Tobi1kenobi
commented
3 years ago Hi,
- CELLECT uses rsIDs as input so you will have to convert your chromosomal coordinates if you don't have them.
- The problem seems to be that you are running with python 3. In our wiki tutorial we provide directions on how to install a conda environment with python 2.7 and all the other requirements for this script.
Hope this is helpful.
All the best, Tobi
ckrilow
I have a few questions regarding the munge_sumstats.py script: 1- does the summary statistics file, passed via --sumstats, require to have RS ids? For example, if we pass a column named 'Marker' with values such as this; chr11:88249377, will the script work? 2- Secondly, when executing the following command, I get the following error and I can not tell if this is because of the summary stats file that I am passing or something else. I have included the command I have used, an example format of the summary statistics file, and the output. For what it is worth I have successfully ran the mtag_munge.py script with two other summary stats files, though they do have RS Ids in them (my data is not all annotated with RS IDs*)
CMD Used: python ldsc/mtag_munge.py --sumstats --snp MarkerName --a1 Allele1 --a2 Allele2 --n-value 45975 --merge-alleles data/ldsc/w_hm3.snplist --keep-pval --p P-value --out /out/gwas
Example of summary statistics file content: MarkerName Allele1 Allele2 Freq1 FreqSE Effect StdErr P-value Direction chr11:88249377 t c 0.9913 0.0000 -0.0234 0.0329 0.4771 - chr15:99906873 t c 0.0710 0.0000 -0.0122 0.0371 0.742 - chr8:135908647 a g 0.2019 0.0000 0.0014 0.0062 0.8201 + chr12:3871714 a c 0.9725 0.0000 0.0194 0.0356 0.5858 + chr11:97895884 c g 0.0668 0.0000 0.0386 0.0127 0.002279 +
ERROR converting summary statistics:
Conversion finished at Wed Apr 21 15:50:42 2021 Traceback (most recent call last): File "ldsc/mtag_munge.py", line 753, in munge_sumstats file_cnames = read_header(args.sumstats) if args.input_datgen is None else args.cnames # note keys not cleaned File "ldsc/mtag_munge.py", line 291, in read_header return [x.rstrip('\n') for x in openfunc(fh).readline().split()] File "ldsc/mtag_munge.py", line 291, in
return [x.rstrip('\n') for x in openfunc(fh).readline().split()]
TypeError: a bytes-like object is required, not 'str'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "ldsc/mtag_munge.py", line 961, in munge_sumstats logging.info(traceback.format_exc(ex)) File "/Users/krilowcn/anaconda3/envs/BINF/lib/python3.8/traceback.py", line 167, in format_exc return "".join(format_exception(*sys.exc_info(), limit=limit, chain=chain)) File "/Users/krilowcn/anaconda3/envs/BINF/lib/python3.8/traceback.py", line 120, in format_exception return list(TracebackException( File "/Users/krilowcn/anaconda3/envs/BINF/lib/python3.8/traceback.py", line 508, in init self.stack = StackSummary.extract( File "/Users/krilowcn/anaconda3/envs/BINF/lib/python3.8/traceback.py", line 340, in extract if limit >= 0: TypeError: '>=' not supported between instances of 'TypeError' and 'int'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "ldsc/mtag_munge.py", line 969, in
d = munge_sumstats(parser.parse_args(), write_out=True)
File "ldsc/mtag_munge.py", line 966, in munge_sumstats
T=allele_info.sec_to_str(round(time.time() - START_TIME, 2))))
File "/Users/krilowcn/Desktop/Projects/GSIS/cellect_work/CELLECT/ldsc/lib_mtag_munge/allele_info.py", line 59, in sec_to_str
[d, h, m, s, n] = reduce(lambda ll, b : divmod(ll[0], b) + ll[1:], [(t, 1), 60, 60, 24])
NameError: name 'reduce' is not defined