I have a problem for my job using MEGAHIT. I write command in shell script and then run it in SSH server. Command for MEGAHIT is like this:
#!/bin/bash #PBS -q normal #PBS -l nodes=1:ppn=2 cd $PBS_O_WORKDIR BIN="/app/bin/MEGAHIT_v1.2.9" megahit -1 IA_1.fq.gz -2 IA_2.fq.gz -o IA.asm run_megahitIA.sh (END)
and than i submit the job in qsub using command:
$chmod +x megahitIA.sh $qsub megahitIA.sh
and then i got result for the job in IA.asm directory and in the directory there 3 file which are
intermediate_contigs log tmp
but when i open folder intermediate_contigs there are no file final.contigs.fasta which is the result from the contigs.
I didn't get any error messages for this job. But i didn't get fasta final contigs. How to solved this problem?
Thank you so much