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Old 08-24-2013, 01:44 PM   #1
KSF
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Default GICL Error at step 'pairwise'

Hello,

I'm trying to set up gicl for the purposes of redundancy reduction in merged 454+Illumina pre-assemblies. I received the following error when trying to run the program. I think it may have something to do with the PATH settings but am a novice when it comes to this kind of stuff in Linux (running Fedora 3.6.11 64bit).

>>> --- Initialization [454ILMNcdhit.fa] started at Aug 24 14:13:32 2013
gicl running options:
gicl 454ILMNcdhit.fa -g sge -c8 -n2000 -p99 -l50
Standard log file: gicl_454ILMNcdhit.fa.log
Error log file: err_gicl_454ILMNcdhit.fa.log
Using 8 CPUs for clustering and assembly
-= Rebuilding 454ILMNcdhit.fa indices =-
102665 entries from file 454ILMNcdhit.fa were indexed in file 454ILMNcdhit.fa.cidx
>>> --- pairwise [454ILMNcdhit.fa] started at Aug 24 14:13:39 2013
Launching distributed clustering:
gridx -g sge -p 8 -n 2000 -i 454ILMNcdhit.fa -d cluster -C '/home/rolab/gicl/454ILMNcdhit.fa:99:30:50:G' -c '/home/rolab/gicl/gicl_mgbl.psx'
Running on localhost: /home/rolab/gicl/gridx -g sge -p 8 -n 2000 -i 454ILMNcdhit.fa -d cluster -C /home/rolab/gicl/454ILMNcdhit.fa:99:30:50:G -c /home/rolab/gicl/gicl_mgbl.psx
52 entries from file gridx-psx-454ILMNcdhit.fa.n2000.s0.t0.taskDb were indexed in file gridx-psx-454ILMNcdhit.fa.n2000.s0.t0.taskDb.cidx
sh: qsub: command not found
Error: No Job ID# could be parsed!
() at /home/rolab/gicl/gridx line 727.
Error at 'gridx -g sge -p 8 -n 2000 -i 454ILMNcdhit.fa -d cluster -C '/home/rolab/gicl/454ILMNcdhit.fa:99:30:50:G' -c '/home/rolab/gicl/gicl_mgbl.psx''


Process terminated with an error, at step 'pairwise'!
gicl (454ILMNcdhit.fa) encountered an error at step pairwise
Working directory was /home/rolab/gicl.

Any help would be great, or alternatively an easier approach for redundancy reduction of merged assemblies.

Thanks
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Old 08-25-2013, 05:47 PM   #2
GenoMax
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Default

This is the important bit that I see in the text.

Code:
sh: qsub: command not found
I assume you are submitting the job to a cluster? What is the complete command you are using for this job submission.

Are there any additional clues in the following log files?

Standard log file: gicl_454ILMNcdhit.fa.log
Error log file: err_gicl_454ILMNcdhit.fa.log
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Old 08-26-2013, 08:04 AM   #3
KSF
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Default

Yeah, that's the bit I picked p on too, but wasn't sure if there was something else I was overlooking.

I am trying to run this on a workstation (8 core, 48 Gb RAM).

The command I used to start was:
gicl /home/rolab/454Allcontigs.fa -g sge -c8 -n2000 -p98 -v10 -l50

The workstation is running another process in windows right now so I'll check the other error log in an hour.

Thanks for the help.
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Old 08-26-2013, 08:36 AM   #4
GenoMax
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Are you actually running SGE to manage jobs on this workstation (not how I would imagine a standalone workstation to be set up)?

If you are not then you should probably run TGICL instead of GICL (which is meant to be used with SGE and condor on a cluster): http://compbio.dfci.harvard.edu/tgi/software/
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Old 08-26-2013, 08:55 AM   #5
KSF
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I have to admit, I'm in over my head when it comes to the system setup. The OS was installed by the IT personnel in our dept. I had thought it was setup to be compatible with software run on clusters but I think I see the problem you mean.

I didn't want to run a full assembly of the contigs. I ran a pre-assembly of Illumina PE reads and 454 reads separately and then merged with CD-HIT-EST. I wanted to collapse redundant contigs, which is why I had thought GICL would be a better option than TGICL. Am I mistaken in that understanding?
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