You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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.
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
The text was updated successfully, but these errors were encountered: