[2025-08-14 11:21:49,925] multiqc                                            [DEBUG  ]  This is MultiQC v1.14
[2025-08-14 11:21:49,926] multiqc                                            [DEBUG  ]  Command used: /home/sam/programs/mambaforge/bin/multiqc --interactive .
[2025-08-14 11:21:50,532] multiqc                                            [WARNING]  MultiQC Version v1.30 now available!
[2025-08-14 11:21:50,532] multiqc                                            [DEBUG  ]  Working dir : /home/shared/16TB_HDD_01/sam/gitrepos/RobertsLab/project-cod-temperature/output/14.00-heatwave-genetics-trimmed-bwa-alignments
[2025-08-14 11:21:50,532] multiqc                                            [DEBUG  ]  Template    : default
[2025-08-14 11:21:50,532] multiqc                                            [DEBUG  ]  Running Python 3.10.10 | packaged by conda-forge | (main, Mar 24 2023, 20:08:06) [GCC 11.3.0]
[2025-08-14 11:21:50,533] 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, biobambam2, jcvi, mtnucratio, picard, vep, sentieon, prokka, qc3C, nanostat, samblaster, samtools, sexdeterrmine, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umitools, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, cellranger, snpsplit, odgi, pangolin, nextclade, humid, kat, leehom, adapterRemoval, bbduk, clipandmerge, cutadapt, flexbar, kaiju, 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
[2025-08-14 11:21:50,533] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmp8601mrt4
[2025-08-14 11:21:50,681] multiqc                                            [INFO   ]  Search path : /home/shared/16TB_HDD_01/sam/gitrepos/RobertsLab/project-cod-temperature/output/14.00-heatwave-genetics-trimmed-bwa-alignments
[2025-08-14 11:22:23,619] multiqc                                            [DEBUG  ]  Summary of files that were skipped by the search: [skipped_module_specific_max_filesize: 8265] // [skipped_no_match: 3098] // [skipped_ignore_pattern: 1376] // [skipped_filesize_limit: 344]
[2025-08-14 11:22:24,054] multiqc.plots.bargraph                             [DEBUG  ]  Using matplotlib version 3.7.1
[2025-08-14 11:22:24,055] multiqc.plots.linegraph                            [DEBUG  ]  Using matplotlib version 3.7.1
[2025-08-14 11:22:24,055] multiqc                                            [DEBUG  ]  No samples found: custom_content
[2025-08-14 11:22:24,116] multiqc.modules.picard.picard                      [INFO   ]  Found 344 MarkDuplicates reports
[2025-08-14 11:22:24,407] multiqc.modules.samtools.samtools                  [INFO   ]  Found 344 stats reports
[2025-08-14 11:22:24,458] multiqc.modules.samtools.flagstat                  [DEBUG  ]  Duplicate sample name found! Overwriting: MHW229-RG
[2025-08-14 11:22:24,490] multiqc.modules.samtools.samtools                  [INFO   ]  Found 344 flagstat reports
[2025-08-14 11:22:24,943] multiqc                                            [INFO   ]  Compressing plot data
[2025-08-14 11:22:25,220] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2025-08-14 11:22:25,220] multiqc                                            [INFO   ]  Data        : multiqc_data
[2025-08-14 11:22:25,220] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmp8601mrt4/multiqc_data' to '/home/shared/16TB_HDD_01/sam/gitrepos/RobertsLab/project-cod-temperature/output/14.00-heatwave-genetics-trimmed-bwa-alignments/multiqc_data'
[2025-08-14 11:22:25,280] multiqc                                            [INFO   ]  MultiQC complete