Open lagphase opened 1 month ago
Hi @lagphase, this is happening because prehgt is not set up to run on bacteria by default.
You can see details here of the couple lines of code that need to change to enable prehgt to run on bacteria: https://github.com/Arcadia-Science/prehgt/issues/56
Please let me know if this doesn't provide you with a workable solution
Hello Taylor,
Thank you for the prompt response. I have cloned the repo, modify the download_reference_genomes.nf, cd
into the cloned prehgt directory and do nextflow run,
but I still encountered the same issue. I wonder if I am doing something wrong?
Hmm can you provide a longer log file for this step? That will help me diagnose what might be going on
[22/dcde21] process > ARCADIASCIENCE_PREHGT:PREHGT:download_reference_genomes (Fructilactobacillus) [100%] 1 of 1, failed: 1 ✔
I copied the log below and also attached the trace files. execution_trace_2024-06-18_12-30-53.txt execution_trace_2024-06-18_12-31-53.txt execution_trace_2024-06-18_12-32-36.txt
[- ] ARCADIASCIENCE_PREHGT:PREHGT:download_reference_genomes -
executor > local (1)
executor > local (1)
[16/d9995c] ARC…E_PREHGT:PREHGT:download_reference_genomes (Fructilactobacillus) | 1 of 1, failed: 1 ✔
[- ] ARCADIASCIENCE_PREHGT:PREHGT:combine_and_parse_gff_per_genus -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:build_genus_pangenome -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:translate_pangenome -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:blastp_against_clustered_nr -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:blastp_add_taxonomy_info -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:blastp_to_hgt_candidates_kingdom -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:blastp_to_hgt_candidates_subkingdom -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:compositional_scans_pepstats -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:compositional_scans_to_hgt_candidates -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:combine_hgt_candidates -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:extract_hgt_candidates -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:kofamscan_hgt_candidates -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:hmmscan_hgt_candidates - [- ] ARCADIASCIENCE_PREHGT:PREHGT:combine_results_genus -
[- ] ARCADIASCIENCE_PREHGT:PREHGT:combine_results -
-[Arcadia-Science/prehgt] Pipeline completed successfully, but with errored process(es) - [16/d9995c] NOTE: Process `ARCADIASCIENCE_PREHGT:PREHGT:download_reference_genomes (Fructilactobacillus)` terminated with an error exit status (2) -- Error is ignored
Completed at: 18-Jun-2024 12:47:38
Duration : 15m 2s
CPU hours : (a few seconds)
Succeeded : 0
Ignored : 1
Failed : 1
Thanks for providing these. They don't quite provide all of the information I need. There should be a .nextflow.log
file in the directory that you executed the command in.
In the meantime, I was able to get the pipeline to run from this branch: https://github.com/Arcadia-Science/prehgt/tree/ter/bacteria. I had to add "bacteria" to two lines.
I've uploaded the results here. They're a TSV file, but I tacked on the "txt" to permit me to attach them to this issue. all_results.tsv.txt
Thank you for running the program for me. This will do for now.
Hello there,
I encountered this when trying the workflow:
Do you have any idea? Thanks.