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hillerlab / make_lastz_chains

Portable solution to generate genome alignment chains using lastz
MIT License
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unable to run make lastz chains on slurm cluster- where do I edit config file? #49

Closed pfb2201 closed 8 months ago

pfb2201 commented 9 months ago

Hello! I am trying to make genome alignment chains using your pipeline, but I keep getting an error related to the nextflow submission process. It fails to submit the joblist that it produces, giving me this error message:

N E X T F L O W ~ version 23.04.0 Launching.../TOGA/make_lastz_chains/parallelization/execute_joblist.nf` ERROR ~ Error executing process > 'execute_jobs (12)'

Caused by: Failed to submit process to grid scheduler for execution

Command executed:

sbatch .command.run

Command exit status: 1

Command output: sbatch: error: invalid partition specified: batch sbatch: error: Batch job submission failed: Invalid partition name specified`

I looked into the execute_joblist.nf file, and it calls a config file for submissions. I believe editing the partition in the config file will probably fix this process, but I am not sure where to find it. Any help with this would be much appreciated!

Details about input data: I softmasked the genomes (around 30-40% of genome is soft-masked), and then turned them into 2bit files using faToTwoBit.

pfb2201 commented 8 months ago

I realized you have to add --cluster_queue name_of_partition (cluster-dependent) when calling this script. I am closing the ticket!