[2025-10-27 07:21:11,347] root [DEBUG ] Logging to file: /tmp/tmp1rlf0_kq/multiqc.log [2025-10-27 07:21:11,348] multiqc.core.update_config [DEBUG ] This is MultiQC v1.32 [2025-10-27 07:21:11,348] multiqc.core.update_config [DEBUG ] Running Python 3.13.5 | packaged by Anaconda, Inc. | (main, Jun 12 2025, 16:09:02) [GCC 11.2.0] [2025-10-27 07:21:11,349] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443 [2025-10-27 07:21:11,899] urllib3.connectionpool [DEBUG ] https://api.multiqc.info:443 "GET /version?version_multiqc=1.32&version_python=3.13.5&operating_system=Linux&is_docker=False&is_singularity=False&is_conda=False&is_ci=False&is_notebook=False&ai_summary=False&ai_summary_full=False&ai_provider=seqera HTTP/1.1" 200 178 [2025-10-27 07:21:11,900] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.32, released 2025-10-25 [2025-10-27 07:21:11,902] multiqc.multiqc [DEBUG ] Working dir : /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code [2025-10-27 07:21:11,903] multiqc.multiqc [DEBUG ] Template : default [2025-10-27 07:21:11,904] multiqc.multiqc [DEBUG ] Command used: /home/sr320/.local/bin/multiqc ../analyses/08-nanoplot/ -o ../analyses/08-multiqc [2025-10-27 07:21:11,904] multiqc.core.file_search [INFO ] Search path: /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/08-nanoplot [2025-10-27 07:21:11,906] multiqc.core.file_search [DEBUG ] Analysing modules: bases2fastq, cellranger_arc, cells2stats, sompy, xenium, custom_content, ccs, ngsderive, purple, conpair, isoseq, lima, peddy, percolator, haplocheck, somalier, methylqa, mosdepth, phantompeakqualtools, qualimap, bamdst, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, checkm, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, glimpse, 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, checkm2, qc3C, nanoq, nanostat, samblaster, samtools, bamtools, sambamba, ngsbits, pairtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umicollapse, umitools, truvari, megahit, ganon, gtdbtk, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, hostile, cellranger, snpsplit, odgi, vg, pangolin, nextclade, freyja, humid, kat, leehom, librarian, nonpareil, adapterremoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, seqfu, fastq_screen, afterqc, fastp, fastqc, sequali, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, spaceranger, xenome, xengsort, metaphlan, seqwho, telseq, ataqv, mgikit, mosaicatcher, software_versions [2025-10-27 07:21:11,906] multiqc.core.file_search [DEBUG ] Search keys: adapterremoval, afterqc, anglerfish, ataqv, bakta, bamdst, bamtools, bases2fastq, bbduk, bbmap, bcftools, bcl2fastq, bclconvert, biobambam2, biobloomtools, biscuit, bismark, bowtie1, bowtie2, busco, bustools, ccs, cellranger, cellranger_arc, cells2stats, checkm, checkm2, checkqc, clipandmerge, clusterflow, conpair, custom_content, cutadapt, damageprofiler, dedup, deeptools, diamond, disambiguate, dragen, dragen_fastqc, eigenstratdatabasetools, fastp, fastq_screen, fastqc, featurecounts, fgbio, filtlong, flash, flexbar, freyja, ganon, gatk, gffcompare, glimpse, goleft_indexcov, gopeaks, gtdbtk, haplocheck, happy, hicexplorer, hicpro, hicup, hifiasm, hisat2, homer, hops, hostile, htseq, humid, interop, isoseq, ivar, jcvi, jellyfish, kaiju, kallisto, kat, kraken, leehom, librarian, lima, longranger, macs2, malt, mapdamage, megahit, metaphlan, methylqa, mgikit, minionqc, mirtop, mirtrace, mosaicatcher, mosdepth, motus, mtnucratio, multiqc_data, multivcfanalyzer, nanoq, nanostat, nextclade, ngsbits, ngsderive, nonpareil, odgi, optitype, pairtools, pangolin, pbmarkdup, peddy, percolator, phantompeakqualtools, picard, porechop, preseq, prinseqplusplus, prokka, purple, pychopper, pycoqc, qc3C, qorts, qualimap, quast, rna_seqc, rockhopper, rsem, rseqc, salmon, sambamba, samblaster, samtools, sargasso, seqera_cli, seqfu, sequali, seqwho, seqyclean, sexdeterrmine, sickle, skewer, slamdunk, snippy, snpeff, snpsplit, software_versions, somalier, sompy, sortmerna, sourmash, spaceranger, stacks, star, supernova, telseq, theta2, tophat, trimmomatic, truvari, umicollapse, umitools, varscan2, vcftools, vep, verifybamid, vg, whatshap, xengsort, xenium, xenome [2025-10-27 07:21:12,087] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_no_match: 33|, |skipped_module_specific_max_filesize: 16|, |skipped_ignore_pattern: 10| [2025-10-27 07:21:12,089] multiqc.core.exec_modules [DEBUG ] Running module: custom_content [2025-10-27 07:21:12,090] multiqc.core.exec_modules [DEBUG ] No samples found: custom_content [2025-10-27 07:21:12,090] multiqc.core.exec_modules [DEBUG ] Running module: nanostat [2025-10-27 07:21:12,092] multiqc.modules.nanostat.nanostat [INFO ] Found 2 reports [2025-10-27 07:21:12,093] multiqc.report [DEBUG ] Wrote data file multiqc_nanostat.txt [2025-10-27 07:21:12,093] multiqc.report [DEBUG ] Wrote data file multiqc_nanostat.json [2025-10-27 07:21:12,115] multiqc.plots.table_object [DEBUG ] Table key 'Active channels_fastq' not found in data for 'nanostat_fastq_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,115] multiqc.plots.table_object [DEBUG ] Table key 'Median percent identity_fastq' not found in data for 'nanostat_fastq_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,115] multiqc.plots.table_object [DEBUG ] Table key 'Average percent identity_fastq' not found in data for 'nanostat_fastq_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,115] multiqc.plots.table_object [DEBUG ] Table key 'Total bases aligned_fastq' not found in data for 'nanostat_fastq_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,116] multiqc.plots.plot [DEBUG ] merge_with_previous for nanostat_fastq_stats_table: found old_data = False [2025-10-27 07:21:12,116] multiqc.plots.plot [DEBUG ] merge_with_previous for nanostat_fastq_stats_table: no old data or empty, using new data only [2025-10-27 07:21:12,192] multiqc.plots.plot [DEBUG ] merge_with_previous for nanostat_quality_dist: found old_data = False [2025-10-27 07:21:12,192] multiqc.plots.plot [DEBUG ] merge_with_previous for nanostat_quality_dist: no old data or empty, using new data only [2025-10-27 07:21:12,220] multiqc.base_module [DEBUG ] nanostat: deleting attribute self.nanostat_data [2025-10-27 07:21:12,220] multiqc.base_module [DEBUG ] nanostat: deleting attribute self.has_qscores [2025-10-27 07:21:12,220] multiqc.base_module [DEBUG ] nanostat: deleting attribute self.has_aligned [2025-10-27 07:21:12,221] multiqc.base_module [DEBUG ] nanostat: deleting attribute self.has_seq_summary [2025-10-27 07:21:12,221] multiqc.base_module [DEBUG ] nanostat: deleting attribute self.has_fastq [2025-10-27 07:21:12,221] multiqc.base_module [DEBUG ] nanostat: deleting attribute self.has_fasta [2025-10-27 07:21:12,221] multiqc.base_module [DEBUG ] nanostat: deleting attribute self.general_stats_added [2025-10-27 07:21:12,221] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions [2025-10-27 07:21:12,222] multiqc.core.write_results [DEBUG ] Rendering plots [2025-10-27 07:21:12,231] multiqc.plots.table_object [DEBUG ] Table key 'Active channels_fastq' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,232] multiqc.plots.table_object [DEBUG ] Table key 'Median percent identity_fastq' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,232] multiqc.plots.table_object [DEBUG ] Table key 'Average percent identity_fastq' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,232] multiqc.plots.table_object [DEBUG ] Table key 'Total bases aligned_fastq' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys [2025-10-27 07:21:12,234] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: found old_data = False [2025-10-27 07:21:12,235] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: no old data or empty, using new data only [2025-10-27 07:21:12,271] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.txt [2025-10-27 07:21:12,272] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.json [2025-10-27 07:21:12,275] multiqc.core.ai [DEBUG ] Saved AI prompt to multiqc_data/llms-full.txt [2025-10-27 07:21:12,275] multiqc.core.write_results [INFO ] Existing reports found, adding suffix to filenames. Use '--force' to overwrite. [2025-10-27 07:21:12,275] multiqc.core.write_results [DEBUG ] Exporting plot data to files [2025-10-27 07:21:12,275] multiqc.report [DEBUG ] Wrote data file nanostat_fastq_stats_table.txt [2025-10-27 07:21:12,276] multiqc.report [DEBUG ] Wrote data file nanostat_quality_dist.txt [2025-10-27 07:21:12,276] multiqc.core.write_results [DEBUG ] Moving data file from '/tmp/tmp1rlf0_kq/multiqc_data' to '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/08-multiqc/multiqc_data_1_2' [2025-10-27 07:21:12,319] multiqc.core.write_results [INFO ] Data : /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/08-multiqc/multiqc_data_1_2 [2025-10-27 07:21:12,339] multiqc.core.write_results [DEBUG ] Compressing plot data [2025-10-27 07:21:12,425] multiqc.core.write_results [INFO ] Report : /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/08-multiqc/multiqc_report_2.html