Closed OliverBryan closed 6 months ago
Hi @OliverBryan, after checking the files you attached, I found the issue.
The organism_name
column in the result.xlsx file doesn't match to the genome_id
column in the genome_to_taxid.tsv
file. Here is an example:
GCF_000364605.1_genomic
is in the genome_to_taxid.tsv
file but its corresponding genome name GCF_000364605.1 Nocardioides sp. Iso805N strain=Iso805N, ASM36460v1
in the result.xlsx
. You should use either one of them.
I have updated the genome_to_taxid.tsv
file to fix this, perhaps I did it incorrectly as I am still getting the same error. I have attached my updated genome_to_taxid.tsv
file. I also am now running yacht convert --yacht_output 'result.xlsx' --sheet_name 'raw_result' --genome_to_taxid 'genome_to_taxid.tsv' --mode 'cami' --sample_name 'MySample' --outfile_prefix 'cami_result' --outdir ./
using the raw_result
sheet instead of the min_coverage1.0
sheet, but both commands give the same error.
Hi @OliverBryan, thanks for trying out my suggestion. I can't find the attached files in your last message.
My apologies @chunyuma I forgot to attach it, I have attached it to this message. genome_to_taxid.txt
Hi @OliverBryan, sorry for the late response.
I figured out the issue. When I wrote the script, for some reasons, I didn't expect the genome_id
column in the genome_to_taxid.tsv
file to have a space like GCF_000364605.1 Nocardioides sp. Iso805N strain=Iso805N, ASM36460v1
. I removed the name of each genome in the genome_id
column and then got GCF_000364605.1
. It works now. I have attached the updated genome_to_taxid.txt
file (see below). You can have a try.
But thanks for letting me be aware of it. This should be a bug. I have fixed it in the code in this PR.
Hi @chunyuma,
Everything is working on my end with the updated genome_to_taxid_test.tsv
file, thank you for your help.
Working with data from https://frl.publisso.de/data/frl:6425521/marine/short_read/marmgCAMI2_sample_0_reads.tar.gz and using a trained version of the gtdb database, I ran into the following error using
yacht convert
to convert the output of yacht into the cami format. I ranyacht convert --yacht_output 'result.xlsx' --sheet_name 'min_coverage1.0' --genome_to_taxid 'genome_to_taxid.tsv' --mode 'cami' --sample_name 'MySample' --outfile_prefix 'cami_result' --outdir ./
and got the following error:I have attached my
result.xlsx
filegenome_to_taxid.tsv
file (changed to a .txt file since github does not support .tsv files but nothing else is changed about it) for reference. result.xlsx genome_to_taxid.txt