I was trying to calculate relative abundance for metagenome MAGs. I used genome option, and 0 reads mapped.
[2025-05-06T13:14:55Z INFO bird_tool_utils::clap_utils] CoverM version 0.7.0
[2025-05-06T13:14:55Z INFO coverm] Writing output to file: LIB115088_derepl_ra_0_coverm.tsv
[2025-05-06T13:14:56Z INFO coverm::genome] Of 1473 reference IDs, 1473 were assigned to a genome and 0 were not
[2025-05-06T13:15:15Z INFO coverm::genome] In sample 'LIB115088_aln.sorted', found 0 reads mapped out of 22089560 total (0.00%)
Since contig option created rpkm, tpm results no problem with same aln.sorted.bam and MAGs (aligned 70-90%), I am wondering why genome option did not count aligned reads. I tried both single file --genome-fasta-files MAGs.fasta and directory --genome-fasta-directory /path/MAG/.
I was trying to calculate relative abundance for metagenome MAGs. I used genome option, and 0 reads mapped.
[2025-05-06T13:14:55Z INFO bird_tool_utils::clap_utils] CoverM version 0.7.0
[2025-05-06T13:14:55Z INFO coverm] Writing output to file: LIB115088_derepl_ra_0_coverm.tsv
[2025-05-06T13:14:56Z INFO coverm::genome] Of 1473 reference IDs, 1473 were assigned to a genome and 0 were not
[2025-05-06T13:15:15Z INFO coverm::genome] In sample 'LIB115088_aln.sorted', found 0 reads mapped out of 22089560 total (0.00%)
Since contig option created rpkm, tpm results no problem with same aln.sorted.bam and MAGs (aligned 70-90%), I am wondering why genome option did not count aligned reads. I tried both single file --genome-fasta-files MAGs.fasta and directory --genome-fasta-directory /path/MAG/.