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wwood / galah

More scalable dereplication for metagenome assembled genomes
GNU General Public License v3.0
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checkM table not working #28

Closed Sanrrone closed 1 year ago

Sanrrone commented 1 year ago

Dears, I'm trying to use the --checkm-tab-table which expect 13 columns, Unfortunately there is no file with that description in the new release of CheckM. complete_genomes.tsv: 11 completeness.tsv: 15 contamination.tsv: 14 quality_summary.tsv: 14

Additionally, as a part of other bug. I tried not use checkm flag and I got:

[2023-05-22T12:04:22Z INFO  bird_tool_utils::external_command_checker] Found dashing version v1.0 
thread 'main' panicked at 'Failed to find sufficient version of dashing. You may wish to use the finch precluster method if you are having problems with dashing.: "It appears the available version of dashing is too old (found version v1.0, required is 0.4.0)"', src/external_command_checker.rs:19:10
stack backtrace:
   0: rust_begin_unwind
             at /rustc/84c898d65adf2f39a5a98507f1fe0ce10a2b8dbc/library/std/src/panicking.rs:579:5
   1: core::panicking::panic_fmt
             at /rustc/84c898d65adf2f39a5a98507f1fe0ce10a2b8dbc/library/core/src/panicking.rs:64:14
   2: core::result::unwrap_failed
             at /rustc/84c898d65adf2f39a5a98507f1fe0ce10a2b8dbc/library/core/src/result.rs:1750:5
   3: galah::external_command_checker::check_for_dashing
   4: galah::cluster_argument_parsing::generate_galah_clusterer
   5: galah::cluster_argument_parsing::run_cluster_subcommand
   6: galah::main

which of course v1.0 is not older than 0.4.0. what should I do?

thanks in advance

wwood commented 1 year ago

Hi,

Thanks for your report - you can now (in the edge version, not released yet) use --checkm2-quality-report as input (rather than --checkm-tab-table.

Re dashing, also fixed.