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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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ipdSummary error "M5" #67

Closed jgonzalez10 closed 5 years ago

jgonzalez10 commented 5 years ago

Hi, I'm having trouble with ipdSummary too. The error I'm getting it the following:

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 198, in init self._loadReferenceInfo() File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 73, in _loadReferenceInfo refMD5s = [r["M5"] for r in refRecords] KeyError: 'M5' 2019-05-15 15:55:15,219 [ERROR] 'M5' 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 198, in init self._loadReferenceInfo() File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 73, in _loadReferenceInfo refMD5s = [r["M5"] for r in refRecords] KeyError: 'M5'

Does somebody know what's happening??? Heeelp please!!! Thanks!!!!

natechols commented 5 years ago

How was the aligned BAM file generated?

jgonzalez10 commented 5 years ago

Hi,

As far as I know with Blasr.

natechols commented 5 years ago

Which version of Blasr, and what was the full command?

jgonzalez10 commented 5 years ago

Sorry, I already checked and they were done with pbmm2, an interface of minimap2 used to align PacBio reads along with the kinetics info. I don’t have the exact command because this is a multi person project and I’m just in charge of the base modificactions analysis. Can you help me?

natechols commented 5 years ago

I think you need to update to the latest pbcore - the M5 requirement has been removed there.

jgonzalez10 commented 5 years ago

And how can I do that?

natechols commented 5 years ago

This depends on how pbcore is installed. I recommend using the pbbioconda distribution: https://github.com/PacificBiosciences/pbbioconda

jgonzalez10 commented 5 years ago

I installed all the smrtlink suite in a virtual machine. Therefore I would need a way tu update that. Unless you are suggesting me to install this via conda and try and use it instead of smrtlink?