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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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DAS_tool update, parser_bbmap.py error #598

Closed AroArz closed 1 year ago

AroArz commented 1 year ago

README.md updated version. Initially ran with 2.9 and had some errors that were fixed in 2.13.1

DASTool update to version 1.1.6 fixes this issue

parsers_bbmap.py additional line inatlas/{sample}/logs/assembly/calculate_coverage/pilup_final_contigs.log breaks the script :

Note: Coverage capped at 65535; please use the flag 32bit for higher values.

The solution I implemented is quite ugly but it handles the problem. I can omit it if you don't want it in this PR.

SilasK commented 1 year ago

Thank you @AroArz