Oops! The 'qorts' MultiQC module broke...

[nickluscombe]

$ multiqc --ignore ERR* --dirs QoRTs_output/ --filename multiQC_align
[INFO   ]         multiqc : This is MultiQC v1.6
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Prepending directory to sample names
[INFO   ]         multiqc : Searching 'QoRTs_output/'
Searching 34 files..  [####################################]  100%
[ERROR  ]         multiqc : Oops! The 'qorts' 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:
    QoRTs_output/QC.summary.txt
============================================================
Module qorts raised an exception: Traceback (most recent call last):
  File "/Users/luscomn/anaconda3/envs/bioinfo/bin/multiqc", line 440, in multiqc
    output = mod()
  File "/Users/luscomn/anaconda3/envs/bioinfo/lib/python3.5/site-packages/multiqc/modules/qorts/qorts.py", line 30, in __init__
    self.parse_qorts(f)
  File "/Users/luscomn/anaconda3/envs/bioinfo/lib/python3.5/site-packages/multiqc/modules/qorts/qorts.py", line 68, in parse_qorts
    self.qorts_data[s_name][s[0]] = float(s[i+1])
ValueError: could not convert string to float: 'Code for the strandedness rule used. 0 if data is unstranded, 1 if data is fr_firstStrand, 2 if data is fr_secondStrand.\n'
============================================================
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

(bioinfo)
QC.summary.txt

[ewels]

Hi @nickluscombe,

Sorry it's taken me so long to get to this. Now I'm here, I'm pretty confused though. When I run MultiQC with your file, it works fine without any errors. Looking at the code history, your error looks basically identical to #639 - this was fixed in 62fe089 back in December, which went out in MultiQC v1.4.

Your log says that you're running MultiQC 1.6, so it should be fine if it's the same problem. How do you have MultiQC installed? Is there something strange going on with your installation? My first port of call would be to try reinstalling.

Phil

[ewels]

Closing as I cannot reproduce the error.

[jkokosar]

@ewels I've bumped into the same issue. The problem seem to be the parse_qorts() not properly handling the use of --dirs parameter.

[ewels]

Thanks @jkokosar - do you have a file I can reproduce this with? I don't get the same error, even with basically the exact command used above:

$ ls
QC.summary.txt

$ multiqc --ignore ERR* --dirs . --filename multiQC_align
[INFO   ]         multiqc : This is MultiQC v1.7.dev0 (12f519c)
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Prepending directory to sample names
[INFO   ]         multiqc : Searching '.'
Searching 1 files..  [####################################]  100%
[INFO   ]           qorts : Found 1 logs
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiQC_align.html
[INFO   ]         multiqc : Data        : multiQC_align_data
[INFO   ]         multiqc : MultiQC complete

[jkokosar]

@ewels you can use the file already attached to the issue - just add it to a subfolder, one level down from where you make a multiqc call.

(multiqc) mac qorts$ ls
example_folder
(multiqc) mac qorts$ ls example_folder/
QC.summary.txt
(multiqc) mac qorts$ multiqc --ignore ERR* --dirs . --filename multiQC_align
[INFO   ]         multiqc : This is MultiQC v1.7
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Prepending directory to sample names
[INFO   ]         multiqc : Searching '.'
[ERROR  ]         multiqc : Oops! The 'qorts' 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:
    ./example_folder/QC.summary.txt
============================================================
Module qorts raised an exception: Traceback (most recent call last):
  File "/Users/janez/virtualenvs/multiqc/bin/multiqc", line 440, in multiqc
    output = mod()
  File "/Users/janez/virtualenvs/multiqc/lib/python3.7/site-packages/multiqc/modules/qorts/qorts.py", line 30, in __init__
    self.parse_qorts(f)
  File "/Users/janez/virtualenvs/multiqc/lib/python3.7/site-packages/multiqc/modules/qorts/qorts.py", line 68, in parse_qorts
    self.qorts_data[s_name][s[0]] = float(s[i+1])
ValueError: could not convert string to float: 'Code for the strandedness rule used. 0 if data is unstranded, 1 if data is fr_firstStrand, 2 if data is fr_secondStrand.\n'
============================================================
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

[ewels]

Ahhh, I didn't have it in a subfolder - thanks! 👍

[ewels]

Hi all,

This should now work in the latest v1.8dev of MultiQC. If you could give it a spin to confirm that would be great.. Thanks!

Phil

[jkokosar]

Works for me! Thank you!

[hreinwal]

Hi Phil,
I am using MultiQC 1.7 and qorts 1.3.0 and I just ran in the same error message as posted above. Thanks for making such a quick fix - however I am having problems installing Multiqc 1.8 via conda.
Could you provide some guidelines on how to get the 1.8dev version to run?

I checked via conda search multiqc and the latest available packages are the following:

multiqc  1.6a0  py36h24bf2e0_1  bioconda            
multiqc                        1.6a0  py36h24bf2e0_2  bioconda            
multiqc                          1.6  py27h24bf2e0_0  bioconda            
multiqc                          1.6  py35h24bf2e0_0  bioconda            
multiqc                          1.6  py36h24bf2e0_0  bioconda            
multiqc                          1.7            py_0  bioconda            
multiqc                          1.7            py_1  bioconda            
multiqc                          1.7            py_2  bioconda            
multiqc                          1.7            py_3  bioconda            
multiqc                          1.7            py_4  bioconda

Best,
Hannes

[sdjebali]

Dear all,
I am having the same error with multiqc 1.9 when I run the nf core atacseq pipeline with very lowly sequenced data

here is the trace that follows the error

 [ERROR  ]         multiqc : Oops! The 'deeptools' 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:
       ./deeptools/liver_R138.mLb.clN.plotProfile.tab
 ============================================================
   Module deeptools raised an exception: Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-atacseq-1.2.1/lib/python3.7/site-packages/multiqc/multiqc.py", line 569, in run
      output = mod()
    File "/opt/conda/envs/nf-core-atacseq-1.2.1/lib/python3.7/site-packages/multiqc/modules/deeptools/deeptools.py", line 74, in __init__
      n['plotProfile'] = self.parse_plotProfile()
    File "/opt/conda/envs/nf-core-atacseq-1.2.1/lib/python3.7/site-packages/multiqc/modules/deeptools/plotProfile.py", line 17, in parse_plotProfile
      parsed_data, bin_labels, converted_bin_labels = self.parsePlotProfileData(f)
    File "/opt/conda/envs/nf-core-atacseq-1.2.1/lib/python3.7/site-packages/multiqc/modules/deeptools/plotProfile.py", line 111, in parsePlotProfileData
      d[s_name].update({converted_bin_labels[i-1]:float(cols[i+1])})
  ValueError: could not convert string to float: '--'
  ============================================================
  [INFO   ]        samtools : Found 2 stats reports
  [INFO   ]        samtools : Found 2 flagstat reports
  [INFO   ]        samtools : Found 2 idxstats reports
  [INFO   ]          picard : Found 2 MarkDuplicates reports
  [INFO   ]         multiqc : Compressing plot data
  [INFO   ]         multiqc : Report      : multiqc_report.html
  [INFO   ]         multiqc : Data        : multiqc_data
  [INFO   ]         multiqc : MultiQC complete

As I understand the ./deeptools/liver_R138.mLb.clN.plotProfile.tab file (that I cannot attach here because its format is not supported) has--strings that cannot be converted to floats. It may be due to the fact that this samples has very very few reads but it would be good not to have a complete fail of the pipeline for this reason ?

Let me know if this is not the right place to post this issue.

Thanks,