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giesselmann / STRique

Nanopore raw signal repeat detection pipeline
MIT License
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STRique not providing results after 24 hours #33

Closed fanavarro closed 1 year ago

fanavarro commented 1 year ago

Hi, I am using the docker version of STRique as depicted in the documentation: docker run -it --mount type=bind,source=$(pwd),target=/host giesselmann/strique I am creating the fast5 index with: python3 /app/scripts/STRique.py index /host/fast5 > fast5/reads.fofn And then, I am executing the count command as follows: python3 /app/scripts/STRique.py count --t 8 /host/fast5/reads.fofn /app/models/r9_4_450bps.model strique_input.tsv > strique_output.tsv

However, I've stopped it after 24 hours without showing any kind of log nor printing anything in strique_output in addition to a header. I've checked the cpu activity while STRique was running, but I did not see so much activity.

Am I doing something wrong?

Kind regards, Francisco Abad.

fanavarro commented 1 year ago

My fault, I did not notice about the --algn parameter, so strique was expecting sam files through stdin...