Skip to content

Micro-C data #19

@jeff-godwin

Description

@jeff-godwin

Hello,

I'm using 3d-genome-builder for yeast micro-C data. As mentioned in the example YML files used in the paper, I left the "hicpro_restriction_sites:" blank in the config file. But I'm getting an error -

Error in rule digest_genome:
jobid: 5
input: genome.fasta
output: HiC-Pro/restriction_sites.txt
log: logs/digest_genome.log (check log file(s) for error details)
shell:
/usr/local/bin/HiC-Pro_3.1.0/bin/utils/digest_genome.py -r None -o HiC-Pro/restriction_sites.txt genome.fasta >logs/digest_genome.log 2>&1
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/digest_genome.log:

Unable to detect offset for None. Please, use '^' to specify the cutting position, i.e A^GATCT for HindIII digestion.

Could you please give me some pointers to fix this?

Thank you,
Jeff

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions