KeyError: 'tMean'

[tay45]

Hi all,

I did run the kinecticsTools successfully with single aligned.cmp.h5 file for in-silico control mode. However, I have an error such as "KeyError: tMean" when I run together with the case-control. Could you please share your experience how to solve the issue if you had the same or similar situation? I attached my log at below. Thank you!

Taehyuk

-sh-3.2$ /opt/smrtanalysis/smrtcmds/bin/smrtwrap ipdSummary.py --reference /home/thkang/pDmeth.fa --verbose --outfile ./test/modification --control /opt2/smrtanalysis/userdata/jobs/016/016488/data/aligned_reads.cmp.h5 aligned_reads.cmp.h5 2016-06-23 17:20:19,665 [INFO] Available CPUs: 32 2016-06-23 17:20:19,665 [INFO] Requested worker processes: -1 2016-06-23 17:20:19,695 [INFO] Worker KineticWorkerProcess-2 (PID=23860) started running.................................................................................................................................................................................................................................................................................................................................. 2016-06-23 17:33:29,461 [INFO] Process KineticWorkerProcess-10 (PID=23868) done; exiting. Process KineticsWriter-33: Traceback (most recent call last): File "/opt/smrtanalysis/current/redist/python2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/kineticsTools/ResultWriter.py", line 102, in run self._run() File "/opt/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/kineticsTools/ResultWriter.py", line 87, in _run self.onResult(nextChunk) File "/opt/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/kineticsTools/ResultWriter.py", line 860, in onResult sink.send(resultChunk) File "/opt/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/kineticsTools/ResultWriter.py", line 374, in hdf5CsvConsumer tMean[idx] = float(x['tMean']) KeyError: 'tMean' 2016-06-23 17:33:30,131 [ERROR] Child process exited with exitcode=1. Aborting.

[casidexiao250]

hi; I noticed that you submitted the question that kinecticsTools can successfully run with single aligned.cmp.h5 file for in-silico control mode, but it will raise error when it run together with the case-control. Unfortunately，I also encountered the same problem。Have you solved this problem?

casidexiao

[rhallPB]

When running with a case control, instead of using the --outfile parameter, specify the individual outputs --gff <gff out> --csv <csv out>