When using coverm genome, there is no *_paired_2.fastq available？

[mattewchen]

I am using "coverm genome -1 hr/_paired_1.fastq -2 hr/_paired_2.fastq --genome-fasta-files binning/drep_out/dereplicated_genomes/*.fa -m tpm -o binning/coverm_abundance_tpm.tsv" to calculate MAG abundance. It is only displayed on "2025-11-23T09:39:28Z INFO coverm::genome] In sample 'SA10_paired_1.fastq', found 25155788 reads mapped out of 219586068 total (11.46%)". Is it normal without SA10_paired_2.fastq?
2025-11-23T09:27:50Z INFO bird_tool_utils::clap_utils] CoverM version 0.7.0
[2025-11-23T09:27:50Z INFO coverm] Writing output to file: binning/coverm_abundance_tpm_new.tsv
[2025-11-23T09:27:50Z INFO bird_tool_utils::external_command_checker] Found minimap2 version 2.30-r1287
[2025-11-23T09:27:51Z INFO bird_tool_utils::external_command_checker] Found samtools version 1.22.1
[2025-11-23T09:27:51Z INFO coverm] Profiling 665 genomes
[2025-11-23T09:27:51Z INFO coverm] Generating concatenated reference FASTA file of 665 genomes ..
[2025-11-23T09:28:53Z INFO coverm::mapping_index_maintenance] Generating MINIMAP2_SR index for /tmp/coverm-concatenated-fasta4WpUaV ..
[2025-11-23T09:29:51Z INFO coverm::mapping_index_maintenance] Finished generating MINIMAP2_SR index.
[2025-11-23T09:39:28Z INFO coverm::genome] In sample 'SA10_paired_1.fastq', found 25155788 reads mapped out of 219586068 total (11.46%)
[2025-11-23T09:52:33Z INFO coverm::genome] In sample 'SA15_paired_1.fastq', found 49088186 reads mapped out of 231309454 total (21.22%)
[2025-11-23T10:03:32Z INFO coverm::genome] In sample 'SA20_paired_1.fastq', found 62028975 reads mapped out of 251096286 total (24.70%)
[2025-11-23T10:16:50Z INFO coverm::genome] In sample 'SA30_paired_1.fastq', found 76824713 reads mapped out of 241654744 total (31.79%)
[2025-11-23T10:28:40Z INFO coverm::genome] In sample 'SA40_paired_1.fastq', found 72272049 reads mapped out of 230139068 total (31.40%)
[2025-11-23T10:41:23Z INFO coverm::genome] In sample 'SA50_paired_1.fastq', found 79213391 reads mapped out of 231906664 total (34.16%)
[2025-11-23T10:53:22Z INFO coverm::genome] In sample 'SA55_paired_1.fastq', found 90114323 reads mapped out of 210365306 total (42.84%)
[2025-11-23T11:16:46Z INFO coverm::genome] In sample 'SA62_paired_1.fastq', found 120310344 reads mapped out of 275602064 total (43.65%)
[2025-11-23T11:30:53Z INFO coverm::genome] In sample 'SA68_paired_1.fastq', found 124588837 reads mapped out of 254732848 total (48.91%)
[2025-11-23T11:48:15Z INFO coverm::genome] In sample 'SA75_paired_1.fastq', found 169391151 reads mapped out of 290322340 total (58.35%)

[wwood]

Yes, when there is a pair it just reports the first of the pair as the name.

[mattewchen]

@wwood Thank you, this has been bothering me all along. I thought it was a mistake in my operation