instrain_compare clustering failure

[elisacaffrey]

Hi Matt, I am running instrain_compare. The run finished without a problem, but only generated the genomeWide_compare.tsv and comparisonsTable.tsv and not the strain_clusters.tsv. The inStrainCompare_dendrograms.pdf file was created but is corrupted, so I cannot open it to visualize. When I checked the log.log, it reports a clustering failure for all genomes (screenshot of the end below).

I ran the same command twice with the same output. What do you think might be the issue?

Thank you! Elisa

[MrOlm]

Hi @elisacaffrey - hmmm interesting. Can you send me the command used to run inStrain compare?

Thanks, Matt

[elisacaffrey]

Sure thing, here it is: nextflow run /home/mattolm/user_data/Nextflow/nf-core-genomeresolvedmetagenomics/aux_instrain_compare.nf -with-report report_compare_batch0105_v2.html --input instraincompare_batch0105_05172024.csv --outdir batch09_results_v3/ --stb s3://sonn-highavail/databases/MiFoDB/MiFoDB_beta/MiFoDB_beta_v3/MiFoDB_beta_v3_prok.stb

[MrOlm]

Ah I see- try adding --is_compare_args " --database_mode" to your nextflow command

[elisacaffrey]

Great, thank you! I'll try running the updated command now.

[elisacaffrey]

Run complete and problem solved, thank you!