I'm not sure if this elevates to an issue, since I'm just starting to use CoverM and am really unsure about the command structure (hard to tell which flags are needed and which not). Sorry if I'm cluttering the issues list!
I'm getting an error that says a genome is not a fasta file because it does not end in .fna (even though it does). Granted, I have other files in the genome directory which are not .fna but I was hoping they would be ignored.

Here is my command:
coverm genome -t 40 --single PATHTOMETAS -d PATHTOMAGS -x .fna -p minimap2-sr --min-read-percent-identity 0.9 --methods relative_abundance --bam-file-cache-directory bam_cache/ --discard-unmapped -v

[2020-12-08T20:55:57Z INFO coverm] CoverM version 0.5.0
[2020-12-08T20:55:57Z INFO coverm] Using min-covered-fraction 10%
[2020-12-08T20:55:57Z INFO coverm] Using min-read-percent-identity 90%
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020571-bin.11.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs_dreped.tar.gz' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/2582580591.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020551-bin.8.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020573-bin.18.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/GEODES117-bin.31.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020501-bin.15.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/refList.txt' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/archive_edited_fasta_id' as a genome FASTA file
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020490-bin.6.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020558-bin.31.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020542-bin.8.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs_original_fasta_id' as a genome FASTA file
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/2582580531.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020517-bin.16.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs_edited_fasta_id' as a genome FASTA file
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/GEODES118-bin.197.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020547-bin.20.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020539-bin.6.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020509-bin.3.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs-fastaIDedited.tar.gz' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:55:57Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/2582580577.fna' as a genome FASTA file, as it does not end with the extension '.fna'
thread 'main' panicked at 'Failed to parse genome paths: "Found 0 genomes from the genome-fasta-directory, cannot continue."', src/bin/coverm.rs:782:18
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace
(coverM) [trina.mcmahon@scarcity-11 coverM_mapping]$ ps
PID TTY TIME CMD
3710272 pts/2 00:00:00 bash
3711189 pts/2 00:00:00 ps
(coverM) [trina.mcmahon@scarcity-11 coverM_mapping]$ coverm genome -t 40 --single /home/GLBRCORG/trina.mcmahon/Cyanos/data/metaGs/ -d /home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/ -x .fna -p minimap2-sr --min-read-percent-identity 0.9 --methods relative_abundance --bam-file-cache-directory bam_cache/ --discard-unmapped -v
[2020-12-08T20:57:20Z INFO coverm] CoverM version 0.5.0
[2020-12-08T20:57:20Z INFO coverm] Using min-covered-fraction 10%
[2020-12-08T20:57:20Z DEBUG coverm] Cached regular coverage taker with columns to normlise: [0] and rpkm_column: None
[2020-12-08T20:57:20Z INFO coverm] Using min-read-percent-identity 90%
[2020-12-08T20:57:20Z DEBUG coverm] Filter parameters set as FilterParameters { flag_filters: FlagFilter { include_improper_pairs: true, include_supplementary: true, include_secondary: false }, min_aligned_length_single: 0, min_percent_identity_single: 0.9, min_aligned_percent_single: 0.0, min_aligned_length_pair: 0, min_percent_identity_pair: 0.0, min_aligned_percent_pair: 0.0 }
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020571-bin.11.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs_dreped.tar.gz' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/2582580591.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020551-bin.8.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020573-bin.18.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/GEODES117-bin.31.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020501-bin.15.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/refList.txt' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/archive_edited_fasta_id' as a genome FASTA file
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020490-bin.6.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020558-bin.31.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020542-bin.8.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs_original_fasta_id' as a genome FASTA file
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/2582580531.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020517-bin.16.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs_edited_fasta_id' as a genome FASTA file
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/GEODES118-bin.197.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020547-bin.20.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020539-bin.6.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/3300020509-bin.3.fna' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/16cyanoMAGs-fastaIDedited.tar.gz' as a genome FASTA file, as it does not end with the extension '.fna'
[2020-12-08T20:57:20Z INFO bird_tool_utils::clap_utils] Not using directory entry '/home/GLBRCORG/trina.mcmahon/Cyanos/data/dereplicated_MAGs/2582580577.fna' as a genome FASTA file, as it does not end with the extension '.fna'
thread 'main' panicked at 'Failed to parse genome paths: "Found 0 genomes from the genome-fasta-directory, cannot continue."', src/bin/coverm.rs:782:18
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace