Sailor Cannot Find Files

[lastarr15]

I have been trying to run Sailor using the following script:
#!/bin/bash
#SBATCH -n 10
#SBATCH -p main
#SBATCH --qos main
#SBATCH -N 1

module load singularity
pip install cwlref-runner
cd /home/lastarr/D2005.1_sailor
./sailor-1.0.4 D2005.1sailor_D1

Everything is in the correct directory (/home/lastarr/D2005.1_sailor) and is properly formatted. When I submit this job, the following results:

self.setup(dedup(referenced_files), basedir)
File "/opt/conda/lib/python2.7/site-packages/cwltool/pathmapper.py", line 225, in setup
self.visit(fob, stagedir, basedir, staged=True)
File "/opt/conda/lib/python2.7/site-packages/cwltool/pathmapper.py", line 214, in visit
self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir, copy=copy, staged=staged)
File "/opt/conda/lib/python2.7/site-packages/schema_salad/sourceline.py", line 150, in exit
raise self.makeError(unicode(exc_value))
ValidationException: D2005.1sailor_D1:9:3: [Errno 2] No such file or directory: '/home/lastarr/D2005.1_sailor/home/lastarr/D2005.1_sailor/D1Aligned.sortedByCoord.out.bam'
[step split_strands] Cannot make job: D2005.1sailor_D1:9:3: [Errno 2] No such file or directory: '/home/lastarr/D2005.1_sailor/home/lastarr/D2005.1_sailor/D1Aligned.sortedByCoord.out.bam'
[workflow rnaediting2strands.workflow.cwl] outdir is /home/lastarr/D2005.1_sailor/D2005/.tmp/interm/EDZJxh
{}
Final process status is permanentFail
cp: cannot stat '/home/lastarr/D2005.1_sailor/D2005/.tmp/outdir/*': No such file or directory

Any help would be great. I am in my home directory when I run this. Thanks!

[byee4]

The error seems to be complaining about missing files, if you know the files do exist, it might be a singularity bind issue. If you are using singularity, you might need to bind the directory or set your SINGULARITY_BINDPATH SECURE: MESSAGE FROM lastarr15 ON 7/29/22, 3:13 PM I have been trying to run Sailor using the following script: #!/bin/bash #SBATCH -n 10 #SBATCH -p main #SBATCH --qos main #SBATCH -N 1 module load singularity pip install cwlref-runner cd /home/lastarr/D2005.1_sailor ./sailor-1.0.4 D2005.1sailor_D1 Everything is in the correct directory (/home/lastarr/D2005.1_sailor) and is properly formatted. When I submit this job, the following results: self.setup(dedup(referenced_files), basedir) File "/opt/conda/lib/python2.7/site-packages/cwltool/pathmapper.py", line 225, in setup self.visit(fob, stagedir, basedir, staged=True) File "/opt/conda/lib/python2.7/site-packages/cwltool/pathmapper.py", line 214, in visit self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir, copy=copy, staged=staged) File "/opt/conda/lib/python2.7/site-packages/schema_salad/sourceline.py", line 150, in exit raise self.makeError(unicode(exc_value)) ValidationException: D2005.1sailor_D1:9:3: [Errno 2] No such file or directory: '/home/lastarr/D2005.1_sailor/home/lastarr/D2005.1_sailor/D1Aligned.sortedByCoord.out.bam' [step split_strands] Cannot make job: D2005.1sailor_D1:9:3: [Errno 2] No such file or directory: '/home/lastarr/D2005.1_sailor/home/lastarr/D2005.1_sailor/D1Aligned.sortedByCoord.out.bam' [workflow rnaediting2strands.workflow.cwl] outdir is /home/lastarr/D2005.1_sailor/D2005/.tmp/interm/EDZJxh {} Final process status is permanentFail cp: cannot stat '/home/lastarr/D2005.1_sailor/D2005/.tmp/outdir/*': No such file or directory Any help would be great. I am in my home directory when I run this. Thanks! — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/YeoLab/sailor/issues/14__;!!LLK065n_VXAQ!ncOBy0L2MqwnTO24dVNzGAAdHp7VdZkUz9TNRfMc-yzxVxDT9lyqcNDe8EdfiOCQhA4eja_v9rVd9-lU1bTj2rjeUNO4$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AB7TJP4Z5A5AZ6XUHTVZF2LVWRJPXANCNFSM55CCVEXA__;!!LLK065n_VXAQ!ncOBy0L2MqwnTO24dVNzGAAdHp7VdZkUz9TNRfMc-yzxVxDT9lyqcNDe8EdfiOCQhA4eja_v9rVd9-lU1bTj2oydyM00$>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>