search

parklab / NGSCheckMate

Software program for checking sample matching for NGS data
MIT License
126 stars 48 forks source link

Issues with file names #10

Closed zhujack closed 6 years ago

zhujack commented 6 years ago

Thanks for the package. I have been using alternative fastq method. But the following code often gives me errors: python $NCM_HOME/vaf_ncm.py -I $vafDir -O $outDir -N NGSCheckMate

Traceback (most recent call last): File "/home/zhujack/Downloads/NGSCheckMate/vaf_ncm.py", line 638, in classifying() File "/home/zhujack/Downloads/NGSCheckMate/vaf_ncm.py", line 365, in classifying output_matrix_f.write(key[0:key.index('.')]) ValueError: substring not found

Then I found in vaf_ncm.py:

Lines 344-352 have substring [:-4] Lines 360, 365 also have substring: [0:key.index('.')]

I guess both of the substr do not work for my case. Your help will be greatly appreciated.

Jack

sejooning commented 6 years ago

Hi Jack. Thank you for using the NGSCheckMate. Could you check whether there are only vaf files in $vafDir or not. For using vaf_ncm.py, there should be only vaf files in the input_dir.

Best, Sejoon Lee

zhujack commented 6 years ago

Thanks, Sejoon. My $vafDir only has symbolic links of the vaf files.

Jack