Hi all friends,
I'm running StringTie on the output of STAR. I got bam file from STAR with the following command:
./STAR --runThreadN 8 --genomeDir /home/seta/wrkdir/software/star-2.5.2b/genome --sjdbGTFfile /home/seta/wrkdir/software/star-2.5.2b/genome/anno.gtf --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outFileNamePrefix map1 --readFilesIn /home/seta/wrkdir/Sequensing_files/file1.fastq.gz --readFilesCommand zcat
But when I run the StringTie via the below script:
#! /bin/sh
#$ -S /bin/bash
#$ -N str
#$ -j N
#$ -o str_out
#$ -cwd
#$ -l h_vmem=40G
#$ -pe openmp 4
export OMP_NUM_THEREADS=$NSLOTS
cd /home/seta/wrkdir/software/stringtie-1.3.2d.Linux_x86_64
./stringtie -p 4 -G /home/seta/wrkdir/software/star-2.5.2b/genome/anno.gtf -B -o str1_as/transcripts.gtf -l str1 /home/seta/wrkdir/software/star-2.5.2b/bin/Linux_x86_64/map1Aligned.sortedByCoord.out.bam
But StringTie gave me the error that cannot find the bam file, it's here:
Error: input file /home/seta/wrkdir/software/star-2.5.2b/bin/Linux_x86_64/map1Aligned.sortedByCoord.out.bam
cannot be found!
But when I run the above stringtie command directly on the terminal (not job schedule), it worked well. Please help me what is wrong with the script?
Thanks
This was the problem I was referring to in a previous thread about compilation.
When you compile your own software on a cluster you need to be sure that the location you put it in is accessible from all cluster nodes. At this point you could move the files (that are not accessible based on that error message) to "scratch" space (most clusters will have a common ) and run it from there.
BTW: Keep your data files in a segregated directory. Looks like they are in the program dir now.
I have not the problem with STAR, the issue is related to stringtie. However, could you please let me know how I can sure the location is accessible from all cluster nodes?
I was focusing on the name STAR in your directory path above hence the error. Post updated accordingly. It is a bit odd that your home directory (based on the name) is not accessible on all cluster nodes.