I have this error message when running DEPICT.
Could anybody comment on it?
(py27env) bash-3.2$ /Users/soujin/Work/DEPICT2/src/python/depict.py /Users/soujin/Work/DEPICT2/analyses/analysis.cfg
Will store result files to /Users/soujin/Work/DEPICT2/analyses/YAOSPsqrt
Reading GWAS and mapping by chromosome and position to genotype data
Traceback (most recent call last):
File "/Users/soujin/Work/DEPICT2/src/python/depict.py", line 111, in
map_log = write_plink_input(analysis_path, filename, label, marker_col_name, pvalue_col_name, chr_col_name, pos_col_name, sep, genotype_data_plink_prefix, association_pvalue_cutoff)
File "/Users/soujin/Work/DEPICT2/src/python/depict_library.py", line 355, in write_plink_input
pos = int(words[pos_col])
ValueError: invalid literal for int() with base 10: ''
My input files are meta-analysis output from plink1.9
I checked if there is any missing or incorrectly recorded in the fields for chromosome and basepair positions of the gwas meta-analysis input files, but all rows for those fields are numerical and non-missing.
I have python2.7 installed in a conda
Has anyone faced the same issue and resolved it?
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