ValueError: invalid literal for int() with base 10: 'ref_counts'

[Rui Resende]

Hi, I am trying to run PyClone v0.13.1 but I am getting the following error:

Traceback (most recent call last):

  File "/opt/conda/bin/PyClone", line 11, in <module>

    load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')()

  File "/opt/conda/lib/python2.7/site-packages/pyclone/cli.py", line 78, in main

    args.func(args)

  File "/opt/conda/lib/python2.7/site-packages/pyclone/run.py", line 44, in run_analysis_pipeline

    config_extras_file=args.config_extras_file,

  File "/opt/conda/lib/python2.7/site-packages/pyclone/run.py", line 258, in _setup_analysis

    prior

  File "/opt/conda/lib/python2.7/site-packages/pyclone/run.py", line 305, in _build_mutations_file

    ref_counts = int(row['ref_counts'])

ValueError: invalid literal for int() with base 10: 'ref_counts'

The inputs are tab-delimited files with following format:

mutation_id ref_counts var_counts normal_cn minor_cn major_cn

chr1:878314 32 13 2 0 2

chr1:978603 23 16 2 0 2

chr1:981087 32 21 2 0 2

chr1:982941 54 31 2 0 2

chr1:982994 59 39 2 0 2

chr1:985266 33 16 2 0 2

chr1:986443 18 7 2 0 2

I am running with prior set as total_copy_number.

I'd appreciate any help.

Thank you!

[Andrew]

Hi Rui,

This suggests there is an entry in the ref_counts column the program does not like. Double check the file for any weird values. One easy way to have a mistake is a blank entry, which will get read in as a missing value which may cause errors. 

You can debug this by loading the file with pandas in Python and checking the dtype of the column. Try casting it to an integer and see if that raises an error.

Best wishes,

Andy

[Rui Resende]

Indeed, one of my input files had a problem. Thank you very much!

Best,

Rui