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MultiQC ignoring first line of TSV file #2550

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4 tasks done
MTDouglas opened this issue May 9, 2024 · 2 comments
Open
4 tasks done

MultiQC ignoring first line of TSV file #2550

MTDouglas opened this issue May 9, 2024 · 2 comments

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@MTDouglas
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Description of bug

Not quite sure if this is a bug per say, but I'm having trouble getting MultiQC to handle a .tsv file that doesn't have a header while using custom_content. I'm using this within the context of a nextflow pipeline and it should be able to handle a .tsv file per sample. Below is the custom_data section I am using in my multiqc_config.yml:

custom_data:
  readitandkeep_table:
    id: "readitandkeep_table"
    file_format:  "tsv"
    section_name: "ReaditAndKeep Results"
    description:  "# of inputted reads vs #of remaining reads post scrubbing"
    plot_type: "table"
    headers:
      "Input reads file 1":
        description: "Total number of raw reads in fastq1"
        format: "{:,.2f}"
      "Input reads file 2":
        description: "Total number of raw reads in fastq2"
        format: "{:,.2f}"
      "Kept reads 1":
        description: "Total number of reads post scrubbing in fastq1"
        format: "{:,.2f}"
      "Kept reads 2":
        description: "Total number of reads post scrubbing in fastq2"
        format: "{:,.2f}"
    pconfig:
      id: "readitandkeep_summary"
      table_title:  "ReaditandKeep Results"
      
    
sp:
  readitandkeep_table:
    fn: "*_readitkeep_summary.tsv"

The .yaml data file procuced looks like this:

Input reads file 2:
  '4688.0': 4688.0
Kept reads 1:
  '4688.0': 1492.0
Kept reads 2:
  '4688.0': 1492.0

Any insight would be much appreciated!

File that triggers the error

T1_readitkeep_summary.zip

MultiQC Error log

[2024-05-09 15:36:14,837] multiqc                                            [DEBUG  ]  This is MultiQC v1.21
[2024-05-09 15:36:14,840] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yml
[2024-05-09 15:36:14,840] multiqc                                            [DEBUG  ]  New config: {'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/readandkeeptest" target="_blank">nf-core/readandkeeptest</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/readandkeeptest" target="_blank">documentation</a>.\n', 'max_table_rows': 1000, 'data_format': 'yaml', 'run_modules': ['fastqc', 'samtools', 'bowtie2', 'custom_content'], 'module_order': [{'fastqc': {'name': 'Preprocess: FastQC (raw reads)'}}, {'samtools': {'name': 'Samtools'}}, {'bowtie2': {'name': 'Bowtie2'}}], 'report_section_order': {'readitandkeep_table': {'after': 'fastqc'}, 'nf-core-readandkeeptest-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-readandkeeptest-summary': {'order': -1002}}, 'custom_data': {'readitandkeep_table': {'id': 'readitandkeep_table', 'file_format': 'tsv', 'section_name': 'ReaditAndKeep Results', 'description': '# of inputted reads vs #of remaining reads post scrubbing', 'plot_type': 'table', 'pconfig': {'id': 'readitandkeep_summary', 'table_title': 'ReaditandKeep Results'}}}, 'export_plots': True}
[2024-05-09 15:36:14,840] multiqc                                            [DEBUG  ]  Added to filename patterns: [{'readitandkeep_table': {'fn': '*_readitkeep_summary.tsv'}}]
[2024-05-09 15:36:14,843] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yml
[2024-05-09 15:36:14,843] multiqc                                            [DEBUG  ]  New config: {'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/readandkeeptest" target="_blank">nf-core/readandkeeptest</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/readandkeeptest" target="_blank">documentation</a>.\n', 'max_table_rows': 1000, 'data_format': 'yaml', 'run_modules': ['fastqc', 'samtools', 'bowtie2', 'custom_content'], 'module_order': [{'fastqc': {'name': 'Preprocess: FastQC (raw reads)'}}, {'samtools': {'name': 'Samtools'}}, {'bowtie2': {'name': 'Bowtie2'}}], 'report_section_order': {'readitandkeep_table': {'after': 'fastqc'}, 'nf-core-readandkeeptest-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-readandkeeptest-summary': {'order': -1002}}, 'custom_data': {'readitandkeep_table': {'id': 'readitandkeep_table', 'file_format': 'tsv', 'section_name': 'ReaditAndKeep Results', 'description': '# of inputted reads vs #of remaining reads post scrubbing', 'plot_type': 'table', 'pconfig': {'id': 'readitandkeep_summary', 'table_title': 'ReaditandKeep Results'}}}, 'export_plots': True}
[2024-05-09 15:36:14,843] multiqc                                            [DEBUG  ]  Added to filename patterns: [{'readitandkeep_table': {'fn': '*_readitkeep_summary.tsv'}}]
[2024-05-09 15:36:14,843] multiqc                                            [DEBUG  ]  Command used: /usr/local/bin/multiqc --force --config multiqc_config.yml -d .
[2024-05-09 15:36:15,838] multiqc                                            [DEBUG  ]  Latest MultiQC version is v1.21, released 2024-02-28
[2024-05-09 15:36:15,838] multiqc                                            [DEBUG  ]  Working dir : /nf-core-pipleine/work/43/0e3504215fbaaf1c4cfa8eeec1b279
[2024-05-09 15:36:15,838] multiqc                                            [DEBUG  ]  Template    : default
[2024-05-09 15:36:15,838] multiqc                                            [DEBUG  ]  Running Python 3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:53:32) [GCC 12.3.0]
[2024-05-09 15:36:15,838] multiqc                                            [INFO   ]  Prepending directory to sample names
[2024-05-09 15:36:15,839] multiqc                                            [INFO   ]  Only using modules: fastqc, samtools, bowtie2, custom_content
[2024-05-09 15:36:15,839] multiqc                                            [DEBUG  ]  Analysing modules: custom_content, fastqc, samtools, bowtie2
[2024-05-09 15:36:15,840] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmp_mn0l3k9
[2024-05-09 15:36:15,842] multiqc                                            [INFO   ]  Search path : /nf-core-pipleine/work/43/0e3504215fbaaf1c4cfa8eeec1b279
[2024-05-09 15:36:15,844] multiqc                                            [DEBUG  ]  Ignored 320 search patterns as didn't match running modules.
[2024-05-09 15:36:15,864] multiqc                                            [DEBUG  ]  Summary of files that were skipped by the search: [skipped_no_match: 8]
[2024-05-09 15:36:15,912] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_readitandkeep_summary.yaml
[2024-05-09 15:36:15,974] multiqc.modules.custom_content.custom_content      [INFO   ]  readitandkeep_table: Found 1 samples (table)
[2024-05-09 15:36:15,974] multiqc.modules.custom_content.custom_content      [INFO   ]  software_versions: Found 1 sample (html)
[2024-05-09 15:36:15,974] multiqc.modules.custom_content.custom_content      [INFO   ]  nf-core-readandkeeptest-methods-description: Found 1 sample (html)
[2024-05-09 15:36:15,974] multiqc.modules.custom_content.custom_content      [INFO   ]  nf-core-readandkeeptest-summary: Found 1 sample (html)
[2024-05-09 15:36:16,002] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 2 reports
[2024-05-09 15:36:16,004] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_fastqc.yaml
[2024-05-09 15:36:16,077] multiqc.plots.plotly.heatmap                       [DEBUG  ]  Heatmap size: 495x200, px per element: 45.00x100.00
[2024-05-09 15:36:16,096] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_samtools_stats.yaml
[2024-05-09 15:36:16,110] multiqc.modules.samtools.samtools                  [INFO   ]  Found 2 stats reports
[2024-05-09 15:36:16,115] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_samtools_flagstat.yaml
[2024-05-09 15:36:16,123] multiqc.modules.samtools.samtools                  [INFO   ]  Found 2 flagstat reports
[2024-05-09 15:36:16,124] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_samtools_idxstats.yaml
[2024-05-09 15:36:16,126] multiqc.modules.samtools.samtools                  [INFO   ]  Found 2 idxstats reports
[2024-05-09 15:36:16,129] multiqc.modules.bowtie2.bowtie2                    [INFO   ]  Found 2 reports
[2024-05-09 15:36:16,130] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_bowtie2.yaml
[2024-05-09 15:36:16,136] multiqc.utils.software_versions                    [DEBUG  ]  Reading software versions from config.software_versions
[2024-05-09 15:36:16,138] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_software_versions.yaml
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'ReaditAndKeep Results'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'ReaditAndKeep Results'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'ReaditAndKeep Results'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'ReaditAndKeep Results'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'Samtools'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Samtools'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Samtools'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Samtools'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'Bowtie2'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Bowtie2'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Bowtie2'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Bowtie2'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'Software Versions'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Software Versions'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Software Versions'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Software Versions'.
[2024-05-09 15:36:16,138] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_table' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-09 15:36:16,139] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-09 15:36:16,151] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_general_stats.yaml
[2024-05-09 15:36:16,154] multiqc                                            [DEBUG  ]  Compressing plot data
[2024-05-09 15:36:16,232] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_data.json
[2024-05-09 15:36:16,232] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2024-05-09 15:36:16,232] multiqc                                            [INFO   ]  Data        : multiqc_data
[2024-05-09 15:36:16,233] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmp_mn0l3k9/multiqc_data' to '/nf-core-pipleine/work/43/0e3504215fbaaf1c4cfa8eeec1b279/multiqc_data'
[2024-05-09 15:36:16,234] multiqc                                            [DEBUG  ]  Full report path: /nf-core-pipleine/work/43/0e3504215fbaaf1c4cfa8eeec1b279/multiqc_report.html
[2024-05-09 15:36:16,234] multiqc                                            [INFO   ]  Plots       : multiqc_plots
[2024-05-09 15:36:16,234] multiqc                                            [DEBUG  ]  Moving plots directory from '/tmp/tmp_mn0l3k9/multiqc_plots' to '/nf-core-pipleine/work/43/0e3504215fbaaf1c4cfa8eeec1b279/multiqc_plots'
[2024-05-09 15:36:16,445] multiqc                                            [INFO   ]  MultiQC complete

Before submitting

  • I have read the troubleshooting documentation.
  • I am using the latest release of MultiQC.
  • I have included a full MultiQC log, not truncated.
  • I have attached an input file (.zip if necessary) that triggers the error.
@MTDouglas
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Author

I have edited the .tsv file to now contain headers and have changed the plot type to graph and get an actual output! However it seems to not work with multiple samples. Each sample has a unique name and the -d has been specified. Any input as to why multiple samples are not being displayed in the plot below would be helpful!

Changed .tsv file example:

Type	Counts
Input reads file 1	4688
Input reads file 2	4688
Kept reads 1	1492
Kept reads 2	1492

multiqc_config.yml specification:

custom_data:
  readitandkeep_graph:
    id: "readitandkeep_graph"
    file_format: "tsv"
    description:  "Outputs of ReadItAndKeep per sample"
    section_name: "ReaditAndKeep Graph"
    plot_type:  "bargraph"
    pconfig:
      title: "Read Counts"
    
sp:
  readitandkeep_graph: 
    fn: "*_readitkeep_summary.tsv"

Graph generated with run with 2 samples but only one samples output is graphed:

image

@MTDouglas
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Author

Here is the second .tsv file that is being run as well. This is the sample that is being plotted above despite both having the same structure

Type	Counts
Input reads file 1	26713
Input reads file 2	26713
Kept reads 1	2443
Kept reads 2	2443
 


MultiQC updated log output as well:
[2024-05-13 11:34:54,682] multiqc                                            [DEBUG  ]  This is MultiQC v1.21
[2024-05-13 11:34:54,686] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yml
[2024-05-13 11:34:54,686] multiqc                                            [DEBUG  ]  New config: {'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/readandkeeptest" target="_blank">nf-core/readandkeeptest</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/readandkeeptest" target="_blank">documentation</a>.\n', 'max_table_rows': 1000, 'data_format': 'yaml', 'run_modules': ['fastqc', 'samtools', 'bowtie2', 'custom_content'], 'module_order': [{'custom_contnet': None, 'name': 'ReaditAndKeep'}, {'fastqc': {'name': 'Preprocess: FastQC (raw reads)'}}, {'samtools': {'name': 'Samtools'}}, {'bowtie2': {'name': 'Bowtie2'}}], 'report_section_order': {'readitandkeep_graph': {'after': 'fastqc'}, 'nf-core-readandkeeptest-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-readandkeeptest-summary': {'order': -1002}}, 'custom_data': {'readitandkeep_graph': {'id': 'readitandkeep_graph', 'file_format': 'tsv', 'description': 'Outputs of ReadItAndKeep per sample', 'section_name': 'ReaditAndKeep Graph', 'plot_type': 'bargraph', 'pconfig': {'title': 'Read Counts'}}, 'readitandkeep_genstats': {'id': 'readitandkeep_genstats', 'file_format': 'tsv', 'plot_type': 'table'}}, 'export_plots': True}
[2024-05-13 11:34:54,686] multiqc                                            [DEBUG  ]  Added to filename patterns: [{'readitandkeep_graph': {'fn': '*_readitkeep_summary.tsv'}, 'readitandkeep_genstats': {'fn': '*_readitkeep_summary.tsv'}}]
[2024-05-13 11:34:54,689] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yml
[2024-05-13 11:34:54,689] multiqc                                            [DEBUG  ]  New config: {'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/readandkeeptest" target="_blank">nf-core/readandkeeptest</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/readandkeeptest" target="_blank">documentation</a>.\n', 'max_table_rows': 1000, 'data_format': 'yaml', 'run_modules': ['fastqc', 'samtools', 'bowtie2', 'custom_content'], 'module_order': [{'custom_contnet': None, 'name': 'ReaditAndKeep'}, {'fastqc': {'name': 'Preprocess: FastQC (raw reads)'}}, {'samtools': {'name': 'Samtools'}}, {'bowtie2': {'name': 'Bowtie2'}}], 'report_section_order': {'readitandkeep_graph': {'after': 'fastqc'}, 'nf-core-readandkeeptest-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-readandkeeptest-summary': {'order': -1002}}, 'custom_data': {'readitandkeep_graph': {'id': 'readitandkeep_graph', 'file_format': 'tsv', 'description': 'Outputs of ReadItAndKeep per sample', 'section_name': 'ReaditAndKeep Graph', 'plot_type': 'bargraph', 'pconfig': {'title': 'Read Counts'}}, 'readitandkeep_genstats': {'id': 'readitandkeep_genstats', 'file_format': 'tsv', 'plot_type': 'table'}}, 'export_plots': True}
[2024-05-13 11:34:54,689] multiqc                                            [DEBUG  ]  Added to filename patterns: [{'readitandkeep_graph': {'fn': '*_readitkeep_summary.tsv'}, 'readitandkeep_genstats': {'fn': '*_readitkeep_summary.tsv'}}]
[2024-05-13 11:34:54,689] multiqc                                            [DEBUG  ]  Command used: /usr/local/bin/multiqc --force --config multiqc_config.yml -d .
[2024-05-13 11:34:55,578] multiqc                                            [DEBUG  ]  Latest MultiQC version is v1.21, released 2024-02-28
[2024-05-13 11:34:55,578] multiqc                                            [DEBUG  ]  Working dir : ''nf-core-readandkeeptest/work/08/04cc6af9023e392e502f1786c2e9e8
[2024-05-13 11:34:55,578] multiqc                                            [DEBUG  ]  Template    : default
[2024-05-13 11:34:55,578] multiqc                                            [DEBUG  ]  Running Python 3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:53:32) [GCC 12.3.0]
[2024-05-13 11:34:55,578] multiqc                                            [INFO   ]  Prepending directory to sample names
[2024-05-13 11:34:55,579] multiqc                                            [INFO   ]  Only using modules: fastqc, samtools, bowtie2, custom_content
[2024-05-13 11:34:55,579] multiqc                                            [DEBUG  ]  Analysing modules: custom_content, fastqc, samtools, bowtie2
[2024-05-13 11:34:55,579] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmpo8vhlbp4
[2024-05-13 11:34:55,580] multiqc                                            [INFO   ]  Search path : ''nf-core-readandkeeptest/work/08/04cc6af9023e392e502f1786c2e9e8
[2024-05-13 11:34:55,581] multiqc                                            [DEBUG  ]  Ignored 320 search patterns as didn't match running modules.
[2024-05-13 11:34:55,598] multiqc                                            [DEBUG  ]  Summary of files that were skipped by the search: [skipped_no_match: 8]
[2024-05-13 11:34:55,665] multiqc.modules.custom_content.custom_content      [DEBUG  ]  No samples found: custom content (readitandkeep_genstats)
[2024-05-13 11:34:55,666] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_readitandkeep_graph-plot.yaml
[2024-05-13 11:34:55,745] multiqc.modules.custom_content.custom_content      [INFO   ]  readitandkeep_graph: Found 1 samples (bargraph)
[2024-05-13 11:34:55,745] multiqc.modules.custom_content.custom_content      [INFO   ]  software_versions: Found 1 sample (html)
[2024-05-13 11:34:55,745] multiqc.modules.custom_content.custom_content      [INFO   ]  nf-core-readandkeeptest-methods-description: Found 1 sample (html)
[2024-05-13 11:34:55,745] multiqc.modules.custom_content.custom_content      [INFO   ]  nf-core-readandkeeptest-summary: Found 1 sample (html)
[2024-05-13 11:34:55,794] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 4 reports
[2024-05-13 11:34:55,798] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_fastqc.yaml
[2024-05-13 11:34:55,879] multiqc.plots.plotly.heatmap                       [DEBUG  ]  Heatmap size: 495x320, px per element: 45.00x80.00
[2024-05-13 11:34:55,903] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_samtools_stats.yaml
[2024-05-13 11:34:55,921] multiqc.modules.samtools.samtools                  [INFO   ]  Found 4 stats reports
[2024-05-13 11:34:55,928] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_samtools_flagstat.yaml
[2024-05-13 11:34:55,940] multiqc.modules.samtools.samtools                  [INFO   ]  Found 4 flagstat reports
[2024-05-13 11:34:55,941] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_samtools_idxstats.yaml
[2024-05-13 11:34:55,944] multiqc.modules.samtools.samtools                  [INFO   ]  Found 4 idxstats reports
[2024-05-13 11:34:55,947] multiqc.modules.bowtie2.bowtie2                    [INFO   ]  Found 4 reports
[2024-05-13 11:34:55,950] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_bowtie2.yaml
[2024-05-13 11:34:55,956] multiqc.utils.software_versions                    [DEBUG  ]  Reading software versions from config.software_versions
[2024-05-13 11:34:55,958] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_software_versions.yaml
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'ReaditAndKeep Graph'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'ReaditAndKeep Graph'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'ReaditAndKeep Graph'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'ReaditAndKeep Graph'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Preprocess: FastQC (raw reads)'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'Samtools'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Samtools'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Samtools'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Samtools'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'Bowtie2'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Bowtie2'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Bowtie2'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Bowtie2'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'Software Versions'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'Software Versions'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Software Versions'.
[2024-05-13 11:34:55,958] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'Software Versions'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'nf-core/readandkeeptest Methods Description'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'nf-core/readandkeeptest Software Versions'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'readitandkeep_graph' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-methods-description' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-13 11:34:55,959] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-readandkeeptest-summary' not found for module 'nf-core/readandkeeptest Workflow Summary'.
[2024-05-13 11:34:55,980] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_general_stats.yaml
[2024-05-13 11:34:55,983] multiqc                                            [DEBUG  ]  Compressing plot data
[2024-05-13 11:34:56,082] multiqc.utils.util_functions                       [DEBUG  ]  Wrote data file multiqc_data.json
[2024-05-13 11:34:56,083] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2024-05-13 11:34:56,083] multiqc                                            [INFO   ]  Data        : multiqc_data
[2024-05-13 11:34:56,083] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpo8vhlbp4/multiqc_data' to '''nf-core-readandkeeptest/work/08/04cc6af9023e392e502f1786c2e9e8/multiqc_data'
[2024-05-13 11:34:56,084] multiqc                                            [DEBUG  ]  Full report path: nf-core-readandkeeptest/work/08/04cc6af9023e392e502f1786c2e9e8/multiqc_report.html
[2024-05-13 11:34:56,084] multiqc                                            [INFO   ]  Plots       : multiqc_plots
[2024-05-13 11:34:56,085] multiqc                                            [DEBUG  ]  Moving plots directory from '/tmp/tmpo8vhlbp4/multiqc_plots' to '''nf-core-readandkeeptest/work/08/04cc6af9023e392e502f1786c2e9e8/multiqc_plots'
[2024-05-13 11:34:56,315] multiqc                                            [INFO   ]  MultiQC complete

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