Weisheng Wu

I see now the mapcount step was killed. I overlooked that line in the log: ``` Output in /nfs/turbo/umms-bishus-sparc/bfx_analysis/Bishu_bishus_CU2-Metagenomics_weishwu/outputs/squeezemeta_coassembly_with_drepGenomes/coassembly_with_drepGenomes/intermediate/10.coassembly_with_drepGenomes.mapcount Killed ``` It took 10 days and was killed after finishing...

Wait. These files have count data that look normal: ``` results/10.coassembly_with_drepGenomes.mappingstat results/11.coassembly_with_drepGenomes.mcount intermediate/10.coassembly_with_drepGenomes.contigcov ``` So it looks like the read counting did go through, but not sure why `10.coassembly_with_drepGenomes.mapcount` is...

Yes it does. Should I try rerunning it with an even larger memory?

When I reran it, SQM went to STEP 12 because it detected ``` results/10.coassembly_with_drepGenomes.mappingstat results/11.coassembly_with_drepGenomes.mcount intermediate/10.coassembly_with_drepGenomes.contigcov ``` Then the same error was triggered because `10.coassembly_with_drepGenomes.mapcount` is empty. I tried deleting...

Because `10.coassembly_with_drepGenomes.mapcount` is an output of STEP 10. I had to delete all the STEP 10 outputs to make SQM rerun STEP 10 to generate `10.coassembly_with_drepGenomes.mapcount`, otherwise this file couldn't...

Ah, never mind. After indexing, SQM is aware of those bams and goes directly into counting. Sorry I was kind of hasty.

I've increased memory to 600G but I'm not sure whether this will be sufficient. It looks like SQM will still take 4-5 days to finish counting for 524 samples, even...

Thanks! I'll rerun the job on our local server without using a cluster node. I added `cp $mapcountfile ${mapcountfile}.presort;` in front of `sort` at line 309 in `10.mapsamples.pl` to save...

I'll test your new version. Thanks a lot!

[sqm_co.log.gz](https://github.com/user-attachments/files/19760441/sqm_co.log.gz) My run on the local server was terminated by an error. Is this an expected behavior since I used the `-test 13` parameter? ``` [11 days, 1 hours, 4...