summarise error

[ereyred]

Hello! I did:
$ CAT_pack add_names -i {classification file} -o out.txt -t {taxonomy folder} --only_official
and everything looks good but then when I try to run summarise:
$ CAT_pack summarise -c {contigs fasta} -i out.txt -o {output file}
it tells me that the named classification file is not a classification file:
ERROR: out.txt is not a CAT classification file.

What's going on??
Thanks
E

[thauptfeld]

Hi!

Could you post what comes out when you do

head out.txt

? Then I can see why it would complain about the classification file. Also, what output file are you adding names to and trying to summarise?

Best,
Tina

[ereyred]

ORF number of hits (r: 10) lineage top bit-score superkingdom phylum class order family genus species

vRA1_NODE_10015_length_6181_cov_25.230517_g1063_i9||full_1 ORF has no hit to database
vRA1_NODE_10015_length_6181_cov_25.230517_g1063_i9||full_2 ORF has no hit to database
vRA1_NODE_10015_length_6181_cov_25.230517_g1063_i9||full_3 3 1;10239;2731341;2731360;2731618;2731619* 57.8 Viruses Uroviricota Caudoviricetes* no support no support no support no support
vRA1_NODE_10016_length_6181_cov_24.993451_g1063_i10||full_1 ORF has no hit to database
vRA1_NODE_10016_length_6181_cov_24.993451_g1063_i10||full_2 ORF has no hit to database
vRA1_NODE_10016_length_6181_cov_24.993451_g1063_i10||full_3 3 1;10239;2731341;2731360;2731618;2731619* 57.8 Viruses Uroviricota Caudoviricetes* no support no support no support no support
vRA1_NODE_10021_length_6180_cov_10.015883_g28_i61||full_1 ORF has no hit to database
vRA1_NODE_10021_length_6180_cov_10.015883_g28_i61||full_2 ORF has no hit to database
vRA1_NODE_10021_length_6180_cov_10.015883_g28_i61||full_3 ORF has no hit to database