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prodigal process expects gzipped file #541
Description
Description of the bug
The prodigal process expects a gzipped file, also the singularity environment doesn't contain pigz.
I can hack it by replacing the first instance of pigz with cat, and the subsequent pigz -nm ones with gzip -n, and replace the version echo at the end by a fixed random-ish string.
Command used and terminal output
Relevant files
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System information
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Activity
jfy133 commentedon Oct 23, 2026
This may require an update to the module it seems, although where is the input files coming from @moritzbuck
That said, I was surprised at first to hear this error. But I just saw we only have tests for
pyrodigal🙈 norprodigalitsself. Out of curiosity, why did you want to use prodigal vs. pyrodigal? Pyrodigal should be much faster -a nd we have considered in the past removing support for prodigal itself.(Sorry for the very late reply!)