ITS genes not being found

[rissidaniel]

Hello, Please, I have done the "ufcg download -t full" and when I run the profile analysis with --set NUC , the tool is not finding any ITS gene for any of the genomes. The other --set options are working.

command:

ufcg profile --input ./genomes/ --output results_phylo_2_nuc --set NUC --thread 28 -k -w tmp_results_phylo_2_nuc

How can I solve this? Thank you in advance

[endixk]

Hello,

I found that the download package actually lacked ITS database, which is required for the extraction.

I uploaded the updated package that will allow your command to run properly.

Could you please try to run ufcg download -t core once, and run your command again?

Sorry for the inconvenience!

[JWDebler]

Hi, not sure if I have the same problem, but running ufcg profile --input genomes --output output --set NUC --force 1 --thread 10 --metadata metadata.tsv gives me a FAILED : ITS sequence not found. for every genome. I installed via conda and tried both ufcg download -t core and ufcg download -t full. Cheers

Edit: it is now running after I changed NUC to PRO. I couldn't find anything about this setting in the manual other than one sentence in the tutorial saying "We want to extract protein markers from the sequences. Type 'PRO' to continue."

[ignadb]

Hi, thanks for developing ufcg; it's very useful! It seems the problem still persists for me. I ran a command with --set NUC and got the ITS sequence not found message for all genomes. Tried downloading the database as suggested above and reran the command without success either with NUC or PRO. I am not sure if this is relevant; I found only two folders (busco,pro) in ../steineggerlab/ufcg/1.0.5/confid/model. Also there is no hmm profile for ITS in the pro folder. Do you have any suggestion about this?

I followed the instruction for installation from Github. Thanks a lot in advance!

[endixk]

Hello @ignadb, It seems the change I made in the recent update on MMseqs2 parameters ruined its nucleotide search capacity 😞 This could be quickly fixed but it will take some time for the amendment being reflected on the conda mirror. Please wait for the new release or install the program manually from the recent clone.

[alisqq]

Hello @endixk, has this issue been resolved? i reinstalled ufcg (i tried both conda and git) yesterday and the pipeline still doesn't find ITS sequences in the genomes.

edit: nevermind, it worked with git clone install!

[jackscanlan]

Hi @endixk, thanks so much for your work on this tool, it's really impressive. Just wondering if the recent commits, including df9d3e6 referenced above, could please be included in a new tag of the ufcg Docker container? I'd love to be able to extract NUC/BUSCO sequences using the container for a Nextflow pipeline I'm working on.

[endixk]

Hello @jackscanlan, sorry for the late reply.

I also think this is a good time to release a new minor version including these updates.

I will work on it soonish and leave a note here when it's done :)