PBSuite_15.2.20 Jelly.py output error

[Gunnar Hönig]

Hello,

I set up PBSuite_15.2.20 as stated in the documentation. I could run all steps with the test file, but get the following error with my own files in the last step (output):

2015-02-26 14:27:55,005 [DEBUG] Moving from ref0000004.50e5 to ref0000004.49e3 (p=1)
2015-02-26 14:27:55,005 [DEBUG] improved gap
2015-02-26 14:27:55,005 [DEBUG] Getting fill sequence for ref0000004.49e3_ref0000004.50e5
Traceback (most recent call last):
File "/home/gunnar/Programme/PBSuite_15.2.20//bin//Collection.py", line 949, in <module>
c.run()
File "/home/gunnar/Programme/PBSuite_15.2.20//bin//Collection.py", line 909, in run
self.outputContigs()
File "/home/gunnar/Programme/PBSuite_15.2.20//bin//Collection.py", line 792, in outputContigs
seq = data.getSequence()
File "/home/gunnar/Programme/PBSuite_15.2.20//bin//Collection.py", line 181, in getSequence
if gapLen < self.GAPINFLATE:
AttributeError: FillingMetrics instance has no attribute 'GAPINFLATE'

Thanks for your help.

[Paul B.]

I'm experiencing the EXACT issue that Gunnar describes above. I, too, can run the test data to completion with no problems. In other words, Jelly.py output / Collection.py seemed to work fine. However, now that I'm trying with my own data, it fails and I get the identical Traceback:

...
2015-02-26 09:23:03,586 [DEBUG] Getting fill sequence for ref0000032.0e3_ref0000032.1e5
Traceback (most recent call last):
File "/appl/PBSuite_15.2.20/bin/Collection.py", line 949, in <module>
c.run()
File "/appl/PBSuite_15.2.20/bin/Collection.py", line 909, in run
self.outputContigs()
File "/appl/PBSuite_15.2.20/bin/Collection.py", line 792, in outputContigs
seq = data.getSequence()
File "/appl/PBSuite_15.2.20/bin/Collection.py", line 181, in getSequence
if gapLen < self.GAPINFLATE:
AttributeError: FillingMetrics instance has no attribute 'GAPINFLATE'

The output stage seems to 'finish', but the output files jelly.out.fasta and jelly.out.qual are empty.

I'm currently using version PBSuite_15.2.20, networkx v1.1, python 2.7.6,

Many thanks for any help here!
Sincerely,
Paul

[Adam English]

This was a bug that our qc checks didn't catch before the version freeze.
I've uploaded a patched version in PBSuite_15.2.20.p1.tgz

[Paul B.]

Awesome - thanks Adam. Downloading now...

[Paul B.]

The patch works!! Thanks again, Adam!

[Gunnar Hönig]

Yes I just wanted to add my thanks. It is working now. Amazing reaction time.