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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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error creating reference table #10

Closed shawpa closed 10 years ago

shawpa commented 10 years ago

I am trying to run the newref.py script but I am getting the following error.

python C:\Users\shawpa\Desktop\wisecondor-master\wisecondor-master\newref.py P:\Cores\hiseq2000\annie\wisecondor\ref_pickle\gc_corrected\ P:\Cores\hiseq2000\annie\wisecondor\reftable.pickle

Settings used:

ignore 0 refdir P:\Cores\hiseq2000\annie\wisecondor\ref_pickle\gc_corrected\ refout P:\Cores\hiseq2000\annie\wisecondor\reftable.pickle

Processing:

Loading reference samples Building reference table Targeting chromosome: 1 Calculating distances to chromosome Traceback (most recent call last): File "C:\Users\shawpa\Desktop\wisecondor-master\wisecondor-master\newref.py", line 114, in jChroms[jChrom] = getDistanceTable(controls,iChrom,jChrom) File "C:\Users\shawpa\Desktop\wisecondor-master\wisecondor-master\newref.py". line 58, in getDistanceTable iLen = max([len(controls[key][iChrom]) for key in controls.keys()]) ValueError: max() arg is an empty sequence

I believe that I have followed all the proper steps. I first made a gccount table of my genomic reference(hg19). I converted sam files to pickle files and did a GC correction on each of those files. Those are the files I am trying to feed into this command. I am not sure how big the files should be but it seems like the pickle files are very small and all the GC corrected files are all the same size at 59Kb. Is this normal? I can send you any of the files if it helps. I have no idea what to do with this error I am getting.

Annie

rstraver commented 10 years ago

Hi Annie,

Could you tell me the file extensions used in here? P:\Cores\hiseq2000\annie\wisecondor\ref_pickle\gc_corrected\

I believe there was a little mixup on file extenstions and people tended to name the gc-corrected files .pickle, while the script would go about looking for .gcc files, throwing an error like you posted (basically, it says there are no control samples available, so it can't find any files to use for it's reference)

I just checked my files and those are also all 59.4kB to 59.7kB, it's the right file size considering there is not a lot of data in them, and they barely vary in size because they all contain the about same amount of numbers.

Roy

shawpa commented 10 years ago

I did name my files with "pickle" at the end. Didn't know what they should be named otherwise. I renamed them .gcc files and now everything seems to be running smoothly. Thanks for your help.