Fernando Puente-Sánchez

This is an issue that happens in some (not all) HPC environments, when the databases are mounted in a remote drive. Each SQLite query takes a lot to be processed....

Closing due to lack of activity, feel free to reopen

1) Because you didn't ask it to. See the manual of v1.6 (option `--filter` in `sqm_mapper.pl`) to see how it's done. 2) You can preprocess your reads with `sqm_mapper.pl` to...

You need to define what you want to consider "common contaminants" in the scope of your study, and prepare the files for those yourself. We can not help with that.

What is the output of `perl /opt/SqueezeMeta-1.5.2/bin/MaxBin/run_MaxBin.pl -thread 30 -contig /srv/data/my_shared_data_folder/amrcattle/metagenome_analysis_results/mgm4754670.3/temp/bincontigs.fasta -abund_list /srv/data/my_shared_data_folder/amrcattle/metagenome_analysis_results/mgm4754670.3/intermediate/binners/maxbin/abund.list -out /srv/data/my_shared_data_folder/amrcattle/metagenome_analysis_results/mgm4754670.3/intermediate/binners/maxbin/maxbin -markerpath /opt/SqueezeMeta-1.5.2/db/marker.hmm` ?

Yep

Funny enough @jtamames was the one that report this issue in the MaxBin repo... https://sourceforge.net/p/maxbin2/tickets/6/ What happens if you add `-min_contig_length 200` to the command above?

Yes El jue., 22 sept. 2022 18:51, EorgeKit ***@***.***> escribió: > by the way does squeezemeta operate with python3? > > — > Reply to this email directly, view it...

What version of SqueezeMeta are you using? Can you share the `syslog` file isnide the project directory with us?

Ah, ok, that issue got fixed in 1.5.2 so you can just update to the latest version and it should work