Closed moldach closed 4 years ago
I'd start out looking at the log files in output_dir/L1522785992-normal_normal_genome/validate/batch-mFDMVoNMPeFmRcZqbfVSqx-*
It sounds like all the jobs failed, so you can pick any of those directories.
Hi @oneillkza thank,
Looks like the error is due to a blat dependency (I was wrong...)
Traceback (most recent call last):
File "/home/moldach/bin/mavis/bin/mavis", line 10, in <module>
sys.exit(main())
File "/home/moldach/bin/mavis/lib/python3.8/site-packages/mavis/main.py", line 297, in main
args.aligner_version = get_aligner_version(args.aligner)
File "/home/moldach/bin/mavis/lib/python3.8/site-packages/mavis/align.py", line 152, in get_aligner_v$
raise ValueError("unable to parse blat version number from:'{}'".format(proc))
ValueError: unable to parse blat version number from:'/bin/sh: blat: command not found'
Now blat
is available on the HPC to users via module load blat
. If I run which blat
I can see that the pathway is: /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/blat/3.5/bin/blat
How can I tell Mavis where to look for blat
?
Hmm -- as near as I can tell it just looks for it to be on the path. Are you running module load blat
at the start of the script? I believe what that does is set up path/environment variables, so as long as those propagate it should work fine.
Hi again, I've confirmed that using module load blat
on my remote server makes blat
accessible in the path. Therefore including this at the start of the script solved my problem.
Thank you very much!
MAVIS version: 2.2.6
Python version: 3.8.2
OS: CentOS Linux 7
I'm running into issues trying to run Mavis on the SLURM scheduler.
I'm getting errors when trying the Mavis (Full) tutorial which is (supposed) to submit to a SLURM scheduler.
Getting tutorial data
Generating the Config file
Setting up the pipeline
Submitting Jobs to the Cluster
Looking at
squeue
immediately I see:However, soon after, I see a non-zero exit code:
Running the following to check the jobs:
Shows that the jobs failed but I’m not sure why? I was able to run the Mavis Mini-Tutorial locally using
salloc
on SLURM so I don't think its a dependency issue.I would appreciate your help trying to solve this issue.