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CSB5 / OPERA-MS

OPERA-MS - Hybrid Metagenomic Assembler
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Polishing [9/9] takes long time ! #94

Open Hedi65 opened 1 month ago

Hedi65 commented 1 month ago

Dear developer

i am trying to build a hybrid assembly with Illumina pair reads and nanopore data from sequence biofilms, so i expected a highly complex environment compare to human gut microbiota. each of the Illumina reads are about 7.3 GB (uncompressed, fastq file) and the nanopore data is about 2.7 GB (uncompressed, fastq file). OPERA-MS is still in Polishing [9/9] step since almost 24h ago. is it normal to take such long time ?

Thanks

jsgounot commented 1 month ago

Hi Hedi,

the polishing step is basically running Pilon on your final assemblies, which is known to be slow. I can't offer a precise answer as I don't know how many assemblies you have, and (most importantly) the number of CPUs. But based on your reads depth, I'd wait at least a couple of more days before thinking about killing the process. You can also check the log file (pilon.err) in the intermediate polishing directory.

Regards, JS

Hedi65 commented 1 month ago

thanks. i allocated 70 cores and 1 TB of memory . the pilon.err file is empty.

jsgounot commented 1 month ago

Ok, then I'd definitely wait for at least a couple of days then.