matrix_constructor.py stops at 55 %

[Edouard94]

Hello team,

A bit of context first, we are trying to produce a preliminary matrix and tree, where we had to speed up our SGTs parsing by deleting the sequences for the one we did not have time to parse yet. But eventually, each ortholog has its parsed tree.

Running apply_to_db.py and prep_final_dataset.py went well (I just had the warning 'There are empty files in the output. Please check for errors'). But when running matrix_constructor.py -i prep_final_dataset_out_Mar.28.2024 -o matrix_constructor_Edouard -t 18, it seems the process always stop when encountering the file nsfNP597649.fas, which looks fine.

[Fri Mar 29 10:44:03 2024]
rule remove_gaps:
    input: /home/Shared/PhyloFisher_MicrosporidiainInsectGenomes/Microsporidiatoadd/matrix_constructor_Edouard_concatenate_only/trimal/nsfNP597649.trimal
    output: /home/Shared/PhyloFisher_MicrosporidiainInsectGenomes/Microsporidiatoadd/matrix_constructor_Edouard_concatenate_only/trimal/nsfNP597649.final
    log: /home/Shared/PhyloFisher_MicrosporidiainInsectGenomes/Microsporidiatoadd/matrix_constructor_Edouard_concatenate_only/logs/trimal/nsfNP597649.log
    jobid: 643
    wildcards: gene=nsfNP597649

Job counts:
        count   jobs
        1       remove_gaps
        1
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem.
[Fri Mar 29 10:44:05 2024]
Finished job 643.
536 of 967 steps (55%) done
Exiting because a job execution failed. Look above for error message
Complete log: /home/Shared/PhyloFisher_MicrosporidiainInsectGenomes/Microsporidiatoadd/.snakemake/log/2024-03-29T102020.202337.snakemake.log

By the way all the trimal and divvier logs are emtpy in the obtained matrix folder.

I attach here the fas file in question nsfNP597649.txt and the complete matrix log 2024-03-29T102020.202337.snakemake.log and hope you will be able to help me on this issue.

Thank you and my best wishes, Edouard