Problems running CoverM Demo data

[Ruser111]

Hello,

When I run the command to calculate the coverage for the demo data (coverm genome --coupled sample_1.1.fq.gz sample_1.2.fq.gz --genome-fasta-files genome_1.fna genome_2.fna genome_3.fna genome_4.fna genome_5.fna genome_6.fna genome_7.fna genome_8.fna -t 8 -m mean relative_abundance covered_fraction -o output_coverm.tsv), I got the following error messages:

[2026-02-04T00:04:49Z INFO bird_tool_utils::clap_utils] CoverM version 0.7.0
[2026-02-04T00:04:49Z INFO coverm] Writing output to file: output_coverm.tsv
[2026-02-04T00:04:49Z INFO bird_tool_utils::external_command_checker] Found minimap2 version 2.30-r1287

thread 'main' panicked at /opt/conda/conda-bld/coverm_1752623530827/_build_env/.cargo/git/checkouts/bird_tool_utils-fb1eb8c77c447961/9741c97/src/external_command_checker.rs:148:6:
Unable to parse version number 'samtools)' from executable samtools
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

Thanks!

[wwood]

It seems there is something astray with your Sam tools install, perhaps.

What happens when you run samtools --version outside of coverm?

[Ruser111]

This is what I got:

samtools: /path/anaconda3/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /path/anaconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /path/anaconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /path/anaconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools 1.21
Using htslib 1.21
Copyright (C) 2024 Genome Research Ltd.

Samtools compilation details:
Features: build=configure curses=yes
CC: /opt/conda/conda-bld/samtools_1734249775320/_build_env/bin/x86_64-conda-linux-gnu-cc
CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /path/anaconda3/include
CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /path/anaconda3/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1734249775320/work=/usr/local/src/conda/samtools-1.21 -fdebug-prefix-map=/path/anaconda3=/usr/local/src/conda-prefix
LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/path/anaconda3/lib -Wl,-rpath-link,/path/anaconda3/lib -L/path/anaconda3/lib
HTSDIR:
LIBS:
CURSES_LIB: -ltinfow -lncursesw

HTSlib compilation details:
Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/path/anaconda3/libexec/htslib htscodecs=1.6.1
CC: /opt/conda/conda-bld/htslib_1726172129301/_build_env/bin/x86_64-conda-linux-gnu-cc
CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /path/anaconda3/include
CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /path/anaconda3/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1726172129301/work=/usr/local/src/conda/htslib-1.21 -fdebug-prefix-map=/path/anaconda3=/usr/local/src/conda-prefix -fvisibility=hidden
LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/path/anaconda3/lib -Wl,-rpath-link,/path/anaconda3/lib -L/path/anaconda3/lib -fvisibility=hidden -rdynamic

[wwood]

Looks like the stuff up front is causing the issue.

Id maybe recommend installing coverm with Pixi instead?

[Ruser111]

Looks like the stuff up front is causing the issue.

Id maybe recommend installing coverm with Pixi instead?

Pixi did not work for me but I found another solution. You are right that the problem is samtools is not properly installed. So I conda installed samtools first, followed by installing CoverM. That way the problems with samtools are gone. It works for me now.

Thank you so much!