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wwood / galah

More scalable dereplication for metagenome assembled genomes
GNU General Public License v3.0
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Dashing failed #19

Open SilasK opened 2 years ago

SilasK commented 2 years ago

I tested Galah on a small and on a large dataset. In both, I get

[2022-09-14T07:35:31Z INFO  galah::dashing] Running dashing to get approximate distances ..
[2022-09-14T07:35:31Z ERROR bird_tool_utils::command] Error when running dashing process. Exitstatus was : ExitStatus(unix_wait_status(4))
[2022-09-14T07:35:31Z ERROR bird_tool_utils::command] The STDERR was: "Dashing version: v0.4.0\n"
[2022-09-14T07:35:31Z ERROR bird_tool_utils::command] The STDOUT was: ""
[2022-09-14T07:35:31Z ERROR bird_tool_utils::command] Cannot continue after dashing failed.

I can use the finch method as a work around.

I installled galah with conda Here is my full command.

galah cluster  --genome-fasta-directory genomes/all_bins --genome-fasta-extension fasta  --genome-info genomes/quality.csv  --ani 97.5  --min-aligned-fraction 0.5    --min-completeness 50  --max-contamination 10  --quality-formula Parks2020_reduced  --threads 8  --output-representative-fasta-directory genomes/dereplicated_genomes  --output-cluster-definition genomes/clustering/allbins2genome_oldname.tsv
wwood commented 2 years ago

Hi,

I think this is likely due to a compilation issue with dashing - does running it outside of galah work?