Skip to content

Error with "nbunch" #76

@ZhezhiGao

Description

@ZhezhiGao

Hi there, I ran into an error when I was trying the quickstart command:
advntr genotype --vntr_id 301645 --alignment_file CSTB_2_5_testdata.bam --working_directory test/ -m vntr_data/hg19_selected_VNTRs_Illumina.db

looks like it failed to align:
`
Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 0 reads
301645
Error`

and the log file in working directory has the following information:
ERROR:Error when finding repeat count from alignment file (illumina) for vntr id 301645: topological_sort() got an unexpected keyword argument 'nbunch'. Skipping genotyping for this VNTR.`

any suggestions please?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions