Open ahorn720 opened 4 years ago
I should mention that when I tried using the example input file... it seems to work just fine.
the only things I can tell that are different between the example file and mine are that I've filled my SNVID column with items like the following: `
SNVID
chr1:1048090:rs747114622:C:T
chr1:1128169:.:T:C
chr1:1240555:.:A:C
chr1:1459342:.:G:A
chr1:1530556:rs186520555:G:A
The problem is that there is a space in the path to your input file. Please try: python clonefinder.py snv "/Users/ahorning/Google Drive/Stanford_postdoc/Research/FAP Samples_EdEsplin/DNAseq_WGS/scripts/RupingPipelineLocalCopies/post-VAP/Bulk_A001_A002/clonefinder/A001_HETsegmentsonly.txt" If you still get the same error, please move your input file from the Google Drive into your PC.
Thank you very much for your help. You helped me figure out that there was certainly something wrong with my input file.
Turns out, I had quotes in my input file I didn't realize. I fixed this by using the write.table(..., quote = FALSE)
argument in my R code.
Its running now so hopefully it works :)
from
/Users/ahorning/CloneFinderAPI/clonefinder
I ran
python clonefinder.py snv /Users/ahorning/Google Drive/Stanford_postdoc/Research/FAP Samples_EdEsplin/DNAseq_WGS/scripts/RupingPipelineLocalCopies/post-VAP/Bulk_A001_A002/clonefinder/A001_HETsegmentsonly.txt
and got this error:
2019-12-10 12:56:13.751637 loading config file: options.ini config parameters loaded successfully parsing command-line parameters... Errors in options.ini Traceback (most recent call last): File "clonefinder.py", line 37, in <module> parser.input_data_file = params.input_data_file NameError: name 'params' is not defined
Im not sure what went wrong...