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
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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