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
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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))
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
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
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
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