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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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KeyError: 'FRAMERATEHZ' #66

Open istolarek opened 5 years ago

istolarek commented 5 years ago

I have aligned P4C2 pacbio data with blasr sorted bam file with samtools and indexed with pbindex

after running ipdSummary I get the following error:

'FRAMERATEHZ' Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/pbcommand/cli/core.py", line 136, in _pacbio_main_runner return_code = exe_main_func(*args, kwargs) File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 719, in args_runner return kt.start() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 393, in start return self.run() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 455, in run ret = self._mainLoop() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 626, in _mainLoop self.loadSharedAlignmentSet(self.args.alignment_set) File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 602, in loadSharedAlignmentSet referenceFastaFname=self.args.reference) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2551, in init super(AlignmentSet, self).init(*files, *kwargs) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1876, in init super(ReadSet, self).init(files, kwargs) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 470, in init self.updateCounts() File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2392, in updateCounts self.assertIndexed() File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2193, in assertIndexed self._assertIndexed((IndexedBamReader, CmpH5Reader)) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1833, in _assertIndexed self._openFiles() File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1953, in _openFiles resource = IndexedBamReader(location) File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 385, in init super(IndexedBamReader, self).init(fname, referenceFastaFname) File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 199, in init self._loadReadGroupInfo() File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 116, in _loadReadGroupInfo rgFrameRate = ds["FRAMERATEHZ"] KeyError: 'FRAMERATEHZ' 2019-03-12 09:32:30,684 [ERROR] 'FRAMERATEHZ' Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/pbcommand/cli/core.py", line 136, in _pacbio_main_runner return_code = exe_main_func(*args, kwargs) File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 719, in args_runner return kt.start() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 393, in start return self.run() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 455, in run ret = self._mainLoop() File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 626, in _mainLoop self.loadSharedAlignmentSet(self.args.alignment_set) File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 602, in loadSharedAlignmentSet referenceFastaFname=self.args.reference) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2551, in init super(AlignmentSet, self).init(*files, *kwargs) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1876, in init super(ReadSet, self).init(files, kwargs) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 470, in init self.updateCounts() File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2392, in updateCounts self.assertIndexed() File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2193, in assertIndexed self._assertIndexed((IndexedBamReader, CmpH5Reader)) File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1833, in _assertIndexed self._openFiles() File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1953, in _openFiles resource = IndexedBamReader(location) File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 385, in init super(IndexedBamReader, self).init(fname, referenceFastaFname) File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 199, in init self._loadReadGroupInfo() File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 116, in _loadReadGroupInfo rgFrameRate = ds["FRAMERATEHZ"] KeyError: 'FRAMERATEHZ'

weedcentipede commented 5 years ago

For correcting this error you have to extract .bam file from .bax.h5 files (please refer to bax2bam), then you could use blasr (There other programs to do this) to align the reads against a reference with the previous extracted bam as input reads.

For further info see issue #58