[2024-07-26 12:38:02,730] multiqc [DEBUG ] This is MultiQC v1.14
[2024-07-26 12:38:02,755] multiqc [DEBUG ] Loading config settings from: multiqc_config.yaml
[2024-07-26 12:38:02,755] multiqc [DEBUG ] New config: {'custom_logo': '/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/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 nf-core/eager analysis pipeline. For information about how to interpret these results, please see the documentation.\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 12:38:02,755] 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 12:38:02,755] multiqc [DEBUG ] Command used: /opt/conda/envs/nf-core-eager-2.4.7/bin/multiqc -f multiqc_config.yaml .
[2024-07-26 12:38:04,242] multiqc [WARNING] MultiQC Version v1.23 now available!
[2024-07-26 12:38:04,242] multiqc [DEBUG ] Working dir : /work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1
[2024-07-26 12:38:04,242] multiqc [DEBUG ] Template : default
[2024-07-26 12:38:04,242] 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 12:38:04,243] 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 12:38:04,243] 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 12:38:04,243] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpn8m6ojm2
[2024-07-26 12:38:04,427] multiqc [INFO ] Search path : /work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/multiqc_config.yaml
[2024-07-26 12:38:04,427] multiqc [INFO ] Search path : /work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1
[2024-07-26 12:38:04,428] multiqc [DEBUG ] Ignored 251 search patterns as didn't match running modules.
[2024-07-26 12:38:04,820] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_no_match: 123]
[2024-07-26 12:38:05,260] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.7.1
[2024-07-26 12:38:05,262] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.7.1
[2024-07-26 12:38:05,262] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting './fastqc_raw/L2_4_CD2_S74_R2_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 12:38:05,353] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting './fastqc_raw/L2_4_CD2_S74_R1_001_raw_fastqc.zip' as it matched the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 12:38:05,370] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping './fastqc/L2_4_CD2_S74_R1_001.fastq_L0.pe.combined_fastqc.zip' as it didn't match the path_filters for 'FastQC (pre-Trimming)'
[2024-07-26 12:38:05,370] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
[2024-07-26 12:38:12,113] multiqc.modules.adapterRemoval.adapterRemoval [INFO ] Found 1 reports
[2024-07-26 12:38:18,023] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping './fastqc_raw/L2_4_CD2_S74_R2_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 12:38:18,023] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping './fastqc_raw/L2_4_CD2_S74_R1_001_raw_fastqc.zip' as it didn't match the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 12:38:18,024] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting './fastqc/L2_4_CD2_S74_R1_001.fastq_L0.pe.combined_fastqc.zip' as it matched the path_filters for 'FastQC (post-Trimming)'
[2024-07-26 12:38:18,038] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports
[2024-07-26 12:38:24,607] multiqc.modules.base_module [DEBUG ] samtools/flagstat - Selecting './flagstat/L2_4_CD2_S74_flagstat.stats' as it matched the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 12:38:24,609] multiqc.modules.base_module [DEBUG ] samtools/flagstat - Skipping './flagstat_filtered/L2_4_CD2_S74_postfilterflagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (pre-samtools filter)'
[2024-07-26 12:38:24,610] multiqc.modules.samtools.samtools [INFO ] Found 1 flagstat reports
[2024-07-26 12:38:24,613] multiqc.modules.base_module [DEBUG ] samtools/flagstat - Skipping './flagstat/L2_4_CD2_S74_flagstat.stats' as it didn't match the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 12:38:24,613] multiqc.modules.base_module [DEBUG ] samtools/flagstat - Selecting './flagstat_filtered/L2_4_CD2_S74_postfilterflagstat.stats' as it matched the path_filters for 'Samtools Flagstat (post-samtools filter)'
[2024-07-26 12:38:24,614] multiqc.modules.samtools.samtools [INFO ] Found 1 flagstat reports
[2024-07-26 12:38:25,351] multiqc.modules.picard.picard [INFO ] Found 1 MarkDuplicates reports
[2024-07-26 12:38:25,355] multiqc.modules.base_module [DEBUG ] preseq - Selecting './preseq/L2_4_CD2_S74.filtered.preseq' as it matched the path_filters for 'Preseq'
[2024-07-26 12:38:25,356] multiqc.modules.preseq.preseq [INFO ] Found 1 reports
[2024-07-26 12:38:28,593] multiqc.modules.mtnucratio.mtnucratio [INFO ] Found 1 reports
[2024-07-26 12:38:28,600] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Custom Qualimap thresholds: 1, 2, 3, 4, 5
[2024-07-26 12:38:30,471] multiqc.modules.qualimap.qualimap [INFO ] Found 1 BamQC reports
[2024-07-26 12:38:34,983] multiqc.modules.bcftools.bcftools [INFO ] Found 1 stats reports
[2024-07-26 12:38:34,992] multiqc.modules.custom_content.custom_content [INFO ] software_versions: Found 1 sample (html)
[2024-07-26 12:38:34,992] multiqc.modules.custom_content.custom_content [INFO ] nf-core-eager-summary: Found 1 sample (html)
[2024-07-26 12:38:34,992] multiqc.modules.custom_content.custom_content [INFO ] endorSpy: Found 1 General Statistics columns
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'FastQC (pre-Trimming)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'FastQC (pre-Trimming)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Adapter Removal'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Adapter Removal'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'FastQC (post-Trimming)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'FastQC (post-Trimming)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Samtools Flagstat (pre-samtools filter)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Samtools Flagstat (pre-samtools filter)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Samtools Flagstat (post-samtools filter)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Samtools Flagstat (post-samtools filter)'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Picard'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Picard'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Preseq'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Preseq'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'DamageProfiler'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'DamageProfiler'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'mtnucratio'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'mtnucratio'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'QualiMap'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'QualiMap'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Bcftools'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'Bcftools'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'nf-core/eager Software Versions'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'nf-core/eager Software Versions'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'nf-core/eager Workflow Summary'.
[2024-07-26 12:38:34,993] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-eager-summary' not found for module 'nf-core/eager Workflow Summary'.
[2024-07-26 12:38:35,001] multiqc.utils.mqc_colour [DEBUG ] general_stats_table: Colour scale RdYlGrn not found - defaulting to GnBu
[2024-07-26 12:38:35,007] multiqc [INFO ] Compressing plot data
[2024-07-26 12:38:35,081] multiqc [INFO ] Report : multiqc_report.html
[2024-07-26 12:38:35,081] multiqc [INFO ] Data : multiqc_data
[2024-07-26 12:38:35,081] multiqc [DEBUG ] Moving data file from '/tmp/tmpn8m6ojm2/multiqc_data' to '/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/multiqc_data'
[2024-07-26 12:38:35,112] multiqc [INFO ] Plots : multiqc_plots
[2024-07-26 12:38:35,112] multiqc [DEBUG ] Moving plots directory from '/tmp/tmpn8m6ojm2/multiqc_plots' to '/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/multiqc_plots'
[2024-07-26 12:38:35,236] multiqc [INFO ] MultiQC complete