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precimed / mixer

Causal Mixture Model for GWAS summary statistics
GNU General Public License v3.0
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ValueError: Input files have distinct value #45

Closed sherryfan030 closed 3 years ago

sherryfan030 commented 3 years ago

Hi there,

I successfully run codes until the visualization step.it happens an error：

python3 precimed/mixer_figures.py combine --json /home/sherry/mixer/MiXer/DIABETES/T2D_noMHC.csv.gz.fit.rep@.json --out /home/sherry/mixer/MiXer/DIABETES/visualize/T2D_noMHC.fit Traceback (most recent call last): File "precimed/mixer_figures.py", line 15, in args.func(args) File "/home/sherry/mixer/precimed/mixer/figures.py", line 537, in execute_combine_parser if len(set(values)) > 1: raise(ValueError('Input files have distinct value in "{}" field: {}'.format(key, ' '.join(set(values))))) ValueError: Input files have distinct value in "trait1_file" field: /home/sherry/mixer/MiXer/T2D_noMHC.csv.gz MiXer/T2D_noMHC.csv.gz ———————————————————— how to solve it? Thanks!

ofrei commented 3 years ago

@sherryfan030 Hi mixer_figures.py combine complains because it appears to see two different trait files - /home/sherry/mixer/MiXer/T2D_noMHC.csv.gz (full path) and MiXer/T2D_noMHC.csv.gz (relative path). The error is just a sanity check and the code should work just fine if you remove the line that throws an error from figures.py file, and re-run the same command https://github.com/precimed/mixer/blob/master/precimed/mixer/figures.py#L537 Or re-run the analysis using consistent path (either full or relative) across all repeats

sherryfan030 commented 3 years ago

Hi,oferi! Thank you for your reply. After that I try to use consistent path across all MiXeR file and it works.