output error

[lfaino]

Dear Adam,
i get an error when i run the output stage.
the error is:

2014-01-15 15:23:04,902 [DEBUG] Getting fill sequence for ref0001860e3_ref0005597e3
2014-01-15 15:23:04,902 [DEBUG] fill span
2014-01-15 15:23:04,902 [INFO] NoFilling ref0001860e3_ref0005597e3
Traceback (most recent call last):
File "/home/luigi/bin/Jelly_13.10.22//bin/Collection.py", line 925, in <module>
c.run()
File "/home/luigi/bin/Jelly_13.10.22//bin/Collection.py", line 883, in run
self.cleanGraph()
File "/home/luigi/bin/Jelly_13.10.22//bin/Collection.py", line 527, in cleanGraph
mySpanScore
UnboundLocalError: local variable 'mySpanScore' referenced before assignment

I checked the Collection.py file and at the line 527 the script is:

if seq is None:
#I fixed this
logging.debug("About to Fail on %s (node: %s)" % (name, node))

                        #if len(seq.qual) == 0 or seq is None:
                        if len(seq.qual) == 0:
                            logging.info("NoFilling %s " % name)
                            myScoreSpan = 0
                            myScoreSeqs = 0

line 527 mySpanScore
else:
#myScore = data.contribBases / float(data.contribSeqs)
myScoreSpan = data.spanCount
myScoreSeqs = data.contribBases
mySpanScore = data.spanSeedScore
#sum([ord(y)-33 for y in seq.qual])/float(len(seq.qual))

however, if i change the line 527 in

mySpanScore = 0

the process goes finished succesfully but i do not know if the correction is rigth or not.

Can you please give me some more info about the error.

thanks

Luigi

[Aureliano Bombarely Gomez]

Dear Adam and Luigi,

I have the same problem just in case that can help to fix the problem.

2014-01-16 09:32:44,334 [DEBUG] Getting fill sequence for ref0009334e5_ref0057667e5
2014-01-16 09:32:44,335 [DEBUG] fill span
2014-01-16 09:32:44,335 [INFO] NoFilling ref0009334e5_ref0057667e5
Traceback (most recent call last):
File "/home/aure/Software/Jelly_13.10.22/bin//Collection.py", line 925, in <module>
c.run()
File "/home/aure/Software/Jelly_13.10.22/bin//Collection.py", line 883, in run
self.cleanGraph()
File "/home/aure/Software/Jelly_13.10.22/bin//Collection.py", line 527, in cleanGraph
mySpanScore
UnboundLocalError: local variable 'mySpanScore' referenced before assignment

Thank you in advance,

Best

Aureliano

[Adam English]

Would either of you be able to send me the gap-assembly directory you found the problem in? I'll recreate the errors and see what can be done to fix it.

ref0009334e5_ref0057667e5 for Aureliano
and
ref0001860e3_ref0005597e3 for Luigi

Thanks,
~/Adam English

[eernst]

Hi Adam,

I'm seeing the same thing in 14.1.14. Looks like line 527 in Collection.py should be an assignment, but there's just the bare variable "mySpanScore" (maybe should be mySpanScore = 0).

Best,
Evan