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something funny... about amptk HOT 4 CLOSED

nextgenusfs avatar nextgenusfs commented on August 20, 2024
something funny...

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nextgenusfs avatar nextgenusfs commented on August 20, 2024

This would be the same bgzip bug you are having as it is using the same zip and unzip functions. I will remove bgzip from that function in case it is problematic, hopefully it picks up pigz as it suppose to.

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nextgenusfs avatar nextgenusfs commented on August 20, 2024

Oh maybe I spoke too soon.... the error is coming from vsearch looks like. Was this the output of amptk illumina? If so.... well then the fast zip function is probably using bgzip to compress (since pigz isn't getting picked up on your system). I'm guessing that the bgzip compression is somehow different than what vsearch is expecting.

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devonorourke avatar devonorourke commented on August 20, 2024

right. the input .gz file was the output from amptk illumina.
I'll just remember that whenever I get an error any more it's likely something to do with file compression. everything's working otherwise, so no worries.

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nextgenusfs avatar nextgenusfs commented on August 20, 2024

Interested to see what happens on your system now.... b2db5b6
You can just drop the amptklib.py into the lib directory or git pull to try.

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