JonJala
commented
1 year ago Hmm, what is the first line or so of finngen_adeno_tomtag.txt? (the column headers) Just trying to see why it would be having trouble identifying columns.
On Mon, Oct 16, 2023 at 9:58 AM caozilongsupper @.***> wrote:
I have prepared the format files such as chr,bpos,a1,a2,snpid,beta,se,pval,freq,N,z.When I run the MTAG, I am faced with an error. Here is the log: Calling ./mtag.py --stream-stdout --n-min 0.0 --sumstats finngen_adeno_tomtag.txt,finngen_squam_tomtag.txt,finngen_uteri_tomtag.txt --out /share/CZL/result/cancer/Cervix/finngen_mtag.1NS
Beginning MTAG analysis... MTAG will use the Z column for analyses. Read in Trait 1 summary statistics (20155970 SNPs) from finngen_adeno_tomtag.txt ...
<><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><
<><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
ERROR converting summary statistics:
Traceback (most recent call last): File "/share/CZL/MTAG/mtag-master/mtag_munge.py", line 802, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SNP column.
Conversion finished at Mon Oct 16 21:29:12 2023 Total time elapsed: 0.01s Could not find SNP column. Traceback (most recent call last): File "/share/CZL/MTAG/mtag-master/mtag.py", line 1577, in mtag(args) File "/share/CZL/MTAG/mtag-master/mtag.py", line 1343, in mtag DATA_U, DATA, args = load_and_merge_data(args) File "/share/CZL/MTAG/mtag-master/mtag.py", line 273, in load_and_merge_data GWAS_d[p], sumstats_format[p] = _perform_munge(args, GWAS_d[p], gwas_dat_gen, p) File "/share/CZL/MTAG/mtag-master/mtag.py", line 166, in _perform_munge munged_results = munge_sumstats.munge_sumstats(argnames, write_out=False, new_log=False) File "/share/CZL/MTAG/mtag-master/mtag_munge.py", line 802, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SNP column. Analysis terminated from error at Mon Oct 16 21:29:12 2023 Total time elapsed: 43.09s It is much appreciated if you could help me solve such problems!
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caozilongsuper
paturley
I have prepared the format files such as chr,bpos,a1,a2,snpid,beta,se,pval,freq,N,z.When I run the MTAG, I am faced with an error. Here is the log: Calling ./mtag.py \ --stream-stdout \ --n-min 0.0 \ --sumstats finngen_adeno_tomtag.txt,finngen_squam_tomtag.txt,finngen_uteri_tomtag.txt \ --out /share/CZL/result/cancer/Cervix/finngen_mtag.1NS
Beginning MTAG analysis... MTAG will use the Z column for analyses. Read in Trait 1 summary statistics (20155970 SNPs) from finngen_adeno_tomtag.txt ... <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><>< <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
ERROR converting summary statistics:
Traceback (most recent call last): File "/share/CZL/MTAG/mtag-master/mtag_munge.py", line 802, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SNP column.
Conversion finished at Mon Oct 16 21:29:12 2023 Total time elapsed: 0.01s Could not find SNP column. Traceback (most recent call last): File "/share/CZL/MTAG/mtag-master/mtag.py", line 1577, in
mtag(args)
File "/share/CZL/MTAG/mtag-master/mtag.py", line 1343, in mtag
DATA_U, DATA, args = load_and_merge_data(args)
File "/share/CZL/MTAG/mtag-master/mtag.py", line 273, in load_and_merge_data
GWAS_d[p], sumstats_format[p] = _perform_munge(args, GWAS_d[p], gwas_dat_gen, p)
File "/share/CZL/MTAG/mtag-master/mtag.py", line 166, in _perform_munge
munged_results = munge_sumstats.munge_sumstats(argnames, write_out=False, new_log=False)
File "/share/CZL/MTAG/mtag-master/mtag_munge.py", line 802, in munge_sumstats
raise ValueError('Could not find {C} column.'.format(C=c))
ValueError: Could not find SNP column.
Analysis terminated from error at Mon Oct 16 21:29:12 2023
Total time elapsed: 43.09s
It is much appreciated if you could help me solve such problems!