Error with 'variantid' function #46
Description
Please find the code, input file, and error message below. I've checked the python version - tried it with 2.7.15 and Python/3.6.6-intel-2018b, both return to the same error message.
(1) code
python $SUMSTAT variantid
--sumstats$PROC_DIR/$ {TRAIT}_n_z_qc_nolift.csv.gz
--force
--log-append
--ref $REF_DIR/sumstats/misc/ega.grch37.all.haplotypes.m.v2.ref
--out$PROC_DIR/$ {TRAIT}_n_z_qc_nolift_vid.csv
--log$PROC_DIR/$ {TRAIT}_n_z_qc_nolift_vid.csv.log
(2) input file
SNP CHR BP PVAL A1 A2 N Z BETA SE
rs667647 5 29439275 0.9415 T C 11373 -0.07338469044558865 -148.8340 2029.8618
(3) error information
Traceback (most recent call last):
File "/cluster/home/wqcheng/workspace/Applications/python_convert/sumstats.py", line 2158, in
args.func(args, log)
File "/cluster/home/wqcheng/workspace/Applications/python_convert/sumstats.py", line 1187, in make_variantid
df_nodups = pd.merge(df[['index', 'CHR', 'BP']], ref[['CHR', 'BP', 'A1_ref', 'A2_ref']][~ref['DUP']], on=['CHR', 'BP'], how='inner')
File "/cluster/software/Python/3.6.6-intel-2018b/lib/python3.6/site-packages/pandas-0.23.4-py3.6-linux-x86_64.egg/pandas/core/reshape/merge.py", line 61, in merge
validate=validate)
File "/cluster/software/Python/3.6.6-intel-2018b/lib/python3.6/site-packages/pandas-0.23.4-py3.6-linux-x86_64.egg/pandas/core/reshape/merge.py", line 555, in init
self._maybe_coerce_merge_keys()
File "/cluster/software/Python/3.6.6-intel-2018b/lib/python3.6/site-packages/pandas-0.23.4-py3.6-linux-x86_64.egg/pandas/core/reshape/merge.py", line 983, in _maybe_coerce_merge_keys
raise ValueError(msg)
ValueError: You are trying to merge on int64 and object columns. If you wish to proceed you should use pd.concat