Question: Help in MEGAHIT! I have no idea with my result from the process in MEGAHIT.
0
gravatar for nisrinalulu
4 days ago by
nisrinalulu10
nisrinalulu10 wrote:

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

metagenomic next-gen assembly • 122 views
ADD COMMENTlink modified 4 days ago • written 4 days ago by nisrinalulu10
1

Instead of creating multiple posts about the same general topic, please ensure that you invest your own effort into your problem(s) before posting here again.

Here are threads that you have created since yesterday:

ADD REPLYlink written 4 days ago by Kevin Blighe53k

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 🙏

ADD REPLYlink written 4 days ago by nisrinalulu10

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

ADD REPLYlink written 4 days ago by Kevin Blighe53k

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

ADD REPLYlink modified 4 days ago • written 4 days ago by nisrinalulu10

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?

ADD REPLYlink written 4 days ago by Kevin Blighe53k
1

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

ADD REPLYlink written 4 days ago by nisrinalulu10
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