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Help in MEGAHIT! I have no idea with my result from the process in MEGAHIT.

Hi everyone,

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

assembly next-gen metagenomic
• 2,205 views • link
written by nisrinalulu • nisrinalulu

Dear Kevin Blighe,

Yes, thank you for your reminding. I'm really new for this job. Sorry for make uncomfort. Once again thank you for reminding me 🙏

• 0 views • link
written by nisrinalulu • nisrinalulu

Sure thing. - no worries. What is the output of the qsub job? It should output a log and/or error file.

• 0 views • link
written by Kevin Blighe Kevin Blighe

Dear Kevin Blighe,

Thank you for your understanding. I will make more effort for my job.

Yes, in the qsub output there is log file. Here is the result whe i open log file:

2020-01-15 12:14:14 - MEGAHIT v1.2.9 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ (END)

I have no idea how to solved my problem. Thank you

• 0 views • link
written by nisrinalulu • nisrinalulu

You don't appear to be assigning any specific resources to the command via your PBS script. It's possible that not enough are being allocated, so, nothing happens. Can you check with your IT Service Desk about how to allocate resources via QSUB?

• 0 views • link
written by Kevin Blighe Kevin Blighe

Ah, i see. OK Kevin, i'll check with my IT Service Desk. Thank you for your advise.

• 0 views • link
written by nisrinalulu • nisrinalulu

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