Need help in running quiver

[julio514]

Dear PacBio community,
Instead of running smrtpipe to run hgap, I started to run each steps separately. All goes well up until the quiver step. So bacically, I ran, BLASR, converted SAM output file to .cmp.h5 and sorted it. Any elp would be appreciated.

 quiver -v -j8 \
 /path/to/aln.cmp.h5 \
 -r /path/to/filtered_subreads.fa \
 -o /path/to/corrected_variants.gff \
 -o /path/to/corrected.fa \ 

Here is the output:

2013-11-07 16:42:01,534 [INFO] h5py version: 2.0.1
2013-11-07 16:42:01,534 [INFO] hdf5 version: 1.8.4
2013-11-07 16:42:01,535 [INFO] ConsensusCore version: 0.6.0
2013-11-07 16:42:01,535 [INFO] Starting.
Traceback (most recent call last):
  File "/path/to/software/smrtanalysis/analysis/bin/variantCaller.py", line 5, in <module>
    pkg_resources.run_script('GenomicConsensus==0.6.0', 'variantCaller.py')
  File "build/bdist.linux-i686/egg/pkg_resources.py", line 489, in run_script
    keys.append(dist.key)
  File "build/bdist.linux-i686/egg/pkg_resources.py", line 1207, in run_script
    def __init__(self,module):
  File "/path/to/software/smrtanalysis-2.0.1/analysis/lib/python2.7/GenomicConsensus-0.6.0-py2.7.egg/EGG-INFO/scripts/variantCaller.py", line 346, in <module>
    sys.exit(ToolRunner().main())
  File "/path/to/software/smrtanalysis-2.0.1/analysis/lib/python2.7/GenomicConsensus-0.6.0-py2.7.egg/EGG-INFO/scripts/variantCaller.py", line 282, in main
    with CmpH5Reader(options.inputFilename) as peekCmpH5:
  File "/path/to/software/smrtanalysis/analysis/lib/python2.7/pbcore-0.6.0-py2.7.egg/pbcore/io/CmpH5Reader.py", line 769, in __init__
    self._readLocatorById[refId] = makeReadLocator(self, refId)
  File "/path/to/software/smrtanalysis/analysis/lib/python2.7/pbcore-0.6.0-py2.7.egg/pbcore/io/rangeQueries.py", line 138, in makeReadLocator
    offStart, offEnd = offsets[offsets[:,0] == refSeq, 1:3].ravel()
ValueError: need more than 0 values to unpack

[rhall]

blasr -> SAM -> cmp.h5 is the problem. To create a cmp.h5 compatible with quiver the easiest approach is to use pbalign (which calls blasr) with the '--forQuiver' option.

https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst