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#12 SGA Error

New
nobody
None
Medium
Defect
2013-11-22
2013-11-22
Anonymous
No

Originally created by: ptmcken... (code.google.com)@gmail.com

What steps will reproduce the problem?
1. Running the A5_pipeline.pl example assembly.

What is the expected output? What do you see instead?
instead:

$ a5_pipeline.pl phiX_p1.fastq phiX_p2.fastq phiX_assembly.out
[a5] Begin: 17:0 on 10-22-2013
[a5] Found the following libraries:
     raw1:
      id=raw1
      p1=phiX_p1.fastq
      p2=phiX_p2.fastq
[a5] Found 1 libraries
[a5] Starting pipeline at step 1
[a5] Cleaning reads with SGA
[a5] Cleaning reads with SGA
sh: /Volumes/Macintosh: No such file or directory
[a5] Error preprocessing reads with SGA

What version of the product are you using? On what operating system?
MacOsX 2013-03-26

Please provide any additional information below.
I have a feeling this is something silly that I might be overlooking.

Discussion


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