How to run the command line to do the new classification for some unknown sequences

[newuser1971]

When I read the Wiki about the running command line to do the new classification for unknown sequences. There is no example on how to do it. For example, if the sequences file is in fasta format, how to do ? If you can provide an example with detailed steps, that will be great. Thank you!

I ran the command line and got the following error:

treatC.json

================================================================================
Main input

GenomeDescTableFile: data/haibin1/VMR_MSL40.csv
ExpDir: ./output/haibin1
TaxoGrouping_Header: Genus

################################################################################ ##########
Build a database of virus protein profile hidden Markov models (PPHMMs)
################################################################################ ##########
INFO: GRAViTy detected a mismatch in sequence numbers between input genbank and VMR files. Attempting to fix with a genbank pull...
Writing contents of genbank object to file
FATAL ERROR: There was a mismatch between the number of sequences in your VMR an d the sequences you provided.GRAViTy-V2 attempted to pull the additional sequenc es from GenBank, but didn't find themThis means that some of your sequences are not on GenBank: please manually make a GenBank file containing all of your seque nces and point GRAViTy-V2 to its path with the 'GenomeSeqFile' parameter.

[Mayne941]

Hi, yes apologies we don't currently have full CLI support for all of the helper functions. If you're comfortable calling an API from the command line (with cURL) I can provide you with some command scripts? Otherwise I can prioritise building these functions into the CLI very soon, maybe later this week :) Let me know which is best.

[newuser1971]

No problem. If you could please provide some command scripts using cURL, that would be great. At the same time, I can wait for your full CLI. Thank you very much!

[Mayne941]

Please find attached a zip file containing a shell script and accompanying .json run files for a complete GRAViTy run. The zip file should be extracted into your GRAViTy directory and can be run with
'''$ bash curl/complete_pipeline.sh '''
Further details are in comments in the bash script.

The script has been written to use example data in the GRAViTy directory. Please try running this first as it is to check that it works on your machine. If you're running on a HPC, it might not be straightforward to point the shell script to the correct GRAViTy address (ln 10 in shell script).

If this all works fine, you can then modify the .json files to point at your own data.

Let me know how you get on :) Even if this works fine I won't close the issue until I've built these functions into the CLI.

curl.zip

[newuser1971]

I ran the command and got the following error message:

bash curl/complete_pipeline.sh
curl: (48) An unknown option was passed in to libcurl
curl: (48) An unknown option was passed in to libcurl
curl: (48) An unknown option was passed in to libcurl
curl: (48) An unknown option was passed in to libcurl
curl: (48) An unknown option was passed in to libcurl
curl: (48) An unknown option was passed in to libcurl
Check GRAViTy terminal for progress of classification.

[Mayne941]

Hmm might be an issue with cURL on your machine. Worth updating curl / libcurl / curl-dev, see response here:
https://stackoverflow.com/questions/11678085/curl-48-an-unknown-option-was-passed-in-to-libcurl

My version:
curl 8.9.1 (x86_64-conda-linux-gnu) libcurl/8.9.1 OpenSSL/3.0.15 zlib/1.2.13 libssh2/1.11.0 nghttp2/1.57.0
Release-Date: 2024-07-31
Protocols: dict file ftp ftps gopher gophers http https imap imaps ipfs ipns mqtt pop3 pop3s rtsp scp sftp smb smbs smtp smtps telnet tftp
Features: alt-svc AsynchDNS GSS-API HSTS HTTP2 HTTPS-proxy IPv6 Kerberos Largefile libz NTLM SPNEGO SSL threadsafe TLS-SRP UnixSockets