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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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KeyError: 'Ipd' #78

Closed nick-youngblut closed 4 years ago

nick-youngblut commented 4 years ago

I'm running ipdSummary (smrtlink-release_9.0.0.92188) and getting the following error: 

KeyError: 'Ipd'
Child process exited with exitcode=1.  Aborting.

The command that I'm using:

smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/smrtcmds/bin/ipdSummary \
  --identify m6A,m4C --methylFraction    \
  --numWorkers 8           --maxCoverage 0   \
  --log-file tests/output_JM2/kinetic/ipdSummary/ccs/cov0/MT14.log   \
  --gff tests/output_JM2/kinetic/ipdSummary/ccs/cov0/MT14.gff  \
  --csv tests/output_JM2/kinetic/ipdSummary/ccs/cov0/MT14.csv \
  --reference /ebio/abt3_scratch/nyoungblut/LLMETH_105232212974/faidx/reference.fasta \      
  /ebio/abt3_scratch/nyoungblut/LLMETH_105232212974/pbmm2/ccs/MT14.bam

My full output:

Process KineticWorkerProcess-3:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Process KineticWorkerProcess-4:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Process KineticWorkerProcess-2:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Process KineticWorkerProcess-1:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Process KineticWorkerProcess-8:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Process KineticWorkerProcess-7:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Process KineticWorkerProcess-5:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Process KineticWorkerProcess-6:
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 151, in run
    self._run()
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/WorkerProcess.py", line 128, in _run
    datum)  # pylint: disable=assignment-from-none
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 122, in onChunk
    (padStart, padEnd), self.options.methylFraction, self.options.identify)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 231, in _summarizeReferenceRegion
    caseReferenceGroupId, targetBounds, self.caseAlignments)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks
    rawIpds = self._loadRawIpds(hits, start, end, factor)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds
    rawIpd = aln.IPD() * factor
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 47, in f
    return self.baseFeature(featureName, aligned, orientation)
  File "/ebio/abt3_projects/software/bin/smrtlink/install/smrtlink-release_9.0.0.92188/bundles/smrttools/install/smrttools-release_9.0.0.92188/private/thirdparty/python3/python3_3.7.3/site-packages/pbcore/io/align/BamAlignment.py", line 469, in baseFeature
    concreteFeatureName = self.bam._baseFeatureNameMappings[self.qId][featureName]
KeyError: 'Ipd'
Child process exited with exitcode=1.  Aborting.

My conda env:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
certifi                   2020.6.20        py38h32f6830_0    conda-forge
htslib                    1.10.2               hd3b49d5_1    bioconda
krb5                      1.17.1               hfafb76e_1    conda-forge
ld_impl_linux-64          2.34                 h53a641e_7    conda-forge
libcurl                   7.71.1               hcdd3856_2    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         h46ee950_1    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libssh2                   1.9.0                hab1572f_3    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
ncurses                   6.2                  he1b5a44_1    conda-forge
openjdk                   11.0.1            h516909a_1016    conda-forge
openssl                   1.1.1g               h516909a_0    conda-forge
pbbam                     1.3.0                h5b7e6e0_1    bioconda
pbgcpp                    1.9.0                         0    bioconda
pbmm2                     1.3.0                h56fc30b_1    bioconda
pigz                      2.3.4                hed695b0_1    conda-forge
pilon                     1.23                          2    bioconda
pip                       20.1.1                     py_1    conda-forge
python                    3.8.3           cpython_he5300dc_0    conda-forge
python_abi                3.8                      1_cp38    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
setuptools                49.2.0           py38h32f6830_0    conda-forge
sqlite                    3.32.3               hcee41ef_1    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
wheel                     0.34.2                     py_1    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
natechols commented 4 years ago

The BAM file is missing the kinetics information. Looking at the CLI arguments, it seems like maybe the BAM is actually CCS data - is this correct?

nick-youngblut commented 4 years ago

The BAM is CCS data created by ccs, but that's still BAM format, which is the possible input for ipdSummary according to the script docs:

positional arguments:
  alignment_set         BAM or Alignment DataSet

Is the input actually more restrictive than stated in the docs? Maybe an explicit check for whether the input bam file includes kinetic info would be helpful?

natechols commented 4 years ago

Only mapped subreads are currently supported - CCS data are missing the essential fields.