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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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[e] gene_markers_identification crashed #115

Open kaw97 opened 1 year ago

kaw97 commented 1 year ago

I just had my phylophlan run crash after 5 days and would appreciate any help.

I'm running version 3.0.2 installed via conda. I am trying to run phylophlan on a collection of bacterial isolate genomes. It looks like it successfully mapped most of the input genomes, but failed with a few of them and then marker gene identification failed.

Here are my output and error files from slurm and my phylophlan config file: phylophlan.515596.err.txt phylophlan.515596.out.txt alaskan_config.txt

If there's any help you can offer, I'd greatly appreciate it.

fasnicar commented 1 year ago

Hi, thank you for using PhyloPhlAn and reporting this. Have you tried running the command from the error output file?

/home/kyle/miniconda3/envs/phylophlan/bin/diamond blastx --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query janthino_phylophlan/tmp/clean_dna/GCA_000818395.fna --db phylophlan_databases/phylophlan/phylophlan.dmnd --out janthino_phylophlan/tmp/map_dna/GCA_000818395.b6o.bkp

I just removed the -quite param.