PBjelly2 failes at output step

Hi,

I'm running PBjelly version 15.8.24. Collection.py run for 5 days (630k assembly folders) when it finally crashed while writing the final contigs. These are the last few lines of output.err:

2017-01-17 23:23:57,350 [DEBUG] Getting fill sequence for ref0161811e5_ref0980136e3
2017-01-17 23:23:57,350 [DEBUG] fill span
2017-01-17 23:23:57,350 [DEBUG] Moving from ref0980136e3 to ref0980136.1e5 (p=1)
2017-01-17 23:23:57,350 [DEBUG] contig
2017-01-17 23:23:57,350 [DEBUG] who? ref0980136.1e5 ref0980136e3
2017-01-17 23:23:57,350 [DEBUG] Grabbing contig between nodes ref0980136.1e5 & ref0980136e3 - [trim 0, 0]
2017-01-17 23:23:57,350 [DEBUG] contig 919 to 7804
2017-01-17 23:23:57,350 [DEBUG] trimming 0 and 0
2017-01-17 23:23:57,351 [DEBUG] Moving from ref0980136.1e5 to ref0980136.0e3 (p=1)
2017-01-17 23:23:57,501 [DEBUG] improved gap
2017-01-17 23:23:57,501 [DEBUG] Getting fill sequence for ref0980136.0e3_ref0980136.1e5
2017-01-17 23:23:57,501 [DEBUG] No predicted gap size
Traceback (most recent call last):
File "/ctx/software/PBSuite_15.8.24/bin/Collection.py", line 963, in <module>
c.run()
File "/ctx/software/PBSuite_15.8.24/bin/Collection.py", line 923, in run
self.outputContigs()
File "/ctx/software/PBSuite_15.8.24/bin/Collection.py", line 817, in outputContigs
seq.reverseCompliment()
AttributeError: 'NoneType' object has no attribute 'reverseCompliment'</module>

Any idea want went wrong?
Debugging will probably be a huge pain due to the runtime of the output stage. Is it possible to write some kind of temporary files that stores intermediate results from this stage?

Thanks,
Chris

Could you look in the folder for the assembly/ref0980136.0e3_ref0980136.1e5 and see what's there? Should maybe be some logs or sequence files or jsons. Something about that particular assembly is breaking the pipeline.

Hello Chris and Adam,
I am facing same error.

2017-05-09 11:18:44,904 [DEBUG] Getting fill sequence for ref0004924.2e3_ref0004924.3e5
2017-05-09 11:18:44,904 [DEBUG] No predicted gap size
Traceback (most recent call last):
  File "/lustre/software/PBSuite_15.8.24/bin/Collection.py", line 963, in <module>
    c.run()
  File "/lustre/software/PBSuite_15.8.24/bin/Collection.py", line 923, in run
    self.outputContigs()
  File "/lustre/software/PBSuite_15.8.24/bin/Collection.py", line 818, in outputContigs
    liftTracker.append((name, strand, len(seq.seq)))
AttributeError: 'NoneType' object has no attribute 'seq'

It will be very helpful if you could share your ideas to fix this.
Many thanks