Hi, I was wondering if someone might be able to help.
I'm running Velvet on a cluster, specifically a Cray. I compile with Categories=6, OpenMPI set to 1 and Maxkmers set to 99.
When I run Velveth with my 6 libraries in my local directory, like so:
aprun -n 1 -q -N 1 -d $OMP_NUM_THREADS velveth Baudin_velvetKmer51/ 51 -fastq -shortPaired -separate Readset1.fastq Readset2.fastq -fastq -short singleReadset.fastq.........(etc for each of the remaining 5 libraries...shortpaired2, 3, 4, 5, 6) I get no Roadmap from the output. Velveth finishes at loading the sequences only.
The aprun command above is used to assign the job on the cluster with a number of nodes, threads etc.
I've managed to get it running with a single library, but for some reason it doesn't work for multiple libraries.
Has anyone had similar problems running Velvet on a cluster and getting this kind of problem?
Thanks for any help you can provide.
I'm running Velvet on a cluster, specifically a Cray. I compile with Categories=6, OpenMPI set to 1 and Maxkmers set to 99.
When I run Velveth with my 6 libraries in my local directory, like so:
aprun -n 1 -q -N 1 -d $OMP_NUM_THREADS velveth Baudin_velvetKmer51/ 51 -fastq -shortPaired -separate Readset1.fastq Readset2.fastq -fastq -short singleReadset.fastq.........(etc for each of the remaining 5 libraries...shortpaired2, 3, 4, 5, 6) I get no Roadmap from the output. Velveth finishes at loading the sequences only.
The aprun command above is used to assign the job on the cluster with a number of nodes, threads etc.
I've managed to get it running with a single library, but for some reason it doesn't work for multiple libraries.
Has anyone had similar problems running Velvet on a cluster and getting this kind of problem?
Thanks for any help you can provide.
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