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VUmcCGP / wisecondor

WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR): Detect fetal trisomies and smaller CNV's in a maternal plasma sample using whole-genome data.
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Problem with gcc file #17

Closed markb41 closed 9 years ago

markb41 commented 9 years ago

Hi Rstraver

I've created pickle files and gcc files and established reference samples. However when testing a new sample I run into problems with the gcc file as follows: .... Targeting chromosome: 22 Calculating distances to chromosome: 1 Calculating distances to chromosome: 2 Calculating distances to chromosome: 3 Calculating distances to chromosome: 4 Calculating distances to chromosome: 5 Calculating distances to chromosome: 6 Calculating distances to chromosome: 7 Calculating distances to chromosome: 8 Calculating distances to chromosome: 9 Calculating distances to chromosome: 10 Calculating distances to chromosome: 11 Calculating distances to chromosome: 12 Calculating distances to chromosome: 13 Calculating distances to chromosome: 14 Calculating distances to chromosome: 15 Calculating distances to chromosome: 16 Calculating distances to chromosome: 17 Calculating distances to chromosome: 18 Calculating distances to chromosome: 19 Calculating distances to chromosome: 20 Calculating distances to chromosome: 21 Calculating distances to chromosome: 22 Picking reference bins Writing reference to file File "/data/illumina/nipd/temptest5/140691.gcc", line 2 S'20' ^ SyntaxError: invalid syntax Traceback (most recent call last): File "/data/mark/tools/wisecondor/plot.py", line 164, in sampleData = pickle.load(open(args.plotdata,'rb')) IOError: [Errno 2] No such file or directory: '/data/illumina/nipd/NIPD1_1-36/140691.plot'

Do you have any idea of the course of this error and maybe even a solution to the problem?

best regards and thanks

Mark

rstraver commented 9 years ago

It looks like you jumped from creating a reference to trying to plot without running test.py in between, is this from running run.sh or did you run these steps manually? This should happen: .pickle -> .gcc -> .plot -> .pdf yours appears to be missing .gcc -> .plot, done by test.py

markb41 commented 9 years ago

Thanks a lot for your help - my analysis is now running again without any errors.

rstraver commented 9 years ago

Cheers, glad to hear it works!