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.