[2024-07-26 14:10:34,241] multiqc                                            [DEBUG  ]  This is MultiQC v1.14
[2024-07-26 14:10:34,268] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yaml
[2024-07-26 14:10:34,269] multiqc                                            [DEBUG  ]  New config: {'custom_logo': '/work/project/crucial/Sarah/7-EAGER/NC_024032.1_BIS_RESULTS/work/df/382c6ad646541f8ae703c7dc97f9c6/nf-core_eager_logo_outline_drop.png', 'custom_logo_url': 'https://github.com/nf-core/eager/', 'custom_logo_title': 'nf-core/eager', 'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/eager" target="_blank">nf-core/eager</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://github.com/nf-core/eager" target="_blank">documentation</a>.\n', 'run_modules': ['adapterRemoval', 'bowtie2', 'custom_content', 'damageprofiler', 'dedup', 'fastp', 'fastqc', 'gatk', 'kraken', 'malt', 'mtnucratio', 'multivcfanalyzer', 'picard', 'preseq', 'qualimap', 'samtools', 'sexdeterrmine', 'hops', 'bcftools'], 'top_modules': [{'fastqc': {'name': 'FastQC (pre-Trimming)', 'path_filters': ['*_raw_fastqc.zip']}}, 'fastp', 'adapterRemoval', {'fastqc': {'name': 'FastQC (post-Trimming)', 'path_filters': ['*.truncated_fastqc.zip', '*.combined*_fastqc.zip']}}, {'bowtie2': {'path_filters': ['*_bt2.log']}}, 'malt', 'hops', 'kraken', {'samtools': {'name': 'Samtools Flagstat (pre-samtools filter)', 'path_filters': ['*_flagstat.stats']}}, {'samtools': {'name': 'Samtools Flagstat (post-samtools filter)', 'path_filters': ['*_postfilterflagstat.stats']}}, 'dedup', 'picard', {'preseq': {'path_filters': ['*.preseq']}}, 'damageprofiler', 'mtnucratio', 'qualimap', 'sexdeterrmine', 'bcftools', {'multivcfanalyzer': {'path_filters': ['*MultiVCFAnalyzer.json']}}], 'qualimap_config': {'general_stats_coverage': [1, 2, 3, 4, 5]}, 'remove_sections': ['sexdeterrmine-snps'], 'table_columns_visible': {'FastQC (pre-Trimming)': {'percent_duplicates': False, 'percent_gc': True, 'avg_sequence_length': True}, 'fastp': {'pct_duplication': False, 'after_filtering_gc_content': True, 'pct_surviving': False}, 'Adapter Removal': {'aligned_total': False, 'percent_aligned': True}, 'FastQC (post-Trimming)': {'avg_sequence_length': True, 'percent_duplicates': False, 'total_sequences': True, 'percent_gc': True}, 'bowtie2': {'overall_alignment_rate': True}, 'MALT': {'Taxonomic assignment success': False, 'Assig. Taxonomy': False, 'Mappability': True, 'Total reads': False, 'Num. of queries': False}, 'Kraken': {'% Unclassified': True, '% Top 5': False}, 'Samtools Flagstat (pre-samtools filter)': {'flagstat_total': True, 'mapped_passed': True}, 'Samtools Flagstat (post-samtools filter)': {'mapped_passed': True}, 'DeDup': {'dup_rate': False, 'clusterfactor': True, 'mapped_after_dedup': True}, 'Picard': {'PERCENT_DUPLICATION': True}, 'DamageProfiler': {'5 Prime1': True, '5 Prime2': True, '3 Prime1': False, '3 Prime2': False, 'mean_readlength': True, 'median': True}, 'mtnucratio': {'mt_nuc_ratio': True}, 'QualiMap': {'mapped_reads': True, 'mean_coverage': True, '1_x_pc': True, '5_x_pc': True, 'percentage_aligned': False, 'median_insert_size': False}, 'MultiVCFAnalyzer': {'Heterozygous SNP alleles (percent)': True}, 'endorSpy': {'endogenous_dna': True, 'endogenous_dna_post': True}, 'nuclear_contamination': {'Num_SNPs': True, 'Method1_MOM_estimate': False, 'Method1_MOM_SE': False, 'Method1_ML_estimate': True, 'Method1_ML_SE': True, 'Method2_MOM_estimate': False, 'Method2_MOM_SE': False, 'Method2_ML_estimate': False, 'Method2_ML_SE': False}, 'snp_coverage': {'Covered_Snps': True, 'Total_Snps': False}}, 'table_columns_placement': {'FastQC (pre-Trimming)': {'total_sequences': 100, 'avg_sequence_length': 110, 'percent_gc': 120}, 'fastp': {'after_filtering_gc_content': 200}, 'Adapter Removal': {'percent_aligned': 300}, 'FastQC (post-Trimming)': {'total_sequences': 400, 'avg_sequence_length': 410, 'percent_gc': 420}, 'Bowtie 2 / HiSAT2': {'overall_alignment_rate': 450}, 'MALT': {'Num. of queries': 430, 'Total reads': 440, 'Mappability': 450, 'Assig. Taxonomy': 460, 'Taxonomic assignment success': 470}, 'Kraken': {'% Unclassified': 480}, 'Samtools Flagstat (pre-samtools filter)': {'flagstat_total': 551, 'mapped_passed': 552}, 'Samtools Flagstat (post-samtools filter)': {'flagstat_total': 600, 'mapped_passed': 620}, 'endorSpy': {'endogenous_dna': 610, 'endogenous_dna_post': 640}, 'nuclear_contamination': {'Num_SNPs': 1100, 'Method1_MOM_estimate': 1110, 'Method1_MOM_SE': 1120, 'Method1_ML_estimate': 1130, 'Method1_ML_SE': 1140, 'Method2_MOM_estimate': 1150, 'Method2_MOM_SE': 1160, 'Method2_ML_estimate': 1170, 'Method2_ML_SE': 1180}, 'snp_coverage': {'Covered_Snps': 1050, 'Total_Snps': 1060}, 'DeDup': {'mapped_after_dedup': 620, 'clusterfactor': 630}, 'Picard': {'PERCENT_DUPLICATION': 650}, 'DamageProfiler': {'5 Prime1': 700, '5 Prime2': 710, '3 Prime1': 720, '3 Prime2': 730, 'mean_readlength': 740, 'median': 750}, 'mtnucratio': {'mtreads': 760, 'mt_cov_avg': 770, 'mt_nuc_ratio': 780}, 'QualiMap': {'mapped_reads': 800, 'mean_coverage': 805, 'median_coverage': 810, '1_x_pc': 820, '2_x_pc': 830, '3_x_pc': 840, '4_x_pc': 850, '5_x_pc': 860, 'avg_gc': 870}, 'sexdeterrmine': {'RateX': 1000, 'RateY': 1010}, 'MultiVCFAnalyzer': {'Heterozygous SNP alleles (percent)': 1200}}, 'read_count_multiplier': 1, 'read_count_prefix': '', 'read_count_desc': '', 'ancient_read_count_prefix': '', 'ancient_read_count_desc': '', 'ancient_read_count_multiplier': 1, 'decimalPoint_format': '.', 'thousandsSep_format': ',', 'report_section_order': {'software_versions': {'order': -1000}, 'nf-core-eager-summary': {'order': -1001}}, 'export_plots': True, 'table_columns_name': {'FastQC (pre-Trimming)': {'total_sequences': 'Nr. Input Reads', 'avg_sequence_length': 'Length Input Reads', 'percent_gc': '% GC Input Reads', 'percent_duplicates': '% Dups Input Reads', 'percent_fails': '% Failed Input Reads'}, 'FastQC (post-Trimming)': {'total_sequences': 'Nr. Processed Reads', 'avg_sequence_length': 'Length Processed Reads', 'percent_gc': '% GC Processed Reads', 'percent_duplicates': '% Dups Processed Reads', 'percent_fails': '%Failed Processed Reads'}, 'Samtools Flagstat (pre-samtools filter)': {'flagstat_total': 'Nr. Reads Into Mapping', 'mapped_passed': 'Nr. Mapped Reads'}, 'Samtools Flagstat (post-samtools filter)': {'flagstat_total': 'Nr. Mapped Reads Post-Filter', 'mapped_passed': 'Nr. Mapped Reads Passed Post-Filter'}, 'Endogenous DNA Post (%)': {'endogenous_dna_post (%)': 'Endogenous DNA Post-Filter (%)'}, 'Picard': {'PERCENT_DUPLICATION': '% Dup. Mapped Reads'}, 'DamageProfiler': {'mean_readlength': 'Mean Length Mapped Reads', 'median_readlength': 'Median Length Mapped Reads'}, 'QualiMap': {'mapped_reads': 'Nr. Dedup. Mapped Reads', 'total_reads': 'Nr. Dedup. Total Reads', 'avg_gc': '% GC Dedup. Mapped Reads'}, 'Bcftools Stats': {'number_of_records': 'Nr. Overall Variants', 'number_of_SNPs': 'Nr. SNPs', 'number_of_indels': 'Nr. InDels'}, 'MALT': {'Mappability': '% Metagenomic Mappability'}, 'SexDetErrmine': {'RateErrX': 'SexDet Err X Chr', 'RateErrY': 'SexDet Err Y Chr', 'RateX': 'SexDet Rate X Chr', 'RateY': 'SexDet Rate Y Chr'}, 'custom_table_header_config': {'general_stats_table': {'median_coverage': {'format': '{:,.3f}'}, 'mean_coverage': {'format': '{:,.3f}'}}}}}
[2024-07-26 14:10:34,269] multiqc                                            [DEBUG  ]  Added to filename clean extensions: [['_fastp', '.pe.settings', '.se.settings', '.settings', '.pe.combined', '.se.truncated', '.mapped', '.mapped_rmdup', '.mapped_rmdup_stats', '_libmerged_rg_rmdup', '_libmerged_rg_rmdup_stats', '_postfilterflagstat.stats', '_flagstat.stat', '.filtered', '.filtered_rmdup', '.filtered_rmdup_stats', '_libmerged_rg_add', '_libmerged_rg_add_stats', '_rmdup', '.unmapped', '.fastq.gz', '.fastq', '.fq.gz', '.fq', '.bam', '.kreport', '.unifiedgenotyper', '.trimmed_stats', '_libmerged', '_bt2']]
[2024-07-26 14:10:34,269] multiqc                                            [DEBUG  ]  Command used: /opt/conda/envs/nf-core-eager-2.4.7/bin/multiqc -f multiqc_config.yaml .
[2024-07-26 14:10:34,568] multiqc                                            [WARNING]  MultiQC Version v1.23 now available!
[2024-07-26 14:10:34,568] multiqc                                            [DEBUG  ]  Working dir : /work/project/crucial/Sarah/7-EAGER/NC_024032.1_BIS_RESULTS/work/df/382c6ad646541f8ae703c7dc97f9c6
[2024-07-26 14:10:34,568] multiqc                                            [DEBUG  ]  Template    : default
[2024-07-26 14:10:34,568] multiqc                                            [DEBUG  ]  Running Python 3.9.4 | packaged by conda-forge | (default, May 10 2021, 22:13:33)  [GCC 9.3.0]
[2024-07-26 14:10:34,569] multiqc                                            [INFO   ]  Only using modules: adapterRemoval, bowtie2, custom_content, damageprofiler, dedup, fastp, fastqc, gatk, kraken, malt, mtnucratio, multivcfanalyzer, picard, preseq, qualimap, samtools, sexdeterrmine, hops, bcftools
[2024-07-26 14:10:34,569] multiqc                                            [DEBUG  ]  Analysing modules: fastqc, fastp, adapterRemoval, fastqc, bowtie2, malt, hops, kraken, samtools, samtools, dedup, picard, preseq, damageprofiler, mtnucratio, qualimap, sexdeterrmine, bcftools, multivcfanalyzer, custom_content, gatk
[2024-07-26 14:10:34,569] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmpeb96s0kv
[2024-07-26 14:10:34,809] multiqc                                            [INFO   ]  Search path : /work/project/crucial/Sarah/7-EAGER/NC_024032.1_BIS_RESULTS/work/df/382c6ad646541f8ae703c7dc97f9c6/multiqc_config.yaml
[2024-07-26 14:10:34,810] multiqc                                            [INFO   ]  Search path : /work/project/crucial/Sarah/7-EAGER/NC_024032.1_BIS_RESULTS/work/df/382c6ad646541f8ae703c7dc97f9c6
[2024-07-26 14:10:34,811] multiqc                                            [DEBUG  ]  Ignored 251 search patterns as didn't match running modules.
[2024-07-26 14:10:51,466] multiqc                                            [DEBUG  ]  Summary of files that were skipped by the search: [skipped_no_match: 5633]
[2024-07-26 14:10:51,948] multiqc.plots.bargraph                             [DEBUG  ]  Using matplotlib version 3.7.1
[2024-07-26 14:10:51,950] multiqc.plots.linegraph                            [DEBUG  ]  Using matplotlib version 3.7.1
[2024-07-26 14:10:51,966] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_6_MB2_S16_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:51,990] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_11_SH2000-99-394-g_S46_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,006] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_14_SM2_S24_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,024] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_1_MB14_S11_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,041] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_1_MB15_S1_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,058] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_9_MD6_S34_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,075] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_3_BC7_S60_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,095] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_3_MB16_S13_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,113] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_10_MB13_S5_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,130] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_12_MB6_S7_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,147] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_3_EG6_S83_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,163] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_4_SH1979-4-6843-c_S42_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,181] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_4_BC8_S61_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,197] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_1_BC5_S58_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,214] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_12_MD1_S22_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,234] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_14_MB10_S9_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,251] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_15_SH2000-99-390-c_S57_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,267] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_5_BC9_S62_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,285] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_1_SCO_98_S66_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,300] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_10_MB13_S5_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,316] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_15_MB12_S10_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,331] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_15_SH2000-99-390-c_S57_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,347] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_3_BC7_S60_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,363] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_3_SCO_114_S68_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,378] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_13_SH2000-99-390-b_S55_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,393] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_15_BC10_S25_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,409] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_2_SCO_81_S67_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,424] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_6_MB2_S16_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,440] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_10_BC14_S20_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,455] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_4_BC8_S61_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,470] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_4_SH1979-4-6843-c_S42_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,485] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_6_SCO_116_S69_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,501] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_11_MB18_S6_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,516] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_5_BC9_S62_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,532] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_9_MD6_S34_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,548] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_3_SH1979-4-6843-e_S41_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,564] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_11_SH2000-99-394-g_S46_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,579] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_9_MB17_S4_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,595] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_8_SH2000-99-394-e_S45_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,611] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_2_BC6_S59_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,626] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_6_TP1_S75_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,642] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_13_SH2000-99-390-b_S55_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,659] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_13_MB11_S8_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,674] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_6_MB3_S3_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,690] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_14_SH1979-4-6843-a_S56_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,706] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_9_MB17_S4_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,722] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_8_SH2000-99-394-e_S45_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,738] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_6_MB3_S3_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,754] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_8_BC1_S77_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,770] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_11_MD14_S36_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,785] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_3_EG6_S83_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,801] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_7_TP2_S76_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,816] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_5_SM3_S2_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,831] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_10_MD11_S35_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,847] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_7_TP2_S76_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,863] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_7_SH2000-99-394-c_S54_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,878] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_3_SCO_114_S68_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,894] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_15_MB12_S10_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,910] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_8_BC1_S77_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,926] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_1_EG4_S81_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,942] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_3_MB16_S13_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,957] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_7_MB1_S17_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,973] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_1_MB15_S1_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:52,989] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_6_SCO_116_S69_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,004] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_10_MD11_S35_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,020] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_5_SM3_S2_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,036] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_12_MB6_S7_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,052] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_14_SH1979-4-6843-a_S56_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,067] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_2_MD13_S12_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,083] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_13_MB11_S8_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,098] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_13_SH2000-99-394-f_S47_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,114] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_12_SCO_2213_S64_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,132] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_5_SH1979-4-6843-d_S43_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,147] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_2_SCO_81_S67_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,163] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_12_SCO_2213_S64_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,178] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_13_SH2000-99-394-f_S47_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,193] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_7_SH2000-99-394-c_S54_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,209] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_2_BC6_S59_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,226] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_11_MD14_S36_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,241] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_15_BC10_S25_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,257] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_7_MB1_S17_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,273] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L11_1_SCO_98_S66_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,288] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_10_BC14_S20_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,303] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_14_MB10_S9_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,319] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_3_SH1979-4-6843-e_S41_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,334] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_12_MD1_S22_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,350] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_1_EG4_S81_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,366] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_6_TP1_S75_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,382] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_14_SM2_S24_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,397] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_6_SH2001-106_11-b_S44_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,414] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_6_SH2001-106_11-b_S44_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,429] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_1_MB14_S11_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,445] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_6_SH1979-4-6843-b_S53_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,461] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_1_BC5_S58_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,476] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_6_SH1979-4-6843-b_S53_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,491] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_2_MD13_S12_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,506] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L3_11_MB18_S6_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,522] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L6_5_SH1979-4-6843-d_S43_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_11_MD14_S36_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L0_3_EG6_S83_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_10_BC14_S20_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_7_TP2_S76_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L11_6_SCO_116_S69_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_2_MD13_S12_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L9_14_SH1979-4-6843-a_S56_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_12_SCO_2213_S64_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_6_MB3_S3_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L6_11_SH2000-99-394-g_S46_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_8_BC1_S77_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_2_BC6_S59_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_10_MB13_S5_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_3_MB16_S13_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L6_3_SH1979-4-6843-e_S41_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_4_BC8_S61_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L6_6_SH2001-106_11-b_S44_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L6_4_SH1979-4-6843-c_S42_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_11_MB18_S6_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_13_MB11_S8_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_12_MD1_S22_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_1_BC5_S58_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L0_1_EG4_S81_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L11_3_SCO_114_S68_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L6_8_SH2000-99-394-e_S45_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_9_MD6_S34_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_15_MB12_S10_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_14_MB10_S9_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,538] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_6_MB2_S16_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_1_MB14_S11_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L6_13_SH2000-99-394-f_S47_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_9_MB17_S4_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L9_6_SH1979-4-6843-b_S53_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_5_SM3_S2_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L9_13_SH2000-99-390-b_S55_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L11_1_SCO_98_S66_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L9_7_SH2000-99-394-c_S54_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_15_BC10_S25_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_14_SM2_S24_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_3_BC7_S60_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_10_MD11_S35_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_6_TP1_S75_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L9_15_SH2000-99-390-c_S57_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L6_5_SH1979-4-6843-d_S43_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_12_MB6_S7_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_7_MB1_S17_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_5_BC9_S62_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L3_1_MB15_S1_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L11_2_SCO_81_S67_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 14:10:53,539] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 98 reports
[2024-07-26 14:11:06,068] multiqc.modules.adapterRemoval.adapterRemoval      [INFO   ]  Found 49 reports
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_6_MB2_S16_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_11_SH2000-99-394-g_S46_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_14_SM2_S24_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_1_MB14_S11_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_1_MB15_S1_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_9_MD6_S34_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_3_BC7_S60_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_3_MB16_S13_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_10_MB13_S5_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_12_MB6_S7_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_3_EG6_S83_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_4_SH1979-4-6843-c_S42_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,607] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_4_BC8_S61_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_1_BC5_S58_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_12_MD1_S22_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_14_MB10_S9_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_15_SH2000-99-390-c_S57_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_5_BC9_S62_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_1_SCO_98_S66_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_10_MB13_S5_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_15_MB12_S10_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_15_SH2000-99-390-c_S57_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_3_BC7_S60_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_3_SCO_114_S68_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_13_SH2000-99-390-b_S55_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_15_BC10_S25_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_2_SCO_81_S67_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_6_MB2_S16_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_10_BC14_S20_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_4_BC8_S61_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_4_SH1979-4-6843-c_S42_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_6_SCO_116_S69_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_11_MB18_S6_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_5_BC9_S62_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_9_MD6_S34_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_3_SH1979-4-6843-e_S41_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_11_SH2000-99-394-g_S46_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_9_MB17_S4_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_8_SH2000-99-394-e_S45_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,608] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_2_BC6_S59_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_6_TP1_S75_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_13_SH2000-99-390-b_S55_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_13_MB11_S8_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_6_MB3_S3_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_14_SH1979-4-6843-a_S56_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_9_MB17_S4_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_8_SH2000-99-394-e_S45_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_6_MB3_S3_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_8_BC1_S77_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_11_MD14_S36_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_3_EG6_S83_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_7_TP2_S76_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_5_SM3_S2_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_10_MD11_S35_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_7_TP2_S76_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_7_SH2000-99-394-c_S54_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_3_SCO_114_S68_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_15_MB12_S10_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_8_BC1_S77_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_1_EG4_S81_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_3_MB16_S13_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_7_MB1_S17_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_1_MB15_S1_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_6_SCO_116_S69_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_10_MD11_S35_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_5_SM3_S2_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_12_MB6_S7_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,609] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_14_SH1979-4-6843-a_S56_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_2_MD13_S12_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_13_MB11_S8_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_13_SH2000-99-394-f_S47_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_12_SCO_2213_S64_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_5_SH1979-4-6843-d_S43_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_2_SCO_81_S67_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_12_SCO_2213_S64_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_13_SH2000-99-394-f_S47_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_7_SH2000-99-394-c_S54_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_2_BC6_S59_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_11_MD14_S36_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_15_BC10_S25_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_7_MB1_S17_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L11_1_SCO_98_S66_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_10_BC14_S20_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_14_MB10_S9_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_3_SH1979-4-6843-e_S41_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_12_MD1_S22_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_1_EG4_S81_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_6_TP1_S75_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_14_SM2_S24_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_6_SH2001-106_11-b_S44_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_6_SH2001-106_11-b_S44_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_1_MB14_S11_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_6_SH1979-4-6843-b_S53_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_1_BC5_S58_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_6_SH1979-4-6843-b_S53_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,610] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_2_MD13_S12_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,611] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L3_11_MB18_S6_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,611] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L6_5_SH1979-4-6843-d_S43_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,611] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_11_MD14_S36_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,626] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L0_3_EG6_S83_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,639] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_10_BC14_S20_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,735] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_7_TP2_S76_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,748] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L11_6_SCO_116_S69_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,761] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_2_MD13_S12_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,775] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L9_14_SH1979-4-6843-a_S56_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,789] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_12_SCO_2213_S64_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,802] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_6_MB3_S3_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,816] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L6_11_SH2000-99-394-g_S46_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,830] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_8_BC1_S77_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,842] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_2_BC6_S59_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,856] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_10_MB13_S5_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,870] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_3_MB16_S13_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,883] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L6_3_SH1979-4-6843-e_S41_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,897] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_4_BC8_S61_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,911] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L6_6_SH2001-106_11-b_S44_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,925] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L6_4_SH1979-4-6843-c_S42_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,938] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_11_MB18_S6_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,952] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_13_MB11_S8_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,965] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_12_MD1_S22_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,979] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_1_BC5_S58_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:14,992] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L0_1_EG4_S81_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,006] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L11_3_SCO_114_S68_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,019] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L6_8_SH2000-99-394-e_S45_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,032] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_9_MD6_S34_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,046] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_15_MB12_S10_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,059] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_14_MB10_S9_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,073] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_6_MB2_S16_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,086] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_1_MB14_S11_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,099] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L6_13_SH2000-99-394-f_S47_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,112] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_9_MB17_S4_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,125] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L9_6_SH1979-4-6843-b_S53_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,139] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_5_SM3_S2_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,153] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L9_13_SH2000-99-390-b_S55_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,166] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L11_1_SCO_98_S66_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,179] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L9_7_SH2000-99-394-c_S54_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,192] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_15_BC10_S25_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,206] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_14_SM2_S24_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,219] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_3_BC7_S60_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,233] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_10_MD11_S35_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,247] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_6_TP1_S75_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,260] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L9_15_SH2000-99-390-c_S57_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,274] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L6_5_SH1979-4-6843-d_S43_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,287] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_12_MB6_S7_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,301] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_7_MB1_S17_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,314] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_5_BC9_S62_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,328] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L3_1_MB15_S1_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,354] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L11_2_SCO_81_S67_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 14:11:15,367] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 49 reports
[2024-07-26 14:11:25,260] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_2_BC6_S59_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,261] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_4_BC8_S61_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,262] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L9_14_SH1979-4-6843-a_S56_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,262] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_2_MD13_S12_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,262] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_13_MB11_S8_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,263] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_11_MD14_S36_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,263] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L6_5_SH1979-4-6843-d_S43_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,263] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L11_2_SCO_81_S67_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,264] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_6_MB2_S16_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,264] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L11_3_SCO_114_S68_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,264] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_12_MB6_S7_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,265] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L6_13_SH2000-99-394-f_S47_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,265] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_8_BC1_S77_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,265] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L0_1_EG4_S81_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,265] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_12_MD1_S22_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,266] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L6_11_SH2000-99-394-g_S46_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,266] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L6_6_SH2001-106_11-b_S44_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,266] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_1_BC5_S58_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,267] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L9_7_SH2000-99-394-c_S54_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,267] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_15_BC10_S25_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,267] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_12_SCO_2213_S64_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,267] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_10_BC14_S20_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,268] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_10_MD11_S35_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,268] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_1_MB14_S11_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,268] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L6_8_SH2000-99-394-e_S45_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,269] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_9_MD6_S34_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,269] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_15_MB12_S10_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,269] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_7_MB1_S17_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,270] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L9_6_SH1979-4-6843-b_S53_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,270] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_5_BC9_S62_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,270] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_14_MB10_S9_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,270] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_10_MB13_S5_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,271] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_14_SM2_S24_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,271] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_5_SM3_S2_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,271] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L9_13_SH2000-99-390-b_S55_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,272] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L6_4_SH1979-4-6843-c_S42_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,272] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L0_3_EG6_S83_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,272] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_7_TP2_S76_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,272] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_6_TP1_S75_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,273] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L9_15_SH2000-99-390-c_S57_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,273] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_9_MB17_S4_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,273] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_3_MB16_S13_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,274] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_3_BC7_S60_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,274] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L6_3_SH1979-4-6843-e_S41_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,274] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_6_MB3_S3_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,275] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L11_1_SCO_98_S66_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,275] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L11_6_SCO_116_S69_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,275] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_1_MB15_S1_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,275] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L3_11_MB18_S6_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_10_MB13_S5_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L6_11_SH2000-99-394-g_S46_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L6_3_SH1979-4-6843-e_S41_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_1_BC5_S58_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L6_5_SH1979-4-6843-d_S43_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_6_TP1_S75_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_14_SM2_S24_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_12_SCO_2213_S64_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_14_MB10_S9_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_6_MB3_S3_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L9_13_SH2000-99-390-b_S55_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_15_BC10_S25_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_8_BC1_S77_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_9_MD6_S34_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L6_6_SH2001-106_11-b_S44_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L0_1_EG4_S81_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_10_BC14_S20_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L11_3_SCO_114_S68_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L11_1_SCO_98_S66_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_2_BC6_S59_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,276] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L6_13_SH2000-99-394-f_S47_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_3_MB16_S13_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L6_4_SH1979-4-6843-c_S42_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_15_MB12_S10_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_7_TP2_S76_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L0_3_EG6_S83_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_11_MB18_S6_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_4_BC8_S61_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L11_6_SCO_116_S69_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_6_MB2_S16_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L9_7_SH2000-99-394-c_S54_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L9_14_SH1979-4-6843-a_S56_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L9_15_SH2000-99-390-c_S57_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_2_MD13_S12_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_10_MD11_S35_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_1_MB14_S11_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L11_2_SCO_81_S67_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_7_MB1_S17_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L6_8_SH2000-99-394-e_S45_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_5_SM3_S2_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_13_MB11_S8_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_12_MB6_S7_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_3_BC7_S60_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L9_6_SH1979-4-6843-b_S53_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_5_BC9_S62_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_11_MD14_S36_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_12_MD1_S22_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_9_MB17_S4_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,277] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L3_1_MB15_S1_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 14:11:25,280] multiqc.modules.samtools.samtools                  [INFO   ]  Found 49 flagstat reports
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_2_BC6_S59_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_4_BC8_S61_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L9_14_SH1979-4-6843-a_S56_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_2_MD13_S12_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_13_MB11_S8_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_11_MD14_S36_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L6_5_SH1979-4-6843-d_S43_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L11_2_SCO_81_S67_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_6_MB2_S16_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L11_3_SCO_114_S68_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_12_MB6_S7_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L6_13_SH2000-99-394-f_S47_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_8_BC1_S77_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L0_1_EG4_S81_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_12_MD1_S22_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L6_11_SH2000-99-394-g_S46_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L6_6_SH2001-106_11-b_S44_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_1_BC5_S58_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L9_7_SH2000-99-394-c_S54_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_15_BC10_S25_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_12_SCO_2213_S64_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_10_BC14_S20_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_10_MD11_S35_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_1_MB14_S11_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L6_8_SH2000-99-394-e_S45_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,283] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_9_MD6_S34_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_15_MB12_S10_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_7_MB1_S17_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L9_6_SH1979-4-6843-b_S53_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_5_BC9_S62_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_14_MB10_S9_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_10_MB13_S5_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_14_SM2_S24_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_5_SM3_S2_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L9_13_SH2000-99-390-b_S55_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L6_4_SH1979-4-6843-c_S42_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L0_3_EG6_S83_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_7_TP2_S76_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_6_TP1_S75_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L9_15_SH2000-99-390-c_S57_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_9_MB17_S4_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_3_MB16_S13_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_3_BC7_S60_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L6_3_SH1979-4-6843-e_S41_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_6_MB3_S3_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L11_1_SCO_98_S66_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L11_6_SCO_116_S69_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_1_MB15_S1_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L3_11_MB18_S6_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,284] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_10_MB13_S5_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,285] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L6_11_SH2000-99-394-g_S46_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,285] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L6_3_SH1979-4-6843-e_S41_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,285] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_1_BC5_S58_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,285] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L6_5_SH1979-4-6843-d_S43_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,286] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_6_TP1_S75_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,286] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_14_SM2_S24_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,286] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_12_SCO_2213_S64_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,287] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_14_MB10_S9_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,287] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_6_MB3_S3_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,287] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L9_13_SH2000-99-390-b_S55_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,288] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_15_BC10_S25_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,288] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_8_BC1_S77_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,288] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_9_MD6_S34_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,288] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L6_6_SH2001-106_11-b_S44_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,289] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L0_1_EG4_S81_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,289] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_10_BC14_S20_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,289] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L11_3_SCO_114_S68_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,290] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L11_1_SCO_98_S66_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,290] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_2_BC6_S59_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,290] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L6_13_SH2000-99-394-f_S47_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,290] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_3_MB16_S13_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,291] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L6_4_SH1979-4-6843-c_S42_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,291] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_15_MB12_S10_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,291] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_7_TP2_S76_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,292] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L0_3_EG6_S83_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,292] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_11_MB18_S6_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,292] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_4_BC8_S61_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,293] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L11_6_SCO_116_S69_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,293] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_6_MB2_S16_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,293] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L9_7_SH2000-99-394-c_S54_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,293] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L9_14_SH1979-4-6843-a_S56_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,294] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L9_15_SH2000-99-390-c_S57_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,294] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_2_MD13_S12_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,294] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_10_MD11_S35_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,295] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_1_MB14_S11_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,295] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L11_2_SCO_81_S67_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,295] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_7_MB1_S17_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,295] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L6_8_SH2000-99-394-e_S45_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,296] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_5_SM3_S2_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,296] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_13_MB11_S8_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,296] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_12_MB6_S7_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,297] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_3_BC7_S60_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,297] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L9_6_SH1979-4-6843-b_S53_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,297] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_5_BC9_S62_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,298] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_11_MD14_S36_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,298] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_12_MD1_S22_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,298] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_9_MB17_S4_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,298] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L3_1_MB15_S1_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 14:11:25,301] multiqc.modules.samtools.samtools                  [INFO   ]  Found 49 flagstat reports
[2024-07-26 14:11:27,621] multiqc.modules.picard.picard                      [INFO   ]  Found 49 MarkDuplicates reports
[2024-07-26 14:11:27,632] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L11_2_SCO_81_S67.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,633] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_13_MB11_S8.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,633] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_10_MD11_S35.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,633] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_14_SM2_S24.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,635] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_10_BC14_S20.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,637] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L0_3_EG6_S83.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,637] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L6_11_SH2000-99-394-g_S46.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,638] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_3_BC7_S60.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,639] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_2_BC6_S59.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,640] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_2_MD13_S12.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,641] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L9_6_SH1979-4-6843-b_S53.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,641] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_7_MB1_S17.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,643] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L11_3_SCO_114_S68.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,644] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_12_SCO_2213_S64.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,645] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_5_BC9_S62.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,646] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_1_MB14_S11.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,646] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L6_8_SH2000-99-394-e_S45.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,647] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L11_6_SCO_116_S69.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,648] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_4_BC8_S61.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,648] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_3_MB16_S13.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,649] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_9_MD6_S34.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,649] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L9_13_SH2000-99-390-b_S55.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,650] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_14_MB10_S9.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,651] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L11_1_SCO_98_S66.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,652] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L6_4_SH1979-4-6843-c_S42.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,653] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_1_MB15_S1.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,653] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L6_13_SH2000-99-394-f_S47.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,654] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L9_14_SH1979-4-6843-a_S56.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,654] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_6_MB2_S16.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,655] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L9_15_SH2000-99-390-c_S57.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,656] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_11_MB18_S6.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,657] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_1_BC5_S58.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,658] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L6_3_SH1979-4-6843-e_S41.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,659] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_7_TP2_S76.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,660] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_12_MB6_S7.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,661] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L6_6_SH2001-106_11-b_S44.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,662] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_6_TP1_S75.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,663] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_12_MD1_S22.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,664] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L9_7_SH2000-99-394-c_S54.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,665] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_8_BC1_S77.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,666] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_15_MB12_S10.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,667] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_5_SM3_S2.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,668] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_10_MB13_S5.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,670] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L6_5_SH1979-4-6843-d_S43.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,671] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L0_1_EG4_S81.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,671] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_6_MB3_S3.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,672] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_11_MD14_S36.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,673] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L3_9_MB17_S4.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,674] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_15_BC10_S25.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 14:11:27,676] multiqc.modules.preseq.preseq                      [INFO   ]  Found 49 reports
[2024-07-26 14:11:31,629] multiqc.modules.mtnucratio.mtnucratio              [INFO   ]  Found 49 reports
[2024-07-26 14:11:31,717] multiqc.modules.qualimap.QM_BamQC                  [DEBUG  ]  Custom Qualimap thresholds: 1, 2, 3, 4, 5
[2024-07-26 14:11:33,803] multiqc.modules.qualimap.qualimap                  [INFO   ]  Found 49 BamQC reports
[2024-07-26 14:11:47,799] multiqc.modules.bcftools.bcftools                  [INFO   ]  Found 49 stats reports
[2024-07-26 14:11:47,822] multiqc.modules.custom_content.custom_content      [INFO   ]  software_versions: Found 1 sample (html)
[2024-07-26 14:11:47,823] multiqc.modules.custom_content.custom_content      [INFO   ]  nf-core-eager-summary: Found 1 sample (html)
[2024-07-26 14:11:47,823] multiqc.modules.custom_content.custom_content      [INFO   ]  endorSpy: Found 49 General Statistics columns
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'FastQC (pre-Trimming)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'FastQC (pre-Trimming)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Adapter Removal'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Adapter Removal'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'FastQC (post-Trimming)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'FastQC (post-Trimming)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Samtools Flagstat (pre-samtools filter)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Samtools Flagstat (pre-samtools filter)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Samtools Flagstat (post-samtools filter)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Samtools Flagstat (post-samtools filter)'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Picard'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Picard'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Preseq'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Preseq'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'DamageProfiler'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'DamageProfiler'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'mtnucratio'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'mtnucratio'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'QualiMap'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'QualiMap'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Bcftools'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Bcftools'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/eager Software Versions'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'nf-core/eager Software Versions'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/eager Workflow Summary'.
[2024-07-26 14:11:47,823] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'nf-core/eager Workflow Summary'.
[2024-07-26 14:11:47,994] multiqc.utils.mqc_colour                           [DEBUG  ]  general_stats_table: Colour scale RdYlGrn not found - defaulting to GnBu
[2024-07-26 14:11:48,221] multiqc                                            [INFO   ]  Compressing plot data
[2024-07-26 14:11:51,365] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2024-07-26 14:11:51,365] multiqc                                            [INFO   ]  Data        : multiqc_data
[2024-07-26 14:11:51,365] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpeb96s0kv/multiqc_data' to '/work/project/crucial/Sarah/7-EAGER/NC_024032.1_BIS_RESULTS/work/df/382c6ad646541f8ae703c7dc97f9c6/multiqc_data'
[2024-07-26 14:11:51,413] multiqc                                            [INFO   ]  Plots       : multiqc_plots
[2024-07-26 14:11:51,413] multiqc                                            [DEBUG  ]  Moving plots directory from '/tmp/tmpeb96s0kv/multiqc_plots' to '/work/project/crucial/Sarah/7-EAGER/NC_024032.1_BIS_RESULTS/work/df/382c6ad646541f8ae703c7dc97f9c6/multiqc_plots'
[2024-07-26 14:11:51,554] multiqc                                            [INFO   ]  MultiQC complete