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hillerlab / make_lastz_chains

Portable solution to generate genome alignment chains using lastz
MIT License
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lastz step terminated with an error exit status (132) #65

Open munegowda opened 1 month ago

munegowda commented 1 month ago

Hi @kirilenkobm and @MichaelHiller,

Thank you for providing this pipeline!

I am using make_lastz_chains version 2.0.8 in our Slurm cluster. When I run the test example ./make_chains.py target query test_data/test_reference.fa test_data/test_query.fa --pd test_out -f --chaining_memory 16 --cluster_executor slurm --cluster_queue long, the pipeline terminates at the lastz step. In the nextflow.log from the temp_lastz_run directory an exit code 132 leading to the termination is documented.

However, when I run ./make_chains.py target query test_data/test_reference.fa test_data/test_query.fa --pd test_out -f --chaining_memory 16 from an sbatch script where the cluster_executor is local, the pipeline does not terminate.

I'd appreciate your thoughts on what might be causing this issue.

kirilenkobm commented 2 days ago

Hi @munegowda just to make sure - can you pls test on the last of the 1st versions? Not 2.x.x

Best, Bogdan