Jason Hill - 2014-02-10

Edit--

I made a mistake. I thought I was using networkx v1.1 but I was still using v1.8. After making sure the right networkx module was being used everything worked great. Thanks!


Greetings,

I'm excited to use your program to upgrade my assembly. I got as far as the extraction step and all though it looks like it finishes normally:

2014-02-10 14:36:55,296 [INFO] Running /data/programs/PBSuite_14.1.15/bin/Jelly.py extraction PBJprotocol.xml -x --debug
2014-02-10 14:36:55,298 [INFO] Executing Stage: extraction
2014-02-10 14:52:51,216 [INFO] Finished Running Stage: extraction

The extraction.err says otherwise and the assembly step cannot start. The end of the extraction.err and full xml file are below. Help getting through this would be appreciated.

PBJ.xml

<jellyProtocol>
    <reference>/data/projects/shared/Pnapi/pbjelly/Pnapi.DAS2.fasta</reference>  
    <outputDir>/data/projects/shared/Pnapi/pbjelly/output</outputDir>
    <blasr>-minMatch 8 -sdpTupleSize 8 -minPctIdentity 75 -bestn 1 -nCandidates 10 -maxScore -500 -nproc 8 -noSplitSubreads</blasr>
    <input baseDir="/data/Reads/Pnapi/PacBio_reads/pb_018/reads/">
        <job>pb_18_1.filtered_subreads.fastq</job>
    <job>pb_18_2.filtered_subreads.fastq</job>
    </input>
</jellyProtocol>

tail of extraction.err

2014-02-10 15:40:20,149 [DEBUG] Writing m131214_035742_42203_c100603672550000001823105806171405_s1_p0/139504/2547_2996 to 14046_22371
2014-02-10 15:40:20,150 [DEBUG] 21950 only has extending evidence
2014-02-10 15:40:20,150 [DEBUG] []
2014-02-10 15:40:20,151 [DEBUG] 34378 only has extending evidence
2014-02-10 15:40:20,151 [DEBUG] []
2014-02-10 15:40:20,151 [DEBUG] 22290 only has extending evidence
2014-02-10 15:40:20,151 [DEBUG] []
2014-02-10 15:40:20,152 [DEBUG] 54540 only has extending evidence
2014-02-10 15:40:20,152 [DEBUG] []
2014-02-10 15:40:20,152 [DEBUG] 7305 only has extending evidence
2014-02-10 15:40:20,152 [DEBUG] []
2014-02-10 15:40:20,153 [DEBUG] Writing m131214_083608_42203_c100603672550000001823105806171407_s1_p0/62762/0_1418 to 1618_2065
2014-02-10 15:40:20,153 [DEBUG] Writing m131214_083608_42203_c100603672550000001823105806171407_s1_p0/62762/0_1418 to 11854_54005
2014-02-10 15:40:20,153 [DEBUG] Writing m131214_083608_42203_c100603672550000001823105806171407_s1_p0/62762/0_1418 to 6375_54005
2014-02-10 15:40:20,154 [INFO] Flushing Output Queue of 20000 gaps 27905 reads
2014-02-10 15:40:20,154 [DEBUG] flankName 30177
Traceback (most recent call last):
File "/data/programs/PBSuite_14.1.15//bin//Extraction.py", line 315, in <module>
me.run()
File "/data/programs/PBSuite_14.1.15//bin//Extraction.py", line 288, in run
self.extractReads()
File "/data/programs/PBSuite_14.1.15//bin//Extraction.py", line 188, in extractReads
self.flushQueue(outputQueue)
File "/data/programs/PBSuite_14.1.15//bin//Extraction.py", line 211, in flushQueue
outFile = self.openGapOut(gapName)
File "/data/programs/PBSuite_14.1.15//bin//Extraction.py", line 237, in openGapOut
sequence = self.reference[flankName[:10]]
KeyError: '30177'

 
Last edit: Jason Hill 2014-02-16