Describe the bug
mgatk call stops due to issues with config files, doesn't produce output files. I'm guessing that lines like these Workflow defines configfile ../mgatk_output/.internal/parseltongue/snake.scatter.yaml but it is not present or accessible (full checked path: /path/to/mgatk_output/.internal/parseltongue/snake.scatter.yaml). are central to the issue here, thus the title. That config file is not present (no .internal dir)
Describe the bug mgatk call stops due to issues with config files, doesn't produce output files. I'm guessing that lines like these
Workflow defines configfile ../mgatk_output/.internal/parseltongue/snake.scatter.yaml but it is not present or accessible (full checked path: /path/to/mgatk_output/.internal/parseltongue/snake.scatter.yaml).
are central to the issue here, thus the title. That config file is not present (no .internal dir)To Reproduce My script is...
The combined_bams dir has .bam files from bulk ATACseq experiment that had ~10-20% MT reads across libraries (each 1 .bam file here).
Attached file has more output log info log.md
When running
mgatk call
on the test data (i.e.mgatk call -i git/mgatk/tests/humanbam/ -g hg19 -o ../mgatk_output
), I get very similar errors