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Non-SGE Environment #16

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wzylin opened this issue Jan 30, 2017 · 1 comment
Open

Non-SGE Environment #16

wzylin opened this issue Jan 30, 2017 · 1 comment

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@wzylin
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wzylin commented Jan 30, 2017

Hi
I confront some problems when using nanocorr.
Hope you may help me out. Thank you!

  1. how am I use two paired end 1.fasta 2.fasta files to correct the nanopore.fa ? should I combine the paired end files into one?
  2. I used Non-SGE Environment command, but where I can find the output corrected reads?
    errors:
    sh: 1: blast6Filter: not found
    Failed : blast6Filter r_experimental p0007.blast6 > p0007.blast6.r
    sh: 1: blast6Filter: not found
    Failed : blast6Filter r_experimental p0003.blast6 > p0003.blast6.r
    sh: 1: blast6Filter: not found
    Failed : blast6Filter r_experimental p0001.blast6 > p0001.blast6.r
    sh: 1: blast6Filter: not found
    Failed : blast6Filter r_experimental p0004.blast6 > p0004.blast6.r
    sh: 1: blast6Filter: not found

what I summitted to PBS:
#!/bin/bash
#PBS -l nodes=1:ppn=10
#PBS -l mem=40gb
#PBS -l walltime=12:00:00
#PBS -m abe
#PBS -q medium
#PBS -N nanocorr_0001
cd $PBS_O_WORKDIR
source /home/wzylin/opt/nanocorr/nanocorr_ve/bin/activate
cd /home/wzylin/opt/nanocorr/0001
for j in {1..500}; do
echo "SGE_TASK_ID=$j TMPDIR=/tmp /home/wzylin/opt/nanocorr/nanocorr.py /home/wzylin/opt/nanocorr/AC_Trim_1P.fa";
done | parallel -j 10

@MattHodgman
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I also got the error sh: blast6Filter: command not found

Did you figure it out?

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