MiModd variant calling


I am trying to run the MiModd variant calling tool in galaxy and I got the below error.

I first aligned my fastq file using Bowtie2, while setting a read group ID and sample name. I then used MiModd variant calling tool in attempt to produce a bcf file for MiModd deletion calling. I changed the name of the reference genome but that didn’t help. Anyone got any suggestions? or a better suggestion for finding deletions in my data


Fatal error: Exit code 1 ()

Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/bin/mimodd”, line 7, in
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/main.py”, line 1197, in parse
result = funcs-1
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/tmpfiles.py”, line 26, in catch_sigterm_wrapper
ret = f(args, **kwargs)
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/variant_calling.py”, line 114, in varcall
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/fasta.py”, line 28, in assert_valid_ids
MiModD.FormatParseError: Invalid reference genome file : Some sequence names contain characters that are not allowed in MiModD.
non-ASCII, whitespace, non-printable characters and any of the characters "
,;<=>[]" are disallowed in sequence names.
You may manually clean up the file or run “python3 -m MiModD.sanitize” to replace invalid characters automatically.

Hi Kara,
that’s the same source of error caused by your reference genome I’ve been explaining you earlier today on the usegalaxy.eu bug tracker mailing list.
The solution, if you want to proceed with any MiModD tools, is to rename the sequences in that ref genome.

As for better tools to find deletions in your data, a lot depends on what that data actually is. This recent post on the usegalaxy.eu website may help you discover some tools for structural variant calling that we added recently to our toolbox: Galaxy Europe | New and updated CNV and Variant Calling tools

Not all of them may be suitable for your data and some might still have lurking bugs waiting to be discovered, but it may help you get started.