Step 14 Not Progressing

[giovrosin]

Hello,

Im having trouble on step 14. The program has run on this step for 11 days straight. I tried restarting the run with more threads but it doesn't seem like its progressing. I checked the /temp/ and the /intermediate/binners/concoct/ files and there seem to be no updates.

Im working with 77 metagenomes and 102 gb total.

I will anex the syslog and the std output.

Any help is appreciated!

log.zip

[jtamames]

Hello Yes, I myself have experienced some trouble with concoct when analyzing big projects as yours. Are you interested in having bins? If not, you could just stop the process and create the contig table and the final stats. If yes, I could tell you a different way of having bins for your samples. Best, J

[giovrosin]

Yes, my project focuses on taxonomic analyses and assignment of bins so this step is important

[fpusan]

Is CONCOCT still running, and if so is it using all the CPU threads at 100%?

[giovrosin]

yes, they're running at 99%

[fpusan]

Then it may be just that the dataset is too complex for CONCOCT. You can either wait, or avoid CONCOCT and use only METABAT2 for getting your bins, since it can be much faster.

[jtamames]

A different approach that you can follow is analyzing the samples in sequential mode instead of coassembly. That will provide individual MAGs for each sample, that you can later merge together (dereplicate) using their ANIs. A program such as dRep can be used for that purpose. In this way you usually get many more bins, because you are able to retrieve these that are abundant in just a few samples, which could be missed using the coassembly

[giovrosin]

Hello!

Thank you for the reply. First I tried restarting the run using metabat2, but as I understand it's running CONCOT still.

Here is the command and syslog:

SqueezeMeta.pl -p SQM_Superior -binners metabat2 --restart -step 13 --force_overwrite -s /home/cstaats/giovana/sqm_illumina/lista_sqm_sup -f /home/cstaats/giovana/sqm_illumina/TratoSuperior -t 50

syslog.zip

[fpusan]

The way to change the configuration mid run is to edit the SqueezeMeta_conf.pl file inside of the projects directory (so SQM_Superior/SqueezeMeta_conf.pl. There, find the variable $binners and remove concoct. Then try to restart again.

[fpusan]

Closing due to lack of activity, feel free to reopen