search

JonJala / mtag

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
GNU General Public License v3.0
169 stars 54 forks source link

ValueError: Could not find SIGNED_SUMSTAT column #164

Open Haojie818 opened 2 years ago

Haojie818 commented 2 years ago

Hi

I am using mtag for two different traits, then I got error like this. Any idea why is that? Thanks in advance.

Best

Haojie

Calling ./mtag.py \ --se-name StdErr \ --p-name Pvalue \ --bpos-name BP \ --stream-stdout \ --n-name N \ --a2-name Allele2 \ --n-min 20000 \ --a1-name Allele1 \ --snp-name RSID \ --chr-name CHR \ --sumstats /home/result/final_data/SKBMD.txt.gz,/home/result/final_data/LSBMD.txt.gz \ --beta-name Effect \ --out /home/result/MTAG/Model.test

2022/08/02/12:44:22 PM Beginning MTAG analysis... 2022/08/02/12:44:22 PM MTAG will use the Z column for analyses. 2022/08/02/12:45:30 PM Read in Trait 1 summary statistics (14406717 SNPs) from /home/result/final_data/SKBMD.txt.gz ... 2022/08/02/12:45:30 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2022/08/02/12:45:30 PM Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><>< 2022/08/02/12:45:30 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2022/08/02/12:45:30 PM ERROR converting summary statistics:

2022/08/02/12:45:30 PM Traceback (most recent call last): File "/home/059904/software/mtag/mtag_munge.py", line 801, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SIGNED_SUMSTAT column.

2022/08/02/12:45:30 PM Conversion finished at Tue Aug 2 12:45:30 2022 2022/08/02/12:45:30 PM Total time elapsed: 0.0s 2022/08/02/12:45:30 PM Could not find SIGNED_SUMSTAT column. Traceback (most recent call last): File "/home/software/mtag/mtag.py", line 1577, in mtag(args) File "/home/software/mtag/mtag.py", line 1343, in mtag DATA_U, DATA, args = load_and_merge_data(args) File "/home/software/mtag/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 "/home/software/mtag/mtag.py", line 166, in _perform_munge munged_results = munge_sumstats.munge_sumstats(argnames, write_out=False, new_log=False) File "/home/software/mtag/mtag_munge.py", line 801, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SIGNED_SUMSTAT column. 2022/08/02/12:45:30 PM Analysis terminated from error at Tue Aug 2 12:45:30 2022 2022/08/02/12:45:30 PM Total time elapsed: 1.0m:7.76s

JonJala commented 2 years ago

It looks like it's having trouble finding the Z column that it's expecting (" 2022/08/02/12:44:22 PM MTAG will use the Z column for analyses.")

On Wed, Aug 3, 2022 at 4:10 AM Haojie818 @.***> wrote:

Hi

I am using mtag for two different traits, then I got error like this. Any idea why is that? Thanks in advance.

Best

Haojie

Calling ./mtag.py --se-name StdErr --p-name Pvalue --bpos-name BP --stream-stdout --n-name N --a2-name Allele2 --n-min 20000 --a1-name Allele1 --snp-name RSID --chr-name CHR --sumstats /home/result/final_data/SKBMD.txt.gz,/home/result/final_data/LSBMD.txt.gz --beta-name Effect --out /home/result/MTAG/Model.test

2022/08/02/12:44:22 PM Beginning MTAG analysis... 2022/08/02/12:44:22 PM MTAG will use the Z column for analyses. 2022/08/02/12:45:30 PM Read in Trait 1 summary statistics (14406717 SNPs) from /home/result/final_data/SKBMD.txt.gz ... 2022/08/02/12:45:30 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2022/08/02/12:45:30 PM Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><>< 2022/08/02/12:45:30 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2022/08/02/12:45:30 PM ERROR converting summary statistics:

2022/08/02/12:45:30 PM Traceback (most recent call last): File "/home/059904/software/mtag/mtag_munge.py", line 801, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SIGNED_SUMSTAT column.

2022/08/02/12:45:30 PM Conversion finished at Tue Aug 2 12:45:30 2022 2022/08/02/12:45:30 PM Total time elapsed: 0.0s 2022/08/02/12:45:30 PM Could not find SIGNED_SUMSTAT column. Traceback (most recent call last): File "/home/software/mtag/mtag.py", line 1577, in mtag(args) File "/home/software/mtag/mtag.py", line 1343, in mtag DATA_U, DATA, args = load_and_merge_data(args) File "/home/software/mtag/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 "/home/software/mtag/mtag.py", line 166, in _perform_munge munged_results = munge_sumstats.munge_sumstats(argnames, write_out=False, new_log=False) File "/home/software/mtag/mtag_munge.py", line 801, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find SIGNED_SUMSTAT column. 2022/08/02/12:45:30 PM Analysis terminated from error at Tue Aug 2 12:45:30 2022 2022/08/02/12:45:30 PM Total time elapsed: 1.0m:7.76s

— Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/164, or unsubscribe https://github.com/notifications/unsubscribe-auth/APIOF52XA672YJA63LRMYNTVXISO7ANCNFSM55N364TA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

CharlesLambert70 commented 2 years ago

Hi,

I also have the same problem. This is my code. python /home/gyu/mtag/mtag.py \ --sumstats MAGIC_INSULIN_SECRETION_AUCins_AUCgluc_for_release_HMrel27_MTAG.txt,MAGIC_INSULIN_SECRETION_DI_for_release_HMrel27_MTAG.txt,MAGIC_INSULIN_SECRETION_ISI_for_release_HMrel27_MTAG.txt \ --snp_name spnid \ --out ./new \ --no_chr_data \ --beta_name beta \ --p_name pval \ --se_name se\ --n_min 0.0 \ --stream_stdout

If I use the option "--use_beta_se", it will raise the error "RuntimeError("Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software. Dec 2, 2021")".

However, the help document has described that "--beta_name: If specified, it will override the z-score column." Since I specify the "--beta_name", it should override z-score column. However, the MTAG still report that "Beginning MTAG analysis... MTAG will use the Z column for analyses."

So is there anything wrong with current version of MTAG?

JonJala commented 2 years ago

After checking the code, it appears that the usage documentation is erroneous (or at least incomplete....the --use-beta-se option would also need to be specified for MTAG to use the beta column). We can update that. In the meantime, the easiest way forward probably would be to use a z score column in your data, which you might need to calculate yourself, as the beta_se mode for MTAG has some bugs in it that have been a difficult to track down.

Hope that helps.

On Tue, Aug 30, 2022 at 9:52 PM CharlesLambert70 @.***> wrote:

Hi,

I also have the same problem. This is my code. python /home/gyu/mtag/mtag.py --sumstats MAGIC_INSULIN_SECRETION_AUCins_AUCgluc_for_release_HMrel27_MTAG.txt,MAGIC_INSULIN_SECRETION_DI_for_release_HMrel27_MTAG.txt,MAGIC_INSULIN_SECRETION_ISI_for_release_HMrel27_MTAG.txt

--snp_name spnid --out ./new --no_chr_data --beta_name beta --p_name pval --se_name se --n_min 0.0 --stream_stdout

If I use the option "--use_beta_se", it will raise the error "RuntimeError("Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software. Dec 2, 2021")".

However, the help document has described that "--beta_name: If specified, it will override the z-score column." Since I specify the "--beta_name", it should override z-score column. However, the MTAG still report that " Beginning MTAG analysis... MTAG will use the Z column for analyses."

So is there anything wrong with current version of MTAG?

— Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/164#issuecomment-1232356670, or unsubscribe https://github.com/notifications/unsubscribe-auth/APIOF5YHPJM4FDTYRC66N5TV323GLANCNFSM55N364TA . You are receiving this because you commented.Message ID: @.***>

CharlesLambert70 commented 2 years ago

Thanks! @JonJala