How to get the output on multiple files into one file in sbatch script?

Question

[newbie]

Hi,

I have 120 sorted.bam files. I would like to check the strandedness of each sample. Whether unstranded or stranded. All 120 sorted.bams are in this directory /data/bams

For that, I kept all the sample names in the samples.txt file. And I started using a shell sbatch script like below:

#!/bin/bash
#SBATCH --job-name=strandspecify_Job
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=1G
#SBATCH --time=0:30:00
#SBATCH --qos=30min
#SBATCH --output=outputs/Inferstrand_%j_%a.out # Standard output
#SBATCH --error=outputs/Inferstrand_%j_%a.err # Standard error
#SBATCH --array=1-120%5

LBID=$(head -$SLURM_ARRAY_TASK_ID /data/samples.txt | tail -1)
Path=/data/bams

ml load RSeQC/2.6.4-goolf-1.7.20-Python-2.7.11-R-3.2.4
python infer_experiment.py -r gencode.v27.annotation.bed -i $Path/${LBID}.sorted.bam

All the Standard output files have information only about a Fraction of reads like below:

Fraction of reads failed to determine: 0.0658
Fraction of reads explained by "1++,1--,2+-,2-+": 0.4677
Fraction of reads explained by "1+-,1-+,2++,2--": 0.4665

But nowhere it is mentioned the output is from which samples? Is there a way to write all the outputs into one file with the sample name in it to know which output is from which sample?

[h.mon]

Why don't you add:

echo "Processing file ${LBID}"

Just before the call to infer_experiment.py?

[Shred]

Why not using a for loop to call each bam file? You could get the filename into a variable and you could echo first the filename than the output

[newbie]

Can you please show me how to do that?

[JC]

add an echo before calling your python code:

ml load RSeQC/2.6.4-goolf-1.7.20-Python-2.7.11-R-3.2.4
echo ${LBID}.sorted.bam
python infer_experiment.py -r gencode.v27.annotation.bed -i $Path/${LBID}.sorted.bam

[newbie]

Thanks a lot...it looks fine now.