SMRT Tools ipdSummary Error

[bgbrink]

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:

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:

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.

[Mike DS]

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.