PBJelly2 Extraction error

[Urmi Trivedi]

Hello,

I am running into an error at extraction stage for PBJelly2. Here are the details:

2016-10-18 10:40:41,972 [INFO] PBSuite_15.8.24/bin/Extraction.py protocol.xml
2016-10-18 10:41:26,575 [INFO] Opening GML Files
2016-10-18 10:41:26,577 [WARNING] It is unknown if networkx version 1.11 will work.
2016-10-18 10:41:26,577 [WARNING] If you get an error here, please report it!!!
2016-10-18 10:45:25,232 [INFO] Loading Reference Sequence
2016-10-18 11:00:51,937 [INFO] Extracting Reads
2016-10-18 11:00:51,946 [INFO] Parsing pacbio_filtered_subreads_gt500.fastq
2016-10-18 11:18:44,874 [INFO] Loaded 8059179 Reads
2016-10-18 11:18:50,565 [INFO] Flushing Output Queue of 20001 gaps 25018 reads
Traceback (most recent call last):
PBSuite_15.8.24/bin/Extraction.py", line 343, in <module>
me.run()
PBSuite_15.8.24/bin/Extraction.py", line 316, in run
self.extractReads()
PBSuite_15.8.24/bin/Extraction.py", line 212, in extractReads
self.flushQueue(outputQueue)
PBSuite_15.8.24/bin/Extraction.py", line 235, in flushQueue
outFile = self.openGapOut(gapName)
PBSuite_15.8.24/bin/Extraction.py", line 265, in openGapOut
sequence = self.reference[flankName[:10]]
KeyError: u'ref0203868'

Following the suggestions given in previous tickets, I replaced "|" by "_" but that didn't work. I checked the version of networkx and it is 1.11. Can this be the cause of problem? Here is my protocol.xml

<jellyProtocol>
<reference>platanus_scaffold_with_underscore.fasta</reference>
<outputDir>PBJelly2</outputDir>
<blasr>--minMatch 8 --minPctIdentity 70 --bestn 1 --nCandidates 20 --maxScore -500 --nproc 10 --noSplitSubreads</blasr>
<input baseDir="Input">
<job>filtered_subreads_gt500.fastq</job>
</input>
</jellyProtocol>

Many thanks for any help you can provide.

[Greg Cary]

Hello Urmi,

Were you able to address this error? I'm encountering one that is very similar and I'd be happy to hear anything that worked for you or even anything that you tried that was unsuccessful.

Thanks!
Greg

[Cristina Osuna]

Hi,

I had a similar error... Any clue of why this was happening?

I will appreciate any help!

Kinds Regards,

Cristina Osuna