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  • SMRT Tools ipdSummary Error

    Hello everyone,

    I downloaded the latest version of the SMRT Link software (8.0.0.80529) and I am trying to run the ipdSummary tool of the SMRT Tools. We obtained PacBio Sequel II sequencing data of a sample and a control without the modifications in question.

    I aligned both sequencing sets to the reference genome using pbmm2. Then, I tried to run the following command:

    Code:
    ipdSummary --reference reference_Genome.fasta --outfile mod_test --control control.alignmentset.xml sample.alignmentset.xml
    Unfortunately I receive this error and I have been unable to fix it myself:

    Code:
    Process KineticsWriter-2:
    
    Traceback (most recent call last):
    
      File "/work/project/ladsie_002/smrtlink/install/smrtlink-release_8.0.0.80529/bundles/smrttools/install/smrttools-release_8.0.0.80502/private/thirdparty/python/python_2.7.16/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap
    
        self.run()
    
      File "/work/project/ladsie_002/smrtlink/install/smrtlink-release_8.0.0.80529/bundles/smrttools/install/smrttools-release_8.0.0.80502/private/thirdparty/python/python_2.7.16/site-packages/kineticsTools/ResultWriter.py", line 116, in run
    
        self._run()
    
      File "/work/project/ladsie_002/smrtlink/install/smrtlink-release_8.0.0.80529/bundles/smrttools/install/smrttools-release_8.0.0.80502/private/thirdparty/python/python_2.7.16/site-packages/kineticsTools/ResultWriter.py", line 101, in _run
    
        self.onResult(nextChunk)
    
      File "/work/project/ladsie_002/smrtlink/install/smrtlink-release_8.0.0.80529/bundles/smrttools/install/smrttools-release_8.0.0.80502/private/thirdparty/python/python_2.7.16/site-packages/kineticsTools/ResultWriter.py", line 952, in onResult
    
        sink.send(resultChunk)
    
      File "/work/project/ladsie_002/smrtlink/install/smrtlink-release_8.0.0.80529/bundles/smrttools/install/smrttools-release_8.0.0.80502/private/thirdparty/python/python_2.7.16/site-packages/kineticsTools/ResultWriter.py", line 583, in alt_hdf5CsvConsumer
    
        tMean[idx] += float(x['tMean'])
    
    KeyError: 'tMean'
    When I run the command without specifying a custom control with --control, I do not receive this error. However, we are looking for modifications that are not in the in silico database, hence we sequenced both a sample and a control.
    I would be grateful for any support.

  • #2
    I would like to run the smrt tools package (on a mac). Has there been any improvement in using this tool outside of a smrt link setup? I think many people have old pacbio data they would like to analyse but cannot access a running smrt link setup.

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