samtools coverage log file skipped by the search

[charlenelawdes]

Description of bug

I am using multiqc to make reports on samtools stats and samtools coverage logs. MultiQC recognized samtools stats output, but not samtools coverage output.

I tried to increase the file size specific to the samtools/coverage module in the config file, but I got the same outcome.

I used this command :
multiqc --config multiqc_config.yaml .

and my multiqc_config.yaml is :

log_filesize_limit: 2000000000
sp:
  samtools/coverage:
    max_filesize: 2000000000

Here is a small test file that I am using to reproduce the error:

reads_alignment.cov.txt

File that triggers the error

No response

MultiQC Error log

[2024-05-14 19:58:43,904] multiqc                                            [DEBUG  ]  This is MultiQC v1.19
[2024-05-14 19:58:43,907] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yaml
[2024-05-14 19:58:43,907] multiqc                                            [DEBUG  ]  New config: {'log_filesize_limit': 2000000000}
[2024-05-14 19:58:43,907] multiqc                                            [DEBUG  ]  Added to filename patterns: [{'samtools/coverage': {'max_filesize': 2000000000}}]
[2024-05-14 19:58:43,908] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yaml
[2024-05-14 19:58:43,908] multiqc                                            [DEBUG  ]  New config: {'log_filesize_limit': 2000000000}
[2024-05-14 19:58:43,908] multiqc                                            [DEBUG  ]  Added to filename patterns: [{'samtools/coverage': {'max_filesize': 2000000000}}]
[2024-05-14 19:58:43,908] multiqc                                            [DEBUG  ]  Command used: /usr/local/bin/multiqc --config multiqc_config.yaml .
[2024-05-14 19:58:44,492] multiqc                                            [WARNING]  MultiQC Version v1.21 now available!
[2024-05-14 19:58:44,492] multiqc                                            [DEBUG  ]  Working dir : /Users/lawcha/Platform/results/work/73/c938062d5488ffba74d9aef7f21c5b
[2024-05-14 19:58:44,492] multiqc                                            [DEBUG  ]  Template    : default
[2024-05-14 19:58:44,492] multiqc                                            [DEBUG  ]  Running Python 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]
[2024-05-14 19:58:44,493] multiqc                                            [DEBUG  ]  Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, sambamba, gopeaks, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dragen_fastqc, dedup, pbmarkdup, damageprofiler, mapdamage, biobambam2, jcvi, mtnucratio, picard, vep, bakta, prokka, qc3C, nanostat, samblaster, samtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umitools, truvari, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, cellranger, snpsplit, odgi, pangolin, nextclade, freyja, humid, kat, leehom, librarian, adapterRemoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, bracken, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, xenome, xengsort
[2024-05-14 19:58:44,493] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmpx6ffxvse
[2024-05-14 19:58:44,494] multiqc                                            [INFO   ]  Search path : /Users/lawcha/Platform/results/work/73/c938062d5488ffba74d9aef7f21c5b
[2024-05-14 19:58:44,651] multiqc                                            [DEBUG  ]  Summary of files that were skipped by the search: [skipped_module_specific_max_filesize: 19] // [skipped_no_match: 8]
[2024-05-14 19:58:47,847] multiqc.plots.bargraph                             [DEBUG  ]  Using matplotlib version 3.8.2
[2024-05-14 19:58:47,847] multiqc.plots.linegraph                            [DEBUG  ]  Using matplotlib version 3.8.2
[2024-05-14 19:58:47,848] multiqc                                            [DEBUG  ]  No samples found: custom_content
[2024-05-14 19:58:47,923] multiqc.modules.samtools.samtools                  [INFO   ]  Found 1 stats reports
[2024-05-14 19:58:47,923] multiqc.utils.software_versions                    [DEBUG  ]  Reading software versions from config.software_versions
[2024-05-14 19:58:47,926] multiqc                                            [DEBUG  ]  Compressing plot data
[2024-05-14 19:58:47,934] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2024-05-14 19:58:47,935] multiqc                                            [INFO   ]  Data        : multiqc_data
[2024-05-14 19:58:47,935] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpx6ffxvse/multiqc_data' to '/Users/lawcha/Platform/results/work/73/c938062d5488ffba74d9aef7f21c5b/multiqc_data'
[2024-05-14 19:58:47,944] multiqc                                            [DEBUG  ]  Full report path: /Users/lawcha/Platform/results/work/73/c938062d5488ffba74d9aef7f21c5b/multiqc_report.html
[2024-05-14 19:58:48,034] multiqc                                            [INFO   ]  MultiQC complete

Before submitting

• I have read the troubleshooting documentation.
• I am using the latest release of MultiQC.
• I have included a full MultiQC log, not truncated.
• I have attached an input file (.zip if necessary) that triggers the error.