[2024-07-26 13:52:20,242] multiqc                                            [DEBUG  ]  This is MultiQC v1.14
[2024-07-26 13:52:20,293] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yaml
[2024-07-26 13:52:20,294] multiqc                                            [DEBUG  ]  New config: {'custom_logo': '/work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS/work/87/819cd22529c0be4f18f2ec2d249e5d/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 13:52:20,294] 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 13:52:20,294] multiqc                                            [DEBUG  ]  Command used: /opt/conda/envs/nf-core-eager-2.4.7/bin/multiqc -f multiqc_config.yaml .
[2024-07-26 13:52:20,601] multiqc                                            [WARNING]  MultiQC Version v1.23 now available!
[2024-07-26 13:52:20,601] multiqc                                            [DEBUG  ]  Working dir : /work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS/work/87/819cd22529c0be4f18f2ec2d249e5d
[2024-07-26 13:52:20,601] multiqc                                            [DEBUG  ]  Template    : default
[2024-07-26 13:52:20,601] 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 13:52:20,602] 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 13:52:20,602] 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 13:52:20,602] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmpnzot7x_i
[2024-07-26 13:52:20,849] multiqc                                            [INFO   ]  Search path : /work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS/work/87/819cd22529c0be4f18f2ec2d249e5d/multiqc_config.yaml
[2024-07-26 13:52:20,849] multiqc                                            [INFO   ]  Search path : /work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS/work/87/819cd22529c0be4f18f2ec2d249e5d
[2024-07-26 13:52:20,850] multiqc                                            [DEBUG  ]  Ignored 251 search patterns as didn't match running modules.
[2024-07-26 13:52:31,364] multiqc                                            [DEBUG  ]  Summary of files that were skipped by the search: [skipped_no_match: 3559]
[2024-07-26 13:52:31,855] multiqc.plots.bargraph                             [DEBUG  ]  Using matplotlib version 3.7.1
[2024-07-26 13:52:31,857] multiqc.plots.linegraph                            [DEBUG  ]  Using matplotlib version 3.7.1
[2024-07-26 13:52:31,857] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_6_MB8_S31_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,873] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_13_BC11_S38_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,888] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_1_EG1_S71_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,903] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_13_BC11_S38_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,918] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_4_MD4_S29_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,933] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_11_MD2_S21_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,948] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_5_MD10_S30_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,963] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_13_MB5_S23_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,979] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_8_SH2_S88_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:31,994] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_3_EG3_S73_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,009] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_4_MD4_S29_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,023] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_3_MD8_S28_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,038] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_15_BC13_S40_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,053] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_10_MPHB2_S78_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,068] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L8_15_HTMK99-XXII-0-4287_S49_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,083] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_1_MD15_S26_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,098] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_1_MD15_S26_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,113] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_2_EG5_S82_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,127] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_8_MD16_S33_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,142] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_15_BC13_S40_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,157] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_11_MPHB3_S79_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,171] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_6_MB8_S31_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,187] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_13_MB5_S23_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,202] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_5_MD5_S15_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,216] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_3_MD8_S28_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,231] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_14_BC12_S39_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,247] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_1_26-52_S50_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,261] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_2_2777-17_S51_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,277] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_1_26-52_S50_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,292] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_11_SCO_1338_S63_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,306] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_12_MD9_S37_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,321] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_2_EG5_S82_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,336] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_4_MB9_S14_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,351] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_12_MPHB4_S80_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,366] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_5_MD5_S15_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,380] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_2_EG2_S72_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,395] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_8_MD16_S33_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,410] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_7_MD3_S32_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,425] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_7_MD3_S32_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,439] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_8_MB4_S18_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,454] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_11_MD2_S21_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,469] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_11_SCO_1338_S63_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,484] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_3_EG3_S73_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,499] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_2_EG2_S72_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,515] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L9_2_2777-17_S51_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,529] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_2_MD7_S27_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,544] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_9_MD12_S19_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,559] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_10_MPHB2_S78_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,574] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_13_SCO_2764_S65_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,589] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L0_8_SH2_S88_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,603] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_12_MD9_S37_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,619] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_2_MD7_S27_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,634] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_12_MPHB4_S80_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,649] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_9_MD12_S19_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,664] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_1_EG1_S71_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,679] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_14_BC12_S39_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,694] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_4_MB9_S14_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,708] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L10_13_SCO_2764_S65_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,724] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L5_5_MD10_S30_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,739] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L8_15_HTMK99-XXII-0-4287_S49_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,754] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L2_11_MPHB3_S79_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,780] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc_raw/L4_8_MB4_S18_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,803] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_1_MD15_S26_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,803] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_12_MD9_S37_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,803] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_12_MPHB4_S80_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,803] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_2_MD7_S27_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,803] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_3_EG3_S73_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,803] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_10_MPHB2_S78_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,803] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L0_8_SH2_S88_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_13_SCO_2764_S65_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L8_15_HTMK99-XXII-0-4287_S49_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L0_2_EG5_S82_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_13_BC11_S38_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_3_MD8_S28_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_4_MB9_S14_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_6_MB8_S31_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L9_1_26-52_S50_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_5_MD5_S15_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_7_MD3_S32_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_2_EG2_S72_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_11_MD2_S21_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L10_11_SCO_1338_S63_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_9_MD12_S19_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_15_BC13_S40_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_11_MPHB3_S79_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_4_MD4_S29_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_14_BC12_S39_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L9_2_2777-17_S51_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_8_MD16_S33_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L5_5_MD10_S30_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L2_1_EG1_S71_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_13_MB5_S23_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc/L4_8_MB4_S18_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 13:52:32,804] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 62 reports
[2024-07-26 13:52:42,638] multiqc.modules.adapterRemoval.adapterRemoval      [INFO   ]  Found 31 reports
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_6_MB8_S31_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_13_BC11_S38_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_1_EG1_S71_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_13_BC11_S38_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_4_MD4_S29_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_11_MD2_S21_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_5_MD10_S30_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_13_MB5_S23_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,875] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_8_SH2_S88_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_3_EG3_S73_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_4_MD4_S29_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_3_MD8_S28_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_15_BC13_S40_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_10_MPHB2_S78_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L8_15_HTMK99-XXII-0-4287_S49_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_1_MD15_S26_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_1_MD15_S26_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_2_EG5_S82_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_8_MD16_S33_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_15_BC13_S40_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_11_MPHB3_S79_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_6_MB8_S31_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_13_MB5_S23_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_5_MD5_S15_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_3_MD8_S28_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_14_BC12_S39_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_1_26-52_S50_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_2_2777-17_S51_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_1_26-52_S50_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_11_SCO_1338_S63_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_12_MD9_S37_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_2_EG5_S82_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_4_MB9_S14_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_12_MPHB4_S80_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_5_MD5_S15_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_2_EG2_S72_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,876] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_8_MD16_S33_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_7_MD3_S32_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_7_MD3_S32_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_8_MB4_S18_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_11_MD2_S21_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_11_SCO_1338_S63_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_3_EG3_S73_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_2_EG2_S72_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L9_2_2777-17_S51_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_2_MD7_S27_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_9_MD12_S19_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_10_MPHB2_S78_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_13_SCO_2764_S65_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L0_8_SH2_S88_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_12_MD9_S37_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_2_MD7_S27_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_12_MPHB4_S80_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_9_MD12_S19_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_1_EG1_S71_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_14_BC12_S39_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_4_MB9_S14_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L10_13_SCO_2764_S65_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L5_5_MD10_S30_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L8_15_HTMK99-XXII-0-4287_S49_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L2_11_MPHB3_S79_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping './fastqc_raw/L4_8_MB4_S18_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,877] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_1_MD15_S26_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,891] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_12_MD9_S37_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,904] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_12_MPHB4_S80_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,917] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_2_MD7_S27_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,930] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_3_EG3_S73_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,943] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_10_MPHB2_S78_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,956] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L0_8_SH2_S88_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,969] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_13_SCO_2764_S65_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,982] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L8_15_HTMK99-XXII-0-4287_S49_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:49,996] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L0_2_EG5_S82_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,008] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_13_BC11_S38_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,022] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_3_MD8_S28_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,035] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_4_MB9_S14_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,048] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_6_MB8_S31_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,061] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L9_1_26-52_S50_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,074] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_5_MD5_S15_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,087] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_7_MD3_S32_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,100] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_2_EG2_S72_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,112] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_11_MD2_S21_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,125] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L10_11_SCO_1338_S63_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,138] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_9_MD12_S19_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,151] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_15_BC13_S40_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,164] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_11_MPHB3_S79_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,177] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_4_MD4_S29_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,190] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_14_BC12_S39_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,203] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L9_2_2777-17_S51_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,216] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_8_MD16_S33_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,229] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L5_5_MD10_S30_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,242] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L2_1_EG1_S71_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,254] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_13_MB5_S23_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,268] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Selecting './fastqc/L4_8_MB4_S18_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 13:52:50,280] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 31 reports
[2024-07-26 13:52:58,492] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_11_MD2_S21_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,493] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_4_MD4_S29_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,494] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_14_BC12_S39_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,494] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_12_MD9_S37_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,494] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_11_SCO_1338_S63_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,495] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_3_EG3_S73_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,495] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L8_15_HTMK99-XXII-0-4287_S49_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,495] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L0_8_SH2_S88_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,496] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_2_MD7_S27_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,496] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_13_BC11_S38_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,496] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_7_MD3_S32_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,496] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_3_MD8_S28_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,497] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L9_1_26-52_S50_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,497] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L10_13_SCO_2764_S65_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,497] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L9_2_2777-17_S51_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,498] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_5_MD10_S30_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,498] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_6_MB8_S31_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,498] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_15_BC13_S40_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,499] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_8_MD16_S33_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,499] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_11_MPHB3_S79_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,499] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_10_MPHB2_S78_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,499] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_9_MD12_S19_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,500] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_5_MD5_S15_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,500] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_8_MB4_S18_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,500] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_2_EG2_S72_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,501] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_12_MPHB4_S80_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,501] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L0_2_EG5_S82_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,501] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_13_MB5_S23_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,502] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L2_1_EG1_S71_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,502] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L4_4_MB9_S14_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,502] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat/L5_1_MD15_S26_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_2_MD7_S27_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_11_MPHB3_S79_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_15_BC13_S40_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_12_MD9_S37_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_3_MD8_S28_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L9_1_26-52_S50_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_14_BC12_S39_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_13_MB5_S23_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L8_15_HTMK99-XXII-0-4287_S49_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L9_2_2777-17_S51_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_1_MD15_S26_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_6_MB8_S31_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_5_MD10_S30_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_8_MD16_S33_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L0_2_EG5_S82_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_2_EG2_S72_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_13_BC11_S38_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_13_SCO_2764_S65_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_9_MD12_S19_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_12_MPHB4_S80_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_5_MD5_S15_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L0_8_SH2_S88_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L10_11_SCO_1338_S63_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_4_MB9_S14_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_8_MB4_S18_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_4_MD4_S29_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L4_11_MD2_S21_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_1_EG1_S71_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_10_MPHB2_S78_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,503] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L2_3_EG3_S73_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,504] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat_filtered/L5_7_MD3_S32_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 13:52:58,505] multiqc.modules.samtools.samtools                  [INFO   ]  Found 31 flagstat reports
[2024-07-26 13:52:58,508] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_11_MD2_S21_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,508] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_4_MD4_S29_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,508] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_14_BC12_S39_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_12_MD9_S37_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_11_SCO_1338_S63_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_3_EG3_S73_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L8_15_HTMK99-XXII-0-4287_S49_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L0_8_SH2_S88_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_2_MD7_S27_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_13_BC11_S38_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_7_MD3_S32_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_3_MD8_S28_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L9_1_26-52_S50_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L10_13_SCO_2764_S65_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L9_2_2777-17_S51_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_5_MD10_S30_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_6_MB8_S31_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_15_BC13_S40_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_8_MD16_S33_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_11_MPHB3_S79_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_10_MPHB2_S78_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_9_MD12_S19_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_5_MD5_S15_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_8_MB4_S18_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_2_EG2_S72_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_12_MPHB4_S80_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L0_2_EG5_S82_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_13_MB5_S23_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L2_1_EG1_S71_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L4_4_MB9_S14_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Skipping './flagstat/L5_1_MD15_S26_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,509] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_2_MD7_S27_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,510] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_11_MPHB3_S79_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,510] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_15_BC13_S40_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,510] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_12_MD9_S37_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,511] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_3_MD8_S28_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,511] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L9_1_26-52_S50_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,511] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_14_BC12_S39_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,512] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_13_MB5_S23_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,512] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L8_15_HTMK99-XXII-0-4287_S49_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,512] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L9_2_2777-17_S51_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,512] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_1_MD15_S26_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,513] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_6_MB8_S31_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,513] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_5_MD10_S30_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,513] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_8_MD16_S33_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,514] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L0_2_EG5_S82_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,514] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_2_EG2_S72_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,514] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_13_BC11_S38_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,515] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_13_SCO_2764_S65_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,515] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_9_MD12_S19_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,515] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_12_MPHB4_S80_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,515] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_5_MD5_S15_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,516] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L0_8_SH2_S88_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,516] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L10_11_SCO_1338_S63_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,516] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_4_MB9_S14_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,517] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_8_MB4_S18_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,517] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_4_MD4_S29_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,517] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L4_11_MD2_S21_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,518] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_1_EG1_S71_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,518] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_10_MPHB2_S78_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,518] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L2_3_EG3_S73_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,518] multiqc.modules.base_module                        [DEBUG  ]  samtools/flagstat - Selecting './flagstat_filtered/L5_7_MD3_S32_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 13:52:58,520] multiqc.modules.samtools.samtools                  [INFO   ]  Found 31 flagstat reports
[2024-07-26 13:53:00,267] multiqc.modules.picard.picard                      [INFO   ]  Found 31 MarkDuplicates reports
[2024-07-26 13:53:00,275] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_13_MB5_S23.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,276] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_12_MD9_S37.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,277] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L0_8_SH2_S88.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,277] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_9_MD12_S19.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,278] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_14_BC12_S39.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,278] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_15_BC13_S40.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,279] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_10_MPHB2_S78.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,285] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L0_2_EG5_S82.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,286] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L9_1_26-52_S50.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,289] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_13_BC11_S38.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,290] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_13_SCO_2764_S65.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,291] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_6_MB8_S31.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,291] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L8_15_HTMK99-XXII-0-4287_S49.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,293] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_11_MD2_S21.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,293] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_7_MD3_S32.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,294] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_4_MD4_S29.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,294] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_8_MD16_S33.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,296] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_2_EG2_S72.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,296] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_3_EG3_S73.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,296] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_8_MB4_S18.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,297] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_3_MD8_S28.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,299] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L10_11_SCO_1338_S63.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,300] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_5_MD10_S30.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,301] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_1_EG1_S71.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,301] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_1_MD15_S26.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,302] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_12_MPHB4_S80.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,302] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L5_2_MD7_S27.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,303] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_4_MB9_S14.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,304] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L4_5_MD5_S15.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,304] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L9_2_2777-17_S51.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,305] multiqc.modules.base_module                        [DEBUG  ]  preseq - Selecting './preseq/L2_11_MPHB3_S79.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 13:53:00,306] multiqc.modules.preseq.preseq                      [INFO   ]  Found 31 reports
[2024-07-26 13:53:03,656] multiqc.modules.mtnucratio.mtnucratio              [INFO   ]  Found 31 reports
[2024-07-26 13:53:03,703] multiqc.modules.qualimap.QM_BamQC                  [DEBUG  ]  Custom Qualimap thresholds: 1, 2, 3, 4, 5
[2024-07-26 13:53:05,753] multiqc.modules.qualimap.qualimap                  [INFO   ]  Found 31 BamQC reports
[2024-07-26 13:53:18,017] multiqc.modules.bcftools.bcftools                  [INFO   ]  Found 31 stats reports
[2024-07-26 13:53:18,035] multiqc.modules.custom_content.custom_content      [INFO   ]  software_versions: Found 1 sample (html)
[2024-07-26 13:53:18,036] multiqc.modules.custom_content.custom_content      [INFO   ]  nf-core-eager-summary: Found 1 sample (html)
[2024-07-26 13:53:18,036] multiqc.modules.custom_content.custom_content      [INFO   ]  endorSpy: Found 31 General Statistics columns
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'FastQC (pre-Trimming)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'FastQC (pre-Trimming)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Adapter Removal'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Adapter Removal'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'FastQC (post-Trimming)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'FastQC (post-Trimming)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Samtools Flagstat (pre-samtools filter)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Samtools Flagstat (pre-samtools filter)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Samtools Flagstat (post-samtools filter)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Samtools Flagstat (post-samtools filter)'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Picard'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Picard'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Preseq'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Preseq'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'DamageProfiler'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'DamageProfiler'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'mtnucratio'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'mtnucratio'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'QualiMap'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'QualiMap'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Bcftools'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Bcftools'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/eager Software Versions'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'nf-core/eager Software Versions'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/eager Workflow Summary'.
[2024-07-26 13:53:18,036] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-eager-summary' not found for module 'nf-core/eager Workflow Summary'.
[2024-07-26 13:53:18,142] multiqc.utils.mqc_colour                           [DEBUG  ]  general_stats_table: Colour scale RdYlGrn not found - defaulting to GnBu
[2024-07-26 13:53:18,281] multiqc                                            [INFO   ]  Compressing plot data
[2024-07-26 13:53:20,148] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2024-07-26 13:53:20,148] multiqc                                            [INFO   ]  Data        : multiqc_data
[2024-07-26 13:53:20,148] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpnzot7x_i/multiqc_data' to '/work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS/work/87/819cd22529c0be4f18f2ec2d249e5d/multiqc_data'
[2024-07-26 13:53:20,176] multiqc                                            [INFO   ]  Plots       : multiqc_plots
[2024-07-26 13:53:20,176] multiqc                                            [DEBUG  ]  Moving plots directory from '/tmp/tmpnzot7x_i/multiqc_plots' to '/work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS/work/87/819cd22529c0be4f18f2ec2d249e5d/multiqc_plots'
[2024-07-26 13:53:20,296] multiqc                                            [INFO   ]  MultiQC complete