Phasing fails due to trying to tabix index a bcf file

[lordkev]

Hi,

It looks like commit 99c9cbb broke phasing, as bcftools cannot tabix index a bcf file. See error below. Changing the index_for_eagle and phase rules to create / use a csi index instead seems to fix the issue.

rule index_for_eagle:
    input: vcf/batch1_merged_mapped_sorted.bcf.gz
    output: vcf/batch1_merged_mapped_sorted.bcf.gz.tbi
    log: logs/vcf/batch1_merged_mapped_sorted.bcf.gz.tbi.log
    jobid: 14
    reason: Missing output files: vcf/batch1_merged_mapped_sorted.bcf.gz.tbi; Input files updated by another job: vcf/batch1_merged_mapped_sorted.bcf.gz
    wildcards: batch=batch1
    resources: tmpdir=/tmp


            bcftools index -f -t vcf/batch1_merged_mapped_sorted.bcf.gz |& tee logs/vcf/batch1_merged_mapped_sorted.bcf.gz.tbi.log

Activating conda environment: bcftools

EnvironmentNameNotFound: Could not find conda environment: bcftools
You can list all discoverable environments with `conda info --envs`.


[E::bcf_index_build3] TBI indices for BCF files are not supported
index: failed to create index for "vcf/batch1_merged_mapped_sorted.bcf.gz"
[Sun Sep 10 17:10:14 2023]
Error in rule index_for_eagle:
    jobid: 14
    input: vcf/batch1_merged_mapped_sorted.bcf.gz
    output: vcf/batch1_merged_mapped_sorted.bcf.gz.tbi
    log: logs/vcf/batch1_merged_mapped_sorted.bcf.gz.tbi.log (check log file(s) for error details)
    conda-env: bcftools
    shell:

            bcftools index -f -t vcf/batch1_merged_mapped_sorted.bcf.gz |& tee logs/vcf/batch1_merged_mapped_sorted.bcf.gz.tbi.log

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message```

[pavelnikonorov]

Hi @lordkev, thanks for your message, we are investigating this and will back to you ASAP

[pavelnikonorov]

hello @lordkev, sorry that it took so long, please check if it's working now