--threads argument no longer supported

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

GNU General Public License v2.0

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--threads argument no longer supported #147

Closed cpavloud closed 1 year ago

cpavloud commented 2 years ago

Hello!

I am trying to run pilon (v 1.24) on an HPC cluster using slurm. My command (in my sh script) is

java -Xmx200G -jar pilon-1.24.jar --iupac --genome purged.fa --frags SRR_uniq_sorted.bam --diploid --threads 40 --outdir pilon_flye

But I get the error

Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500 --threads argument no longer supported; ignoring!

Is there another flag for the threads in version 1.24?

ethering commented 1 year ago

A belated answer, but the release notes for 1.24 state:

Support for the experimental --threads option has been removed. It was implemented by an ugly hack which no longer works in modern scala, and it was a resource hog in any case. I hope to revisit multithreading again in the future.

https://github.com/broadinstitute/pilon/releases/tag/v1.24