search

wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
297 stars 30 forks source link

ERROR coverm::genomes_and_contigs he contig 'k141_142388_length_1308_cov_6.0000' has been assigned to multiple genomes, at least 'JL17_bin.20' and 'WA23_bin.33' #108

Open ZongzhiWu opened 2 years ago

ZongzhiWu commented 2 years ago

[2022-03-16T05:03:15Z INFO coverm] CoverM version 0.6.1 [2022-03-16T05:03:15Z INFO coverm] Writing output to file: /lustre/home/liutang/41groundwater/14host/01MAGs/05host_abundance/host_rpkm.tsv [2022-03-16T05:03:15Z INFO coverm] Using min-covered-fraction 10% [2022-03-16T05:03:15Z INFO coverm] Using min-read-percent-identity 95% [2022-03-16T05:03:15Z INFO coverm] Using min-read-aligned-percent 90% [2022-03-16T05:04:53Z ERROR coverm::genomes_and_contigs] The contig 'k141_142388_length_1308_cov_6.0000' has been assigned to multiple genomes, at least 'JL17_bin.20' and 'WA23_bin.33'. You may try not using --reference and let coverm generate a reference of concatenated contigs, or rename the contigs in your genome file(s).

wwood commented 2 years ago

Hi,

I'm afraid there's not enough information here to know what the problem might be (other than what the error is suggesting). What command line did you use?