Error with 'variantid' function

[WQ-CHENG]

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

[interCM]

Should be fixed now. Please test it with your specific case.

[WQ-CHENG]

Unfortunately, I got the same error with the updated python script. Please see details below: - path on SAGA: /cluster/projects/nn9114k/weiqiuc/Ref/sumstats/PROC/ENIGMA_ICV_2015 - error file: ENIGMA_ICV_2015_n_z_qc_nolift_vid.csv.log.error I've checked the script I use is the latest one: awk 'NR==1229 || NR==1233' /cluster/projects/nn9114k/weiqiuc/Applications/python_convert/sumstats.py df = pd.read_csv(args.sumstats, sep='\t', dtype={"CHR":str}) ref = pd.read_csv(args.ref, sep='\t', usecols=[cols.CHR, cols.BP, cols.A1, cols.A2], dtype={cols.CHR:str})

…

On Thu, Mar 18, 2021 at 9:20 PM interCM ***@***.***> wrote: Should be fixed now. Please test it with your specific case. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#46 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANOIRTS7TZB7Z72LII4XPDLTEJN7JANCNFSM4ZMOKGGQ> .