medaka error pyabpoa and libgsl.so.25

[CorentinEscobar]

Hi everyone,

I am using medaka in hybracter pipeline. Hybracter creates different conda environments for each step of its pipeline, and notably uses medaka for polishing. When I run the hybracter pipeline I get this error message :

[Mon Jan 15 13:18:40 2024]
Finished job 11.
3 of 18 steps (17%) done
Checking program versions
This is medaka 1.11.3
Program    Version    Required   Pass     
bcftools   Not found  1.11       False    
bgzip      1.17       1.11       True     
minimap2   2.26       2.11       True     
samtools   1.18       1.11       True     
tabix      1.17       1.11       True     
[Mon Jan 15 13:18:41 2024]
Error in rule medaka_round_1:
    jobid: 25
    input: /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/pre_polish/hybracter_RB04_test_chromosome_plus_plasmids.fasta, /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/qc/hybracter_RB04_test_filt_trim.fastq.gz
    output: /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/complete/medaka_rd_1/hybracter_RB04_test/consensus.fasta, /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/versions/hybracter_RB04_test/medaka_complete.version
    log: /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/stderr/medaka_round_1/hybracter_RB04_test.log (check log file(s) for error details)
    conda-env: /home/horigene/anaconda3/envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/conda/348d2d1aa0134c8a68065158ce832239_
    shell:

        medaka_consensus -i /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/qc/hybracter_RB04_test_filt_trim.fastq.gz -d /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/pre_polish/hybracter_RB04_test_chromosome_plus_plasmids.fasta -o /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/complete/medaka_rd_1/hybracter_RB04_test -m r1041_e82_400bps_sup_v4.2.0  -t 16 2> /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/stderr/medaka_round_1/hybracter_RB04_test.log
        medaka --version > /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/versions/hybracter_RB04_test/medaka_complete.version
        touch /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/complete/medaka_rd_1/hybracter_RB04_test/calls_to_draft.bam
        rm /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/complete/medaka_rd_1/hybracter_RB04_test/calls_to_draft.bam
        touch /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/complete/medaka_rd_1/hybracter_RB04_test/consensus_probs.hdf
        rm /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/processing/complete/medaka_rd_1/hybracter_RB04_test/consensus_probs.hdf

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile /mnt/data/horigene/Corentin/20231214_24_genomes_GW/hybracter/stderr/medaka_round_1/hybracter_RB04_test.log:
================================================================================
Cannot import pyabpoa, some features may not be available.
Cannot import pyabpoa, some features may not be available.
Cannot import pyabpoa, some features may not be available.
Cannot import pyabpoa, some features may not be available.
bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
================================================================================

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-01-15T131838.221728.snakemake.log
WorkflowError:
At least one job did not complete successfully.

Have you ever had this problem or do you know how to fix it?

Thanks in advance Corentin

[cjw85]

Oxford Nanopore Technologies is not responsible for the medaka package from the bioconda channel. You should take this matter up with the developers of hybracter and bioconda maintainers.

The error:

bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

appears to be nothing to do with medaka itself.