[2026-09-25 13:11:50,385] root [DEBUG ] Logging to file: /tmp/tmpu53u3np8/multiqc.log [2026-09-25 13:11:50,420] multiqc.core.update_config [DEBUG ] This is MultiQC v1.35 [2026-09-25 13:11:50,420] multiqc.core.update_config [DEBUG ] Running Python 3.14.7 | packaged by conda-forge | (main, Sep 2 2026, 21:08:32) [GCC 15.3.0] [2026-09-25 13:11:50,421] multiqc.core.update_config [INFO ] Report title: SRP139854 read QC [2026-09-25 13:11:50,457] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443 [2026-09-25 13:11:50,915] urllib3.connectionpool [DEBUG ] https://api.multiqc.info:443 "GET /version?version_multiqc=1.35&version_python=3.14.7&operating_system=Linux&is_docker=False&is_singularity=True&is_conda=True&is_uv=False&is_ci=False&is_notebook=False&ai_summary=False&ai_summary_full=False&ai_provider=seqera HTTP/1.1" 200 178 [2026-09-25 13:11:50,915] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.35, released 2026-05-13 [2026-09-25 13:11:50,916] multiqc.multiqc [DEBUG ] Working dir : /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/code [2026-09-25 13:11:50,916] multiqc.multiqc [DEBUG ] Template : default [2026-09-25 13:11:50,917] multiqc.multiqc [DEBUG ] Command used: /mmfs1/gscratch/srlab/sr320/miniforge3/envs/qc-trim/bin/multiqc --force --title SRP139854 read QC --outdir ../output/02-qc-trim/multiqc ../output/02-qc-trim [2026-09-25 13:11:50,917] multiqc.core.file_search [INFO ] Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/output/02-qc-trim [2026-09-25 13:11:50,918] multiqc.core.file_search [DEBUG ] Analysing modules: bases2fastq, cellranger_arc, cells2stats, deacon, hicstuff, hifi_trimmer, methurator, ribotish, ribowaltz, riker, seqkit, 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, sincei, ganon, gtdbtk, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, hostile, cellranger, checkatlas, snpsplit, odgi, vg, pangolin, nextclade, freyja, humid, kat, leehom, librarian, nonpareil, adapterremoval, bbduk, clipandmerge, cutadapt, trim_galore, flexbar, sourmash, kaiju, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, seqfu, fastq_screen, fastqe, 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, sylphtax, seqwho, telseq, ataqv, mgikit, mosaicatcher, software_versions [2026-09-25 13:11:50,918] 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, checkatlas, checkm, checkm2, checkqc, clipandmerge, clusterflow, conpair, custom_content, cutadapt, damageprofiler, deacon, dedup, deeptools, diamond, disambiguate, dragen, dragen_fastqc, eigenstratdatabasetools, fastp, fastq_screen, fastqc, fastqe, featurecounts, fgbio, filtlong, flash, flexbar, freyja, ganon, gatk, gffcompare, glimpse, goleft_indexcov, gopeaks, gtdbtk, haplocheck, happy, hicexplorer, hicpro, hicstuff, hicup, hifi_trimmer, 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, methurator, 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, ribotish, ribowaltz, riker, rna_seqc, rockhopper, rsem, rseqc, salmon, sambamba, samblaster, samtools, sargasso, seqera_cli, seqfu, seqkit, sequali, seqwho, seqyclean, sexdeterrmine, sickle, sincei, skewer, slamdunk, snippy, snpeff, snpsplit, software_versions, somalier, sompy, sortmerna, sourmash, spaceranger, stacks, star, supernova, sylphtax, telseq, theta2, tophat, trim_galore, trimmomatic, truvari, umicollapse, umitools, varscan2, vcftools, vep, verifybamid, vg, whatshap, xengsort, xenium, xenome [2026-09-25 13:11:51,664] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_module_specific_max_filesize: 35|, |skipped_no_match: 28|, |skipped_ignore_pattern: 1| [2026-09-25 13:11:51,667] multiqc.base_module [DEBUG ] Couldn't read file as utf-8: multiqc.parquet, will attempt to skip non-unicode characters 'utf-8' codec can't decode byte 0x98 in position 7: invalid start byte [2026-09-25 13:11:51,669] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading report data from parquet file: ../output/02-qc-trim/multiqc/SRP139854-read-QC_multiqc_report_data/multiqc.parquet [2026-09-25 13:11:52,510] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading module Trim Galore from parquet [2026-09-25 13:11:52,511] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading module FastQC from parquet [2026-09-25 13:11:52,511] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Extracting software versions from HTML content in parquet file [2026-09-25 13:11:52,511] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Collected software version: FastQC = 0.12.1 [2026-09-25 13:11:52,511] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Collected software version: Trim Galore = 2.3.0 [2026-09-25 13:11:52,511] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Skipping Software Versions module from parquet file - extracted data to global software_versions [2026-09-25 13:11:52,511] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading global software versions data from parquet file [2026-09-25 13:11:52,583] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for trim_galore_adapter_length_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,583] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for trim_galore_adapter_length_plot, adding new data [2026-09-25 13:11:52,584] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for trim_galore_poly_trimming_table, type: ViolinPlotInputData [2026-09-25 13:11:52,584] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for trim_galore_poly_trimming_table, adding new data [2026-09-25 13:11:52,586] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_base_sequence_quality_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,586] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_per_base_sequence_quality_plot, adding new data [2026-09-25 13:11:52,587] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_sequence_quality_scores_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,587] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_per_sequence_quality_scores_plot, adding new data [2026-09-25 13:11:52,590] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_sequence_gc_content_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,590] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_per_sequence_gc_content_plot, adding new data [2026-09-25 13:11:52,591] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_base_n_content_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,591] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_per_base_n_content_plot, adding new data [2026-09-25 13:11:52,592] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_sequence_duplication_levels_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,592] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_sequence_duplication_levels_plot, adding new data [2026-09-25 13:11:52,593] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_top_overrepresented_sequences_table, type: ViolinPlotInputData [2026-09-25 13:11:52,593] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_top_overrepresented_sequences_table, adding new data [2026-09-25 13:11:52,595] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_adapter_content_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,595] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_adapter_content_plot, adding new data [2026-09-25 13:11:52,596] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc-status-check-heatmap, type: HeatmapNormalizedInputData [2026-09-25 13:11:52,596] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc-status-check-heatmap, adding new data [2026-09-25 13:11:52,598] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for general_stats_table, type: ViolinPlotInputData [2026-09-25 13:11:52,598] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for general_stats_table, adding new data [2026-09-25 13:11:52,598] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for trim_galore_filtered_reads_plot, type: BarPlotInputData [2026-09-25 13:11:52,598] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for trim_galore_filtered_reads_plot, adding new data [2026-09-25 13:11:52,600] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for trim_galore_adapter_length_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,600] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for trim_galore_adapter_length_plot, merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:52,600] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor trim_galore_adapter_length_plot [2026-09-25 13:11:52,631] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (606, 13), New: (606, 13) [2026-09-25 13:11:52,634] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:52,703] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:52,703] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (606, 13) [2026-09-25 13:11:52,709] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:52,709] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for trim_galore_adapter_length_plot [2026-09-25 13:11:52,709] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_sequence_counts_plot, type: BarPlotInputData [2026-09-25 13:11:52,709] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_sequence_counts_plot, adding new data [2026-09-25 13:11:52,710] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_base_sequence_quality_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,711] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc_per_base_sequence_quality_plot, merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:52,711] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_base_sequence_quality_plot [2026-09-25 13:11:52,714] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (330, 13), New: (330, 13) [2026-09-25 13:11:52,714] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:52,715] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:52,716] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (330, 13) [2026-09-25 13:11:52,718] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:52,718] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc_per_base_sequence_quality_plot [2026-09-25 13:11:52,719] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_sequence_quality_scores_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,720] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc_per_sequence_quality_scores_plot, merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:52,720] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_sequence_quality_scores_plot [2026-09-25 13:11:52,723] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (234, 13), New: (234, 13) [2026-09-25 13:11:52,723] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:52,724] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:52,724] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (234, 13) [2026-09-25 13:11:52,727] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:52,727] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc_per_sequence_quality_scores_plot [2026-09-25 13:11:52,732] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_sequence_gc_content_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,732] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc_per_sequence_gc_content_plot, merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:52,732] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_sequence_gc_content_plot [2026-09-25 13:11:52,748] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (1212, 13), New: (2424, 13) [2026-09-25 13:11:52,749] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (12, 2) [2026-09-25 13:11:52,750] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (1212, 13) [2026-09-25 13:11:52,750] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (3636, 13) [2026-09-25 13:11:52,764] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 2 datasets, 6 samples [2026-09-25 13:11:52,764] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc_per_sequence_gc_content_plot [2026-09-25 13:11:52,766] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_per_base_n_content_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,766] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc_per_base_n_content_plot, merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:52,766] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_base_n_content_plot [2026-09-25 13:11:52,769] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (330, 13), New: (330, 13) [2026-09-25 13:11:52,770] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:52,771] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:52,771] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (330, 13) [2026-09-25 13:11:52,773] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:52,774] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc_per_base_n_content_plot [2026-09-25 13:11:52,775] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_sequence_duplication_levels_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,775] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc_sequence_duplication_levels_plot, merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:52,775] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_sequence_duplication_levels_plot [2026-09-25 13:11:52,776] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (96, 13), New: (96, 13) [2026-09-25 13:11:52,777] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:52,778] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:52,778] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (96, 13) [2026-09-25 13:11:52,780] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:52,780] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc_sequence_duplication_levels_plot [2026-09-25 13:11:52,780] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_overrepresented_sequences_plot, type: BarPlotInputData [2026-09-25 13:11:52,780] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] No existing plot input data for fastqc_overrepresented_sequences_plot, adding new data [2026-09-25 13:11:52,781] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_top_overrepresented_sequences_table, type: ViolinPlotInputData [2026-09-25 13:11:52,781] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc_top_overrepresented_sequences_table, merging ViolinPlotInputData with ViolinPlotInputData [2026-09-25 13:11:52,788] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc_top_overrepresented_sequences_table [2026-09-25 13:11:52,791] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc_adapter_content_plot, type: LinePlotNormalizedInputData [2026-09-25 13:11:52,791] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc_adapter_content_plot, merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:52,791] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_adapter_content_plot [2026-09-25 13:11:52,796] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (600, 13), New: (600, 13) [2026-09-25 13:11:52,797] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (12, 2) [2026-09-25 13:11:52,797] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:52,798] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (600, 13) [2026-09-25 13:11:52,801] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 12 samples [2026-09-25 13:11:52,802] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc_adapter_content_plot [2026-09-25 13:11:52,802] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for fastqc-status-check-heatmap, type: HeatmapNormalizedInputData [2026-09-25 13:11:52,802] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for fastqc-status-check-heatmap, merging HeatmapNormalizedInputData with HeatmapNormalizedInputData [2026-09-25 13:11:52,802] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for fastqc-status-check-heatmap [2026-09-25 13:11:52,804] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Loading plot input data for general_stats_table, type: ViolinPlotInputData [2026-09-25 13:11:52,804] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Found existing plot input data for general_stats_table, merging ViolinPlotInputData with ViolinPlotInputData [2026-09-25 13:11:52,810] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Successfully merged plot input data for general_stats_table [2026-09-25 13:11:52,811] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Processed 1 versions for FastQC: 0.12.1 [2026-09-25 13:11:52,811] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Processed 1 versions for Trim Galore: 2.3.0 [2026-09-25 13:11:52,931] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for trim_galore_adapter_length_plot [2026-09-25 13:11:52,966] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for trim_galore_poly_trimming_table [2026-09-25 13:11:52,970] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_per_base_sequence_quality_plot [2026-09-25 13:11:52,973] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_per_sequence_quality_scores_plot [2026-09-25 13:11:52,980] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_per_sequence_gc_content_plot [2026-09-25 13:11:52,984] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_per_base_n_content_plot [2026-09-25 13:11:52,986] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_sequence_duplication_levels_plot [2026-09-25 13:11:52,991] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_top_overrepresented_sequences_table [2026-09-25 13:11:52,999] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_adapter_content_plot [2026-09-25 13:11:53,005] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc-status-check-heatmap [2026-09-25 13:11:53,010] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for general_stats_table [2026-09-25 13:11:53,015] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for trim_galore_filtered_reads_plot [2026-09-25 13:11:53,019] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_sequence_counts_plot [2026-09-25 13:11:53,022] multiqc.core.special_case_modules.load_multiqc_data [DEBUG ] Created plot object for fastqc_overrepresented_sequences_plot [2026-09-25 13:11:53,023] multiqc.core.exec_modules [DEBUG ] Running module: custom_content [2026-09-25 13:11:53,024] multiqc.core.exec_modules [DEBUG ] No samples found: custom_content [2026-09-25 13:11:53,024] multiqc.core.exec_modules [DEBUG ] Running module: htseq [2026-09-25 13:11:53,028] multiqc.core.exec_modules [DEBUG ] No samples found: htseq [2026-09-25 13:11:53,028] multiqc.core.exec_modules [DEBUG ] Running module: snippy [2026-09-25 13:11:53,029] multiqc.core.exec_modules [DEBUG ] No samples found: snippy [2026-09-25 13:11:53,029] multiqc.core.exec_modules [DEBUG ] Running module: trim_galore [2026-09-25 13:11:53,032] multiqc.modules.trim_galore.trim_galore [INFO ] Found 6 reports [2026-09-25 13:11:53,033] multiqc.plots.plot [DEBUG ] merge_with_previous for trim_galore_filtered_reads_plot: found old_data = True [2026-09-25 13:11:53,033] multiqc.plots.plot [DEBUG ] merge_with_previous for trim_galore_filtered_reads_plot: merging BarPlotInputData with BarPlotInputData [2026-09-25 13:11:53,037] multiqc.plots.plot [DEBUG ] merge_with_previous for trim_galore_filtered_reads_plot: merge completed [2026-09-25 13:11:53,043] multiqc.plots.plot [DEBUG ] merge_with_previous for trim_galore_adapter_length_plot: found old_data = True [2026-09-25 13:11:53,043] multiqc.plots.plot [DEBUG ] merge_with_previous for trim_galore_adapter_length_plot: merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:53,043] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor trim_galore_adapter_length_plot [2026-09-25 13:11:53,049] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (606, 13), New: (1212, 13) [2026-09-25 13:11:53,049] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (12, 2) [2026-09-25 13:11:53,050] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (606, 13) [2026-09-25 13:11:53,051] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (1818, 13) [2026-09-25 13:11:53,057] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 18 samples [2026-09-25 13:11:53,057] multiqc.plots.plot [DEBUG ] merge_with_previous for trim_galore_adapter_length_plot: merge completed [2026-09-25 13:11:53,063] multiqc.report [DEBUG ] Wrote data file multiqc_trim_galore.txt [2026-09-25 13:11:53,112] multiqc.report [DEBUG ] Wrote data file multiqc_trim_galore.json [2026-09-25 13:11:53,112] multiqc.core.exec_modules [INFO ] Updating module "Trim Galore" [2026-09-25 13:11:53,112] multiqc.core.exec_modules [DEBUG ] Running module: fastqc [2026-09-25 13:11:53,206] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'SRR6995993_trimmed_fastqc.zip' as already parsed 'SRR6995993' [2026-09-25 13:11:53,288] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'SRR6995994_trimmed_fastqc.zip' as already parsed 'SRR6995994' [2026-09-25 13:11:53,363] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'SRR6995995_trimmed_fastqc.zip' as already parsed 'SRR6995995' [2026-09-25 13:11:53,393] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'SRR6995996_trimmed_fastqc.zip' as already parsed 'SRR6995996' [2026-09-25 13:11:53,486] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'SRR6995997_trimmed_fastqc.zip' as already parsed 'SRR6995997' [2026-09-25 13:11:53,546] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'SRR6995998_trimmed_fastqc.zip' as already parsed 'SRR6995998' [2026-09-25 13:11:53,546] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2026-09-25 13:11:53,546] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_sequence_counts_plot: found old_data = True [2026-09-25 13:11:53,546] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_sequence_counts_plot: merging BarPlotInputData with BarPlotInputData [2026-09-25 13:11:53,552] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_sequence_counts_plot: merge completed [2026-09-25 13:11:53,559] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_base_sequence_quality_plot: found old_data = True [2026-09-25 13:11:53,559] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_base_sequence_quality_plot: merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:53,559] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_base_sequence_quality_plot [2026-09-25 13:11:53,562] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (330, 13), New: (330, 13) [2026-09-25 13:11:53,562] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:53,563] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:53,563] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (330, 13) [2026-09-25 13:11:53,565] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:53,565] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_base_sequence_quality_plot: merge completed [2026-09-25 13:11:53,570] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_sequence_quality_scores_plot: found old_data = True [2026-09-25 13:11:53,570] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_sequence_quality_scores_plot: merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:53,570] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_sequence_quality_scores_plot [2026-09-25 13:11:53,572] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (234, 13), New: (234, 13) [2026-09-25 13:11:53,573] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:53,573] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:53,573] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (234, 13) [2026-09-25 13:11:53,575] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:53,575] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_sequence_quality_scores_plot: merge completed [2026-09-25 13:11:53,584] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_sequence_gc_content_plot: found old_data = True [2026-09-25 13:11:53,584] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_sequence_gc_content_plot: merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:53,584] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_sequence_gc_content_plot [2026-09-25 13:11:53,601] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (3636, 13), New: (1212, 13) [2026-09-25 13:11:53,602] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (12, 2) [2026-09-25 13:11:53,603] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (3636, 13) [2026-09-25 13:11:53,603] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (4848, 13) [2026-09-25 13:11:53,620] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 2 datasets, 6 samples [2026-09-25 13:11:53,620] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_sequence_gc_content_plot: merge completed [2026-09-25 13:11:53,632] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_base_n_content_plot: found old_data = True [2026-09-25 13:11:53,632] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_base_n_content_plot: merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:53,632] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_per_base_n_content_plot [2026-09-25 13:11:53,635] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (330, 13), New: (330, 13) [2026-09-25 13:11:53,636] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:53,636] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:53,636] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (330, 13) [2026-09-25 13:11:53,639] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:53,639] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_per_base_n_content_plot: merge completed [2026-09-25 13:11:53,644] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_sequence_duplication_levels_plot: found old_data = True [2026-09-25 13:11:53,644] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_sequence_duplication_levels_plot: merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:53,644] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_sequence_duplication_levels_plot [2026-09-25 13:11:53,645] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (96, 13), New: (96, 13) [2026-09-25 13:11:53,646] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (6, 2) [2026-09-25 13:11:53,646] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:53,646] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (96, 13) [2026-09-25 13:11:53,648] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 6 samples [2026-09-25 13:11:53,648] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_sequence_duplication_levels_plot: merge completed [2026-09-25 13:11:53,652] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_overrepresented_sequences_plot: found old_data = True [2026-09-25 13:11:53,652] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_overrepresented_sequences_plot: merging BarPlotInputData with BarPlotInputData [2026-09-25 13:11:53,656] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_overrepresented_sequences_plot: merge completed [2026-09-25 13:11:53,687] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_top_overrepresented_sequences_table: found old_data = True [2026-09-25 13:11:53,687] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_top_overrepresented_sequences_table: merging ViolinPlotInputData with ViolinPlotInputData [2026-09-25 13:11:53,691] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_top_overrepresented_sequences_table: merge completed [2026-09-25 13:11:53,698] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_adapter_content_plot: found old_data = True [2026-09-25 13:11:53,699] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_adapter_content_plot: merging LinePlotNormalizedInputData with LinePlotNormalizedInputData [2026-09-25 13:11:53,699] multiqc.plots.linegraph [DEBUG ] LinePlot merge called for anchor fastqc_adapter_content_plot [2026-09-25 13:11:53,703] multiqc.plots.linegraph [DEBUG ] LinePlot merge: both old and new data present, merging. Old: (600, 13), New: (600, 13) [2026-09-25 13:11:53,704] multiqc.plots.linegraph [DEBUG ] LinePlot merge: new_keys shape: (12, 2) [2026-09-25 13:11:53,704] multiqc.plots.linegraph [DEBUG ] LinePlot merge: old_df_filtered shape: (0, 13) [2026-09-25 13:11:53,705] multiqc.plots.linegraph [DEBUG ] LinePlot merge: merged_df shape: (600, 13) [2026-09-25 13:11:53,708] multiqc.plots.linegraph [DEBUG ] LinePlot merge: created result with 1 datasets, 12 samples [2026-09-25 13:11:53,708] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc_adapter_content_plot: merge completed [2026-09-25 13:11:53,712] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc-status-check-heatmap: found old_data = True [2026-09-25 13:11:53,712] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc-status-check-heatmap: merging HeatmapNormalizedInputData with HeatmapNormalizedInputData [2026-09-25 13:11:53,712] multiqc.plots.plot [DEBUG ] merge_with_previous for fastqc-status-check-heatmap: merge completed [2026-09-25 13:11:53,718] multiqc.report [DEBUG ] Wrote data file multiqc_fastqc.txt [2026-09-25 13:11:53,718] multiqc.report [DEBUG ] Wrote data file multiqc_fastqc.json [2026-09-25 13:11:53,719] multiqc.base_module [DEBUG ] fastqc: deleting attribute self.order_of_duplication_levels [2026-09-25 13:11:53,719] multiqc.base_module [DEBUG ] fastqc: deleting attribute self.status_colours [2026-09-25 13:11:53,719] multiqc.core.exec_modules [INFO ] Updating module "FastQC" [2026-09-25 13:11:53,719] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions [2026-09-25 13:11:53,720] multiqc.report [DEBUG ] Wrote data file multiqc_software_versions.txt [2026-09-25 13:11:53,720] multiqc.core.write_results [DEBUG ] Rendering plots [2026-09-25 13:11:53,731] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: found old_data = True [2026-09-25 13:11:53,731] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: merging ViolinPlotInputData with ViolinPlotInputData [2026-09-25 13:11:53,736] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: merge completed [2026-09-25 13:11:53,744] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.txt [2026-09-25 13:11:53,745] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.json [2026-09-25 13:11:53,750] multiqc.core.ai [DEBUG ] Saved AI prompt to multiqc_data/llms-full.txt [2026-09-25 13:11:53,770] multiqc.core.write_results [DEBUG ] Exporting plot data to files [2026-09-25 13:11:53,770] multiqc.report [DEBUG ] Wrote data file trim_galore_filtered_reads_plot.txt [2026-09-25 13:11:53,771] multiqc.report [DEBUG ] Wrote data file trim_galore_adapter_length_plot.txt [2026-09-25 13:11:53,771] multiqc.report [DEBUG ] Wrote data file fastqc_sequence_counts_plot.txt [2026-09-25 13:11:53,772] multiqc.report [DEBUG ] Wrote data file fastqc_per_base_sequence_quality_plot.txt [2026-09-25 13:11:53,772] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_quality_scores_plot.txt [2026-09-25 13:11:53,774] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_gc_content_plot_Percentages.txt [2026-09-25 13:11:53,776] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_gc_content_plot_Counts.txt [2026-09-25 13:11:53,777] multiqc.report [DEBUG ] Wrote data file fastqc_per_base_n_content_plot.txt [2026-09-25 13:11:53,777] multiqc.report [DEBUG ] Wrote data file fastqc_sequence_duplication_levels_plot.txt [2026-09-25 13:11:53,777] multiqc.report [DEBUG ] Wrote data file fastqc_overrepresented_sequences_plot.txt [2026-09-25 13:11:53,777] multiqc.report [DEBUG ] Wrote data file fastqc_top_overrepresented_sequences_table.txt [2026-09-25 13:11:53,778] multiqc.report [DEBUG ] Wrote data file fastqc_adapter_content_plot.txt [2026-09-25 13:11:53,778] multiqc.report [DEBUG ] Wrote data file fastqc-status-check-heatmap.txt [2026-09-25 13:11:53,778] multiqc.core.write_results [DEBUG ] Moving data file from '/tmp/tmpu53u3np8/multiqc_data' to '/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/output/02-qc-trim/multiqc/SRP139854-read-QC_multiqc_report_data' [2026-09-25 13:11:54,285] multiqc.core.write_results [INFO ] Data : /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/output/02-qc-trim/multiqc/SRP139854-read-QC_multiqc_report_data (overwritten) [2026-09-25 13:11:54,354] multiqc.core.write_results [DEBUG ] Compressing plot data [2026-09-25 13:11:54,451] multiqc.core.write_results [INFO ] Report : /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/output/02-qc-trim/multiqc/SRP139854-read-QC_multiqc_report.html (overwritten)