Question: An odd error with StringTie!!
0
gravatar for seta
2.6 years ago by
seta1.2k
Sweden
seta1.2k wrote:

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

error stringtie rnaseq • 1.3k views
ADD COMMENTlink modified 2.6 years ago by Devon Ryan91k • written 2.6 years ago by seta1.2k

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax71k

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?

ADD REPLYlink written 2.6 years ago by seta1.2k

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax71k
0
gravatar for Devon Ryan
2.6 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

Presumably whatever node this is getting run on can't see that directory (or the NFS is really slow). Try an ls on the node first and make sure you save stdout somewhere.

ADD COMMENTlink written 2.6 years ago by Devon Ryan91k

Thanks. I have not enough experience with such issues and pass your response to our admin. Just for learning, I searched on the net for doing your advice, but nothing found useful. could you please explain or introduce me some links?

ADD REPLYlink written 2.6 years ago by seta1.2k

Your best bet is to bring the cluster admin a coffee on Monday and ask him/her to give you a little overview of how this particular cluster is structured. In some larger clusters, you might find that a certain path is available on some (but not all) nodes. There are typically very good reasons for this, but you'll need an overview so you know what queue you should be submitting things to. Anyway, the admin should understand the error message you're seeing, since obviously if you can see the file on the head node then it's not being seen (at that location at least) on at least some of the cluster nodes.

ADD REPLYlink written 2.6 years ago by Devon Ryan91k

Thanks, Devon. Hope coffee solve the problem!

ADD REPLYlink written 2.6 years ago by seta1.2k

If that doesn't do the trick then I recommend cake as well. I kid you not, it can help.

ADD REPLYlink written 2.6 years ago by Devon Ryan91k
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