PBjelly2 failes at output step

Urmi Trivedi — Tue, 16 May 2017 08:46:11 -0000

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

PBjelly2 failes at output step

Adam English — Fri, 27 Jan 2017 19:02:21 -0000

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.

PBjelly2 failes at output step

Christian — Wed, 18 Jan 2017 11:12:10 -0000

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'

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

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