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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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dedup #670

Closed GelatinousGiant closed 1 month ago

GelatinousGiant commented 4 months ago

Hi,

I am just wondering what is the approximate run time for the dedup algorithim?

I am running on 20 cores each with 50GB of ram and trying to deduplicate a bam file thats ~50GB in size but its been running for >8 hours and only outputted a file ~2GB in size so far.

Is there way to check logs of progress on this step?

Thanks!

armintoepfer commented 1 month ago

You can try --log-level INFO or DEBUG, but no guarantees that it will give you an ETA