Only Log.out and Log.progress.out files after alignment.

Question

[Yihan]

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.

[Ram]

It looks like your job is failing. Redirect the job's STDERR and STDOUT to separate files and examine them.

[GenoMax]

I redacted your email address.

Please add

#SBATCH -o slurm_%J.out
#SBATCH -e slurm_%J.err

to your script to capture outputs as @Ram suggested and check those.

[Yihan]

Thank you!

Answer 1

[Ram]

I wonder what outSAMType BAM SortedB$ means - valid options are BAM Unsorted, BAM SortedByCoordinate and BAM Unsorted SortedByCoordinate

[GenoMax]

Actually this may be reason for run failure. Sorting BAM inside a STAR run needs a large amount of RAM. I see only 64 G assigned for this job.

Yihan : Remove that option and do the BAM sorting in a separate job using samtools.

[Ram]

As a side note: unless a wiggle output is required of STAR, sorting the BAM with it is a bad idea.

[Yihan]

Yes, I think this is the problem... When I copied the script I used previously, the ByCoordinate turns into a $ because of the size of the terminal window. It worked now. Thank you so much.

[Ram]

I've moved my comment to an answer. Please accept it to mark the post as solved.