Using the test dataset included in the package, I have continued problems:
Mapping seems to work: produces alignments that look like this:
m130724_230321_00121_c100518582550000001823079209281361_s1_p0/116034/3824_6124 lambda_NEB3011_1|ref0000001 -720 72.7848 0 6 278 2300 1 2128 2423 28380 50
When I run support, I get no error, but it fails:
*~/pb-jelly-code-0/pbsuite/jelly/Jelly.py support Protocol.xml*
2014-03-21 07:35:39,065 [INFO] Running /home/macmanes/pb-jelly-code-0/pbsuite/jelly/Jelly.py support Protocol.xml
[WARNING] Couldn't find /home/macmanes/pb-jelly-code-0/docs/jellyExample/data/reference/lambda.qual...
assuming there isn't a quality file for the reference
2014-03-21 07:35:39,067 [INFO] Executing Stage: support
2014-03-21 07:35:39,210 [INFO] Finished Running Stage: support
looking inside support/ my .gml file contains:
and my *err file has:
2014-03-21 07:35:39,196 [INFO] Running
2014-03-21 07:35:39,197 [INFO] Building Helper Objects
2014-03-21 07:35:39,197 [INFO] Connecting Alignments
2014-03-21 07:35:39,200 [INFO] Classifying Alignments' Support
2014-03-21 07:35:39,200 [INFO] Saving Support Graph
2014-03-21 07:35:39,201 [INFO] Finished
So, something is amiss, but I'm not sure what..
FWIW, I have the right networkx installed:
pip show networkx
The Protocol.xml file is unchanged from what is distributed:
<blasr>-minMatch 8 -minPctIdentity 70 -bestn 5 -nCandidates 20
-maxScore -500 -nproc 32 -noSplitSubreads</blasr>
Sorry you're having trouble. I'm unsure of a potential fix based on the information you've given me. Could you please re-run Support.py with --debug. Perhaps the verbose logs will give us a better indication of what's happening.
/home/macmanes/pb-jelly-code-0//bin//Support.py /home/macmanes/pb-jelly-code-0/docs/jellyExample/mapping/filtered_subreads.fastq.m4 /home/macmanes/pb-jelly-code-0/docs/jellyExample/data/reference/lambda.gapInfo.bed /home/macmanes/pb-jelly-code-0/docs/jellyExample/support/filtered_subreads.fastq.gml --debug
Sign up for the SourceForge newsletter:
You seem to have CSS turned off.
Please don't fill out this field.