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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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Error in rule sort_gatherVcfs #201

Closed daicy527 closed 1 week ago

daicy527 commented 1 week ago

Dear snparcher developers,

I encounter an error rule sort_gatherVcfs when I run the pipeline. The information is as follows:

Checking the headers and starting positions of 1634 files [E::hts_idx_load3] Could not load local index file 'results/GCA_013397395.1/vcfs/intervals/filtered_L1020.vcf.gz.tbi' : Too many open files Failed to open results/GCA_013397395.1/vcfs/intervals/filtered_L1020.vcf.gz: could not load index [W::bgzf_read_block] EOF marker is absent. The input may be truncated [E::bcf_hdr_read] Failed to read BCF header Could not read VCF/BCF headers from - Cleaning

I have tried to delete and regenerate this file, but the error remains. Many thanks Trying

tsackton commented 1 week ago

You may be running into a limit with the number of open files on your system. You can try setting this with ulimit -n to see if that helps.

daicy527 commented 1 week ago

You may be running into a limit with the number of open files on your system. You can try setting this with ulimit -n to see if that helps.

Thank you Tim, it works.