ipdSummary.py throws Attribute error

[qihualiang]

I am trying to run ipdSummary.py as
ipdSummary.py --reference ReferenceGenome.fasta example1.cmp.h5

But there are below error messages:

Traceback (most recent call last):
File "/home/qliang/0.soft/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/ipdSummary.py", line 715, in
sys.exit(main())
File "/home/qliang/0.soft/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/ipdSummary.py", line 692, in main
rcode = kt.start()
File "/home/qliang/0.soft/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/ipdSummary.py", line 342, in start
return self.run()
File "/home/qliang/0.soft/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/ipdSummary.py", line 405, in run
ret = self._mainLoop()
File "/home/qliang/0.soft/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/ipdSummary.py", line 619, in _mainLoop
self.loadReferenceAndModel(self.args.reference, self.args.infile)
File "/home/qliang/0.soft/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/ipdSummary.py", line 531, in loadReferenceAndModel
contigs = ReferenceUtils.loadReferenceContigs(referencePath, cmpH5Path)
File "/home/qliang/software/python/lib/python2.7/site-packages/kineticsTools-0.5.1-py2.7-linux-x86_64.egg/kineticsTools/ReferenceUtils.py", line 70, in loadReferenceContigs
for x in alignmentSet.referenceInfoTable:
AttributeError: 'str' object has no attribute 'referenceInfoTable'

Is this caused by the reference genome in FASTA format? or why?

[rhall]

I believe that the reference needs to be a formatted reference entry, including xml and and index files, which is generated using referenceUploader.py .

[qihualiang]

I believe that the reference needs to be a formatted reference entry, including xml and and index files, which is generated using referenceUploader.py .

Thank you!

But I have met new error messages moving on, and it seems to be within the .cmp.h5 file now.

File "/home/qliang/0.soft/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/ipdSummary.py", line 69, in _validateResource
raise IOError("Unable to find {p}".format(p=p))
IOError: Unable to find
: not foundg/malaria/6mA_detection/1.pbalign_result/new.1.m26_50_1.cmp.h5: 1: /home/qliang/malaria/6mA_detection/1.pbalign_result/new.1.m26_50_1.cmp.h5: ?HDF
/home/qliang/malaria/6mA_detection/1.pbalign_result/new.1.m26_50_1.cmp.h5: 2: /home/qliang/malaria/6mA_detection/1.pbalign_result/new.1.m26_50_1.cmp.h5: : not found
/home/qliang/malaria/6mA_detection/1.pbalign_result/new.1.m26_50_1.cmp.h5: 1: /home/qliang/malaria/6mA_detection/1.pbalign_result/new.1.m26_50_1.cmp.h5: Syntax error: word unexpected (expecting ")")

[GenoMax]

@qihualiang: Even though Dr. Hall always steps up and provides support you can also directly contact PacBio tech support to get more immediate help with questions.