Error running PBJelly

Question

[mks002]

dear all, While running Pbjelly, I am getting error at extraction level. Can anyone please help out to work this thing

2

018-05-23 16:24:36,150 [INFO] Loaded 6445214 Reads
2018-05-23 16:24:41,994 [INFO] Parsed 338 Reads
Traceback (most recent call last):
  File "/usr/bin/Extraction.py", line 343, in <module>
    me.run()
  File "/usr/bin/Extraction.py", line 316, in run
    self.__extractReads__()
  File "/usr/bin/Extraction.py", line 220, in __extractReads__
    self.flushQueue(outputQueue)
  File "/usr/bin/Extraction.py", line 235, in flushQueue
    outFile = self.openGapOut(gapName)
  File "/usr/bin/Extraction.py", line 265, in openGapOut
    sequence = self.reference[flankName[:10]]
KeyError: 'size282107'

answers are most welcome

Answer 1

[Coryza]

I stumbled upon the exact same error just now. In the end the error leads back to executing an incorrect order of steps in PBJelly (most likely caused by incorrect (order of) indexing). I just re-did the analysis, after learning from my mistakes, and it went all just fine.