Error when running Mimodd deletion calling tool

usegalaxy.org support
1

Hello,

I am running Mimodd deletion calling and I consistently get the following error message:

Matching sample names between bam file and coverage file:
---
sample names found ONLY in coverage file:
/jetstream2/scratch/main/jobs/59620156/working/tmp_indexed_bam_9738.bam
Traceback (most recent call last):
  File "/usr/local/bin/mimodd", line 7, in <module>
    __main__.parse()
  File "/usr/local/lib/python3.6/site-packages/MiModD/__main__.py", line 1197, in parse
    result = funcs[-1](**args)
  File "/usr/local/lib/python3.6/site-packages/MiModD/tmpfiles.py", line 26, in catch_sigterm_wrapper
    ret = f(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/MiModD/deletion_calling.py", line 96, in delcall
    raise RuntimeError ('Some samples in the coverage file could not be matched to entries in the bam file.')
RuntimeError: Some samples in the coverage file could not be matched to entries in the bam file

I used Bowtie2 to map reads against a reference genome and generate my .bam file and Mimodd variant calling to generate my. bcf dataset. My data are PE reads from C. elegans EMS mutagenesis samples and I am using the WS220(ce10) built-in genome as a reference genome.
Does anyone know what might be going wrong?

I am new to the Galaxy community and I appreciate any help you can offer!

Thanks!

2

Welcome, @ilianak

This message

Some samples in the coverage file could not be matched to entries in the bam file

Means that the tool cannot find data in the second input file inside the first input file. Double check that both are based on the same reference genome, and that your sample names are the same.

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