Only Log.out and Log.progress.out files after alignment.
I encountered some problem on command line at the step of alignment.
Here is the script.
#!/bin/bash
#SBATCH --ntasks=20
#SBATCH --mem=64G
#SBATCH --mail-type=END
#SBATCH --mail-user=xxxxx
cd /data/elmallahlab/Yihan/biswas_6991_rawdata
module load STAR/2.7.2b-gcb01
for i in *_R1_001.fastq.gz;
do STAR --quantMode GeneCounts \
--readFilesCommand zcat \
--outSAMtype BAM SortedB$ \
--genomeDir /data/elmallahlab/Yihan/mouse_index \
--readFilesIn $i ${i%_R1_001.fastq.gz}_R2_001.fastq.gz \
--runThreadN 20 \
--outFileNamePrefix /data/elmallahlab/Yihan/biswas_6991_alignment/${i%_R1_001.fastq.gz};
done
After running the script, I couldn't get the Log.final.out and out.tab file for the merged files. I checked the content inside these mergedLog.out and mergedLog.progress.out files using cat, but there is nothing inside.
1 answer
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It looks like your job is failing. Redirect the job's STDERR and STDOUT to separate files and examine them.
I redacted your email address.
Please add
to your script to capture outputs as @Ram suggested and check those.
Thank you!