Hicpro MultiQC module broke

[RxLoutre]

Description of bug:

I have had this issue while running the nf-core for hi-c data. It ran successfully with the full dataset. I was trying to see if a subsample of the initial dataset would speed up analysis while still giving the same results, but MultiQC won't perfom on this one with the following error :

MultiQC Error log:

WARN: Access to undefined parameter `genomes` -- Initialise it to a default value eg. `params.genomes = some_value`
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/hic v1.2.2
----------------------------------------------------
Pipeline Release  : master
Run Name          : elegant_stallman
Input             : /work/sbsuser/test/Dev_Hi-C/reads/Mais_Hi-C-Dovetail-MBS-F252-T937_050620_Novaseq_Dovetail/*_R{1,2}_1Million.fastq
splitFastq        : false
Fasta Ref         : /work/sbsuser/test/Dev_Hi-C/test_cedric/references/Zea_mays_reformatted.fasta
Restriction Motif : ^GATC
Ligation Motif    : GATCGATC
DNase Mode        : false
Remove Dup        : true
Remove MultiHits  : true
Min MAPQ          : 0
Min Fragment Size : 0
Max Fragment Size : 0
Min Insert Size   : 0
Max Insert Size   : 0
Min CIS dist      : 0
Maps resolution   : 1000000,500000
Max Memory        : 120 GB
Max CPUs          : 48
Max Time          : 4d
Output dir        : ./results
Working dir       : /work/sbsuser/test/roxane/nextflow/hi-c/NovaSeq-Mais-Subset/work
Container Engine  : singularity
Container         : nfcore/hic:1.2.2
Current home      : /home/sbsuser
Current user      : sbsuser
Current path      : /work/sbsuser/test/roxane/nextflow/hi-c/NovaSeq-Mais-Subset
Script dir        : /home/sbsuser/.nextflow/assets/nf-core/hic
Config Profile    : genotoul
Config Profile Description: The Genotoul cluster profile
Config Profile Contact: support.bioinfo.genotoul@inra.fr
Config Profile URL: http://bioinfo.genotoul.fr/
Config Files      : /home/sbsuser/.nextflow/config, /home/sbsuser/.nextflow/assets/nf-core/hic/nextflow.config, /work/sbsuser/test/roxane/nextflow/hi-c/NovaSeq-Mais-Subset/nextflow.config, /work/sbsuser/test/roxane/nextflow/hi-c/NovaSeq-Mais-Subset/nextflow.config
----------------------------------------------------
executor >  slurm (7)
executor >  slurm (22)
[96/9f23d5] process > get_software_versions    [100%] 1 of 1 ✔
[5e/874037] process > makeBowtie2Index         [100%] 1 of 1 ✔
[cc/e879be] process > makeChromSize            [100%] 1 of 1 ✔
[5f/337ade] process > getRestrictionFragments  [100%] 1 of 1 ✔
[fe/0e5a46] process > bowtie2_end_to_end       [100%] 2 of 2 ✔
[1a/62fba9] process > trim_reads               [100%] 2 of 2 ✔
executor >  slurm (22)
[96/9f23d5] process > get_software_versions    [100%] 1 of 1 ✔
[5e/874037] process > makeBowtie2Index         [100%] 1 of 1 ✔
[cc/e879be] process > makeChromSize            [100%] 1 of 1 ✔
[5f/337ade] process > getRestrictionFragments  [100%] 1 of 1 ✔
[fe/0e5a46] process > bowtie2_end_to_end       [100%] 2 of 2 ✔
[1a/62fba9] process > trim_reads               [100%] 2 of 2 ✔
[99/d078ba] process > bowtie2_on_trimmed_reads [100%] 2 of 2 ✔
executor >  slurm (22)
[96/9f23d5] process > get_software_versions    [100%] 1 of 1 ✔
[5e/874037] process > makeBowtie2Index         [100%] 1 of 1 ✔
[cc/e879be] process > makeChromSize            [100%] 1 of 1 ✔
[5f/337ade] process > getRestrictionFragments  [100%] 1 of 1 ✔
[fe/0e5a46] process > bowtie2_end_to_end       [100%] 2 of 2 ✔
[1a/62fba9] process > trim_reads               [100%] 2 of 2 ✔
[99/d078ba] process > bowtie2_on_trimmed_reads [100%] 2 of 2 ✔
executor >  slurm (22)
[96/9f23d5] process > get_software_versions    [100%] 1 of 1 ✔
[5e/874037] process > makeBowtie2Index         [100%] 1 of 1 ✔
[cc/e879be] process > makeChromSize            [100%] 1 of 1 ✔
[5f/337ade] process > getRestrictionFragments  [100%] 1 of 1 ✔
[fe/0e5a46] process > bowtie2_end_to_end       [100%] 2 of 2 ✔
[1a/62fba9] process > trim_reads               [100%] 2 of 2 ✔
[99/d078ba] process > bowtie2_on_trimmed_reads [100%] 2 of 2 ✔
executor >  slurm (22)
[96/9f23d5] process > get_software_versions    [100%] 1 of 1 ✔
[5e/874037] process > makeBowtie2Index         [100%] 1 of 1 ✔
[cc/e879be] process > makeChromSize            [100%] 1 of 1 ✔
[5f/337ade] process > getRestrictionFragments  [100%] 1 of 1 ✔
[fe/0e5a46] process > bowtie2_end_to_end       [100%] 2 of 2 ✔
[1a/62fba9] process > trim_reads               [100%] 2 of 2 ✔
[99/d078ba] process > bowtie2_on_trimmed_reads [100%] 2 of 2 ✔
[b5/0e7942] process > merge_mapping_steps      [100%] 2 of 2 ✔
[37/9645af] process > combine_mapped_files     [100%] 1 of 1 ✔
[8a/ff481d] process > get_valid_interaction    [100%] 1 of 1 ✔
[92/2d8930] process > remove_duplicates        [100%] 1 of 1 ✔
[c8/26480b] process > merge_sample             [100%] 4 of 4 ✔
[-        ] process > build_contact_maps       -
[-        ] process > run_ice                  -
[15/47f607] process > generate_cool            [100%] 1 of 1 ✔
[78/974d38] process > multiqc                  [100%] 1 of 1, failed: 1 ✘
[0f/6b7253] process > output_documentation     [100%] 1 of 1 ✔
-[nf-core/hic] Pipeline completed with errors-
Error executing process > 'multiqc'

Caused by:
  Process `multiqc` terminated with an error exit status (1)

Command executed:

  multiqc -f   --config multiqc_config.yaml .

Command exit status:
  1

Command output:
  (empty)

Command error:
  [WARNING]         multiqc : MultiQC Version v1.9 now available!
  [INFO   ]         multiqc : This is MultiQC v1.8
  [INFO   ]         multiqc : Template    : default
  [INFO   ]         multiqc : Searching   : /work/sbsuser/test/roxane/nextflow/hi-c/NovaSeq-Mais-Subset/work/78/974d381edc8e177b9d40b2dd6d704e
  [INFO   ]  custom_content : nf-core-chipseq-summary: Found 1 sample (html)
  [INFO   ]  custom_content : nf-core-chipseq-summary: Found 2751 samples (html)
  [INFO   ]  custom_content : software_versions: Found 1 sample (html)
  [INFO   ]  custom_content : software_versions: Found 432 samples (html)
  [ERROR  ]         multiqc : Oops! The 'hicpro' MultiQC module broke...
    Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
    If possible, please include a log file that triggers the error - the last file found was:
      ./input_4/mstats/Mais-MBS847-Dovetail_AGTTCAGG-CCAACAGA-AHHMY2DRXX_L001Million/Mais-MBS847-Dovetail_AGTTCAGG-CCAACAGA-AHHMY2DRXX_L001_1Million.mRSstat
  ============================================================
  Module hicpro raised an exception: Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-hic-1.2.2/lib/python3.7/site-packages/multiqc/multiqc.py", line 546, in run
      output = mod()
    File "/opt/conda/envs/nf-core-hic-1.2.2/lib/python3.7/site-packages/multiqc/modules/hicpro/hicpro.py", line 41, in __init__
      data['percent_mapped_R2'] = float(data['mapped_R2']) / float(data['total_R2']) * 100.0
  KeyError: 'mapped_R2'
  ============================================================
  [INFO   ]         multiqc : Compressing plot data
  [INFO   ]         multiqc : Report      : multiqc_report.html
  [INFO   ]         multiqc : Data        : multiqc_data
  [INFO   ]         multiqc : Plots       : multiqc_plots
  [INFO   ]         multiqc : MultiQC complete

Work dir:
  /work/sbsuser/test/roxane/nextflow/hi-c/NovaSeq-Mais-Subset/work/78/974d381edc8e177b9d40b2dd6d704e

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

File that triggers the error:

MultiQC run details (please complete the following):

• Command used to run MultiQC:
• MultiQC Version: MultiQC v1.8
• Operating System: Node on slurm, I don't really know what is behind :s
• Python Version: It is not specified in the multiQC report of hi-c pipelines that previously worked
• Method of MultiQC installation: Again, no idea, MultiQC was installed on the cluster indepentely (V1.7) but the one used here is from the nf-core pipeline (1.8) so it should have been installed via nextflow : v20.01.0

Additional context

It seems it actually created something as I go into the directory where the error occured, we can see a multi_qc report in there but he is an empty page with just the versions.

[ewels]

Hi @RxLoutre,

Sorry to hear that you're having problems. Would it be possible to attach the file that triggered the error so that I can try to replicate it?

You can see the (probable) path in the error log:

If possible, please include a log file that triggers the error - the last file found was:
./input_4/mstats/Mais-MBS847-Dovetail_AGTTCAGG-CCAACAGA-AHHMY2DRXX_L001Million/Mais-MBS847-Dovetail_AGTTCAGG-CCAACAGA-AHHMY2DRXX_L001_1Million.mRSstat

Thanks,

Phil

[ewels]

Closing due to lack of example file to replicate the error.

[jzohren]

Hi Phil,

I encountered the same error as @RxLoutre earlier this year when I tried to run the nf-core/hic:1.3.0 pipeline:

nf-core/hic execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'multiqc'

Caused by:
  Process `multiqc` terminated with an error exit status (1)

Command executed:

  multiqc -f    .

Command exit status:
  1

Command output:
  |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 15/15  

Command error:
  
    /// MultiQC 🔍 | v1.11
  
  |           multiqc | Search path : /camp/lab/turnerj/working/jasmin/manuscript/analysis/nf-core/hic/run211129/work/22/b198ac15e9f3e90d5aca44ac40f716
  |    custom_content | software_versions: Found 1 sample (html)
  ╭───────────────── Oops! The 'hicpro' MultiQC module broke... ─────────────────╮
  │ Please copy this log and report it at                                        │
  │ https://github.com/ewels/MultiQC/issues                                      │
  │ Please attach a file that triggers the error. The last file found was:       │
  │ ./input_4/stats/PRD_Pdev031_S9_L001/PRD_Pdev_2031_S9_L001.mRSstat            │
  │                                                                              │
  │ Traceback (most recent call last):                                           │
  │   File "/usr/local/lib/python3.9/site-packages/multiqc/multiqc.py", line 624 │
  │     output = mod()                                                           │
  │   File "/usr/local/lib/python3.9/site-packages/multiqc/modules/hicpro/hicpro │
  │     data["duplicates"] = data["valid_interaction"] - data["valid_interaction │
  │ KeyError: 'valid_interaction'                                                │
  │                                                                              │
  ╰──────────────────────────────────────────────────────────────────────────────╯
  |           multiqc | Compressing plot data
  |           multiqc | Report      : multiqc_report.html
  |           multiqc | Data        : multiqc_data
  |           multiqc | Plots       : multiqc_plots
  |           multiqc | MultiQC complete

I didn't encounter this when I ran the pipeline with the test profile, so I wonder whether it has something to do with my data. I've attached the file that triggered this (I had to append the txt otherwise github wouldn't let me upload it).
PRD_Pdev_2031_S9_L001.mRSstat.txt

Thanks a lot for your help!

[jzohren]

Hi @ewels and @RxLoutre,

Just wanted to let you know that I now know what caused this issue. With the help from @nservant, we discovered that a "_1" or "_2" in the filename will be treated as a suffix for read 1/2 files. This causes incorrect filenames along the way, which means that multiqc can't find all files it's looking for.
I have simply renamed my input files and now the pipeline ran without any problems. Nicolas said this should be fixed in the next release of nf-core/hic.

Best wishes,
Jasmin

[ewels]

Thanks @jzohren! Great that you got it to work. However, MultiQC shouldn't really have an unhandled crash like this, whatever you did. As you've provided a file to replicate the problem I've reopened the issue.

[ewels]

Ok, I've added a bunch of error handling to try to catch these errors. It doesn't really fix the problem as such, but the module at least keeps going so you get a report with something there. It hopefully also makes debugging a little easier:

Thanks for reporting!