I am trying to run Quiver I get this error

[Subhi]

I am trying to run Quiver :
However I get the following error, my input is a bam file and reference.fasta file.

Running job quiver-lv (7370641) on
'HD'
Traceback (most recent call last):
File "/home/l/python2.7/lib/python2.7/site-packages/pbcommand-0.6.1-py2.7.egg/pbcommand/cli/core.py", line 136, in _pacbio_main_runner
return_code = exe_main_func(*args, **kwargs)
File "/home/l/python2.7/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/main.py", line 381, in args_runner
return tr.main()
File "/home/l/python2.7/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/main.py", line 297, in main
with AlignmentSet(options.inputFilename) as peekFile:
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2649, in init
super(AlignmentSet, self).init(*files, **kwargs)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 1936, in init
super(ReadSet, self).init(*files, **kwargs)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 477, in init
self.updateCounts()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2490, in updateCounts
self.assertIndexed()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2320, in assertIndexed
self._assertIndexed((IndexedBamReader, CmpH5Reader))
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 1893, in _assertIndexed
self._openFiles()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2017, in _openFiles
resource = IndexedBamReader(location)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 385, in init
super(IndexedBamReader, self).init(fname, referenceFastaFname)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 196, in init
self._checkFileCompatibility()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 185, in _checkFileCompatibility
checkedVersion = self.version
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 271, in version
return self.peer.header["HD"]["pb"]
KeyError: 'HD'
[ERROR] 'HD'
Traceback (most recent call last):
File "/home/l/python2.7/lib/python2.7/site-packages/pbcommand-0.6.1-py2.7.egg/pbcommand/cli/core.py", line 136, in _pacbio_main_runner
return_code = exe_main_func(*args, **kwargs)
File "/home/l/python2.7/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/main.py", line 381, in args_runner
return tr.main()
File "/home/l/python2.7/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/main.py", line 297, in main
with AlignmentSet(options.inputFilename) as peekFile:
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2649, in init
super(AlignmentSet, self).init(*files, **kwargs)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 1936, in init
super(ReadSet, self).init(*files, **kwargs)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 477, in init
self.updateCounts()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2490, in updateCounts
self.assertIndexed()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2320, in assertIndexed
self._assertIndexed((IndexedBamReader, CmpH5Reader))
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 1893, in _assertIndexed
self._openFiles()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/dataset/DataSetIO.py", line 2017, in _openFiles
resource = IndexedBamReader(location)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 385, in init
super(IndexedBamReader, self).init(fname, referenceFastaFname)
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 196, in init
self._checkFileCompatibility()
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 185, in _checkFileCompatibility
checkedVersion = self.version
File "/home/l/python2.7/lib/python2.7/site-packages/pbcore-1.4.0-py2.7.egg/pbcore/io/align/BamIO.py", line 271, in version
return self.peer.header["HD"]["pb"]
KeyError: 'HD'

[mdsmith]

Hi Subhi, what did you use to generate your bam file? It looks like it has a malformed header. Can you post the header here?

[pb-dseifert]

RSII support has been removed.