Assembling the sequences with MEGAHIT. How to make it works?

Question

[nisrinalulu]

Hi! I am a really for using MEGAHIT. I try to use MEGAHIT with command:

#!/bin/bash
#PBS -q normal
#PBS -l nodes=1:ppn=2

cd $PBS_O_WORKDIR

BIN="/app/bin/vasp_5.2_intelmpi_ifort"
mpirun -n 2 $BIN > LOG1

megahit -1 HA_1.fq.gz -2 HA_2.fq.gz -o out

and the answer is

Output directory /home/husna/out already exists, please change the parameter -o to another value to avoid overwriting

What the mean of parameter -o? I'm not undestand. Then i try another command:

qsub -cwd -pe multislot 24 -N megahit -l mtc=1 -b y \
/vol/cmg/bin/megahit -1 HA_1.fq.gz -2 HA_2.fq.gz -t 24 -o megahit_out

but, it doesn't work.

Anyone please help me how to run MEGAHIT properly. I try to use command in github page but it doesn't work.

[GenoMax]

but, it doesn't work.

Is a statement that gives us no useful information for helping solve your problem. Tell us if you get an error message and post that message here.

Have you tried to use a directory name that does not already exist for -o paramter?

[nisrinalulu]

Yes, i have tried other directory name with this command

megahit -1 HA_1.fq.gz -2 HA_2.fq.gz -o HA.megahit_asm

But the answer is

2020-01-14 20:57:43 - MEGAHIT v1.2.9
megahit: Cannot find file /home/husna/HA_1.fq.gz

[GenoMax]

Error is clear.

/home/husna/HA_1.fq.gz

is not the right location for that file. If that file is is some other directory then you need to use the correct full/relative path for it.

[nisrinalulu]

Actually i want to run job with PBS/qsub to submit job in SSH with this command:

#!/bin/bash
#PBS -q normal
#PBS -l nodes=1:ppn=2
cd $PBS_O_WORKDIR
BIN="/app/bin/vasp_5.2_intelmpi_ifort"
mpirun -n 2 $BIN > LOG1
megahit -1 HA_1.fq.gz -2 HA_2.fq.gz -o out

but i don't know when i have to put qsub command and how to entry my script to qsub. And how to until i get ID job with qsub.

and i don't know those command that i've already put is running or not. And i wonder how to check that our job is running or not in system. Thank you

[Pierre Lindenbaum]

What the mean of parameter -o

http://www.metagenomics.wiki/tools/assembly/megahit

-o/--out-dir <string> output directory, default ./megahit_out

so if your run this cmd twice out already exists and this tool doesn't allow it. Change the name or remove the directory...

[nisrinalulu]

OK, thank you so much. I am going to try it.