MAXBIN2 RUNNING ONLY IN ONE CORE?

[H1889]

Hi, again, I am running the test, in may local machine with these options: NXF_VER=20.10.0 nextflow run ./MUFFIN --output output_dir --cpus 32 --memory 128g -profile local,conda,test

Everything goes well and very fast, however when it starts bowie2 mapping the process only uses one cpu and lasts for hours (at this moment 5 hours):

N E X T F L O W ~ version 20.10.0 Launching ./MUFFIN/main.nf [jovial_khorana] - revision: d488d29b21 executor > local (12) [71/468286] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [e2/5d8557] process > checkm_setup_db [100%] 1 of 1 ✔ [3f/fe885e] process > discard_short (1) [100%] 1 of 1 ✔ [24/be841a] process > merge (1) [100%] 1 of 1 ✔ [a1/96b732] process > fastp [100%] 1 of 1 ✔ [7e/73a2a0] process > spades (1) [100%] 1 of 1 ✔ [17/ea6bbe] process > minimap2 (1) [100%] 1 of 1 ✔ [e1/80871e] process > bwa (1) [100%] 1 of 1 ✔ [31/99bc17] process > metabat2 (1) [100%] 1 of 1 ✔ [79/521710] process > maxbin2 (1) [ 0%] 0 of 1 [5f/6dcc0b] process > concoct (1) [100%] 1 of 1 ✔ [- ] process > refine3 - [- ] process > checkm - [- ] process > sourmash_bins - [- ] process > sourmash_checkm_parser - [skipped ] process > eggnog_download_db [100%] 1 of 1, stored: 1 ✔ [- ] process > eggnog_bin - [- ] process > parser_bin - [71/ae962c] process > readme_output [100%] 1 of 1 ✔

is the maxbin2 phase where the process is stuck? I have checked it with htop and see only one cpu used at 100% by the bowtie2 process.

Thanks

[replikation]

thanks for reporting this there was a missing "2" in the config. therefore maxbin2 did not received the info on a local run to use all cores.

[H1889]

Ok, you are wellcome. Thanks to you for doing a nice pipeline. best