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Old 02-20-2020, 06:17 AM   #1
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Location: Germany

Join Date: Feb 2020
Posts: 1
Default SMRT Tools ipdSummary Error

Hello everyone,

I downloaded the latest version of the SMRT Link software ( 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/", line 267, in _bootstrap

  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/", line 116, in 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/", line 101, in _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/", line 952, in onResult


  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/", 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.
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