SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
HISAT XS attribute timless Bioinformatics 5 03-26-2015 07:04 PM
HTSeq 'gene_id' attribute error meher Bioinformatics 17 11-15-2013 03:02 AM
BAM record error: found spliced alignment without XS attribute paolo.kunder Bioinformatics 0 09-06-2012 06:09 AM
Picard MarkDuplicates throws a java.lang.NegativeArraySizeException rdeborja Bioinformatics 0 01-21-2011 08:28 AM
Cufflinks, attribute not supported Anna Esteve Bioinformatics 2 07-27-2010 02:30 AM

Reply
 
Thread Tools
Old 02-09-2016, 09:11 AM   #1
qihualiang
Junior Member
 
Location: United States

Join Date: Jan 2015
Posts: 8
Default ipdSummary.py throws Attribute error

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?
qihualiang is offline   Reply With Quote
Old 02-10-2016, 10:51 AM   #2
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

I believe that the reference needs to be a formatted reference entry, including xml and and index files, which is generated using referenceUploader.py .
rhall is offline   Reply With Quote
Old 02-11-2016, 09:47 AM   #3
qihualiang
Junior Member
 
Location: United States

Join Date: Jan 2015
Posts: 8
Default

Quote:
Originally Posted by rhall View Post
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 ")")
qihualiang is offline   Reply With Quote
Old 02-11-2016, 10:54 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077
Default

@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.
GenoMax is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:09 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO