error: archaea.markers.tsv not found

[Valentin-Bio-zz]

Hello I'm trying to run autometa over my metagenomic data. I tried running it before with other dataset and it worked well. When I run it with his new dataset I got an error message appointing to a lacking archaea.markers.tsv file. I think that there is no contig identified as an Archeal contig but nut sure.

Here I attach my config file

config_autometa.txt

and here is the error message:

error_autometa.txt

Under my directory where are the partial outputs I have:

1 )SLF_CL2.archaea.5mers.am_clr.bhsne.tsv
2) SLF_CL2.archaea.fna
3) SLF_CL2.bacteria.5mers.tsv
4) SLF_CL2.coverages.tsv
5) SLF_CL2.gc_content.tsv
6) SLF_CL2.orfs.sseqid2taxid.tsv
7) SLF_CL2.unclassified.fna 8) SLF_CL2.archaea.5mers.am_clr.tsv
9) SLF_CL2.bacteria.5mers.am_clr.bhsne.tsv
10) SLF_CL2.bacteria.fna
11) SLF_CL2.eukaryota.fna 12) SLF_CL2.orfs.errortaxids.tsv
13) SLF_CL2.taxids.tsv
14) SLF_CL2.viruses.fna 15) SLF_CL2.archaea.5mers.tsv
16) SLF_CL2.bacteria.5mers.am_clr.tsv
17) SLF_CL2.coverages.bed.tsv
18) SLF_CL2.filtered.fna 19) SLF_CL2.orfs.lca.tsv
20) SLF_CL2.taxonomy.tsv

[Sidduppal]

Hey @Valentin-Bio Thanks for using Autometa. From the error file it looks like your your hmm profiles are not pressed. I suppose you need to run the following two commands before running Autometa. For bacterial markers --> hmmpress -f /GWSPH/home/ecastron/Databases/autometa_db/bacteria.single_copy.hmm For archael markers --> hmmpress -f /GWSPH/home/ecastron/Databases/autometa_db/archaea.single_copy.hmm

The path might be different based on where the makers genes are present.

[evanroyrees]

Hello @Valentin-Bio, were you able to resolve your issue?