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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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coverm cluster to dereplicate --Parsing error in CheckM tab table file #118

Closed uqmwu closed 2 years ago

uqmwu commented 2 years ago

Hi Wood,

I try to use the coverm cluster function to dereplicate the genomes, Here is the command I used, coverm cluster -x fa --genome-fasta-directory /scratch/project/alkane/Mengxiong/C3_anammox/C3_anammox_BINNING/maxbin2_bins --checkm-tab-table /scratch/project/alkane/Mengxiong/C3_anammox/C3_anammox_BINNING/maxbin2_checkm_output/storage/checkm_maxbin2.tsv --min-completeness 70 --max-contamination 10 --output-representative-fasta-directory /scratch/project/alkane/Mengxiong/C3_anammox/C3_anammox_BINNING/drep_out

But I get the error: ERROR checkm] Parsing error in CheckM tab table file - didn't find 13 columns in line StringRecord.

Can you help check what is the issue here? Thank you!

wwood commented 2 years ago

Hi there,

Looks like there is some problem with your input file. It should be the output of when you run checkm lineage_wf --tab_table (I think that's the command, from memory)

ben

uqmwu commented 2 years ago

Thanks ben, I have updated the checkm tab table, but got another error, [2022-06-03T02:27:20Z INFO bird_tool_utils::clap_utils] coverm version 0.3.0 [2022-06-03T02:27:20Z INFO bird_tool_utils::external_command_checker] Found fastANI version 1.32 [2022-06-03T02:27:20Z INFO galah::cluster_argument_parsing] Reading CheckM tab table .. [2022-06-03T02:27:20Z INFO galah::cluster_argument_parsing] Calculating num_contigs etc. for genome quality assessment .. [2022-06-03T02:27:21Z INFO galah::cluster_argument_parsing] Read in genome qualities for 74 genomes. 29 passed quality thresholds thread 'main' panicked at 'Unable to parse version for dashing (error 1)', /root/.cargo/registry/src/github.com-1ecc6299db9ec823/bird_tool_utils-0.3.0/src/external_command_checker.rs:99:14 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace What is the issue here? Thanks!

wwood commented 2 years ago

HI,

That is an entirely unrelated issue, and is due to the way dashing was installed. When installed through conda, it sometimes doesn't work because it is compiled for the wrong CPU architecture. See https://github.com/wwood/CoverM/issues/45

I think I've answered the issue raised here so closing, but feel free to open another ticket if you have further problems. THanks, ben