@gmail.com on 7 Oct 2009 at 5:29

GoogleCodeExporter commented 9 years ago 
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

Original comment by acpa...@gmail.com on 4 May 2011 at 5:02