Error in step05

[LinduniR]

Hi,

I successfully run the GenEpi up to step 04 and getting an error in step 05 as below.

Traceback (most recent call last):
File "/home/n10398406/PD_Data/GenEpi_PD/Trial_chr21_gen/GenEpiL21/bin/GenEpi", line 8, in
sys.exit(main())
File "/home/n10398406/PD_Data/GenEpi_PD/Trial_chr21_gen/GenEpiL21/lib/python3.7/site-packages/genepi/GenEpi.py", line 209, in main
float_score_train, float_score_test = CrossGeneEpistasisLogistic(os.path.join(str_outputFilePath, "singleGeneResult"), str_inputFileName_phenotype, int_kOfKFold=int(args.k), int_nJobs=1)
TypeError: cannot unpack non-iterable float object

What can I do to get rid of this error? Really appreciated if you could help me.
Thank you.

Linduni

[Chester75321]

Hi Linduni, Sorry for the late response. The error happened because there were no SNPs selected in step5. Please check the files in the singleGeneResult folder, which are the output of step4. In the *_Result.csv, I guess that the chi-square p-values of the selected features were not significant enough (log10(p-value) < 5) for further step. And, thanks for the feedback, the GenEpi 2.0.10 will send you a warning message for this situation instead of the type error. Best, Chester LinduniR <notifications@github.com> 於 2020年7月13日 週一 下午7:08寫道：

…

Hi, I successfully run the GenEpi up to step 04 and getting an error in step 05 as below. *Traceback (most recent call last): File "/home/n10398406/PD_Data/GenEpi_PD/Trial_chr21_gen/GenEpiL21/bin/GenEpi", line 8, in sys.exit(main()) File "/home/n10398406/PD_Data/GenEpi_PD/Trial_chr21_gen/GenEpiL21/lib/python3.7/site-packages/genepi/GenEpi.py", line 209, in main float_score_train, float_score_test = CrossGeneEpistasisLogistic(os.path.join(str_outputFilePath, "singleGeneResult"), str_inputFileName_phenotype, int_kOfKFold=int(args.k), int_nJobs=1) TypeError: cannot unpack non-iterable float object* What can I do to get rid of this error? Really appreciated if you could help me. Thank you. Linduni — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADUJNC6XX25TS46S4SHABFLR3LTMBANCNFSM4OYL3LBQ> .

[LinduniR]

Hi Chester, Thank you for your reply. I successfully run the GenEpi and got results for my data. Thank you for your support so far. I have few questions regarding the output files. 1.In crossGeneResult folder has file with the .pkl extension. I tried to open it using pickle.load(), but it didn't work. Any suggestions? 2. In CrossGeneResult folder has Result.csv file. In that file there is one extra column (singleGene Score) which is not mentioned in the GenEpi documents. Following is the headings and few rows of Results.csv file. Would like to know what SingleGene Score is? rsid weight chi-square_log_p-value odds_ratio genotype_frequency geneSymbol singleGeneScore 7:21733475:G:A_BB*7:21758045:T:G_AA -0.28357 5.424037874 0.750207331 0.13234596 DNAH11 0.554608558 4:852659:T:G_BB*4:906131:C:G_AA 0.081056 6.402381867 1.417004049 0.100256337 GAK 0.447900467 4:906131:C:G_AA*4:921733:C:A_BB 0.040279 6.328296421 1.413615654 0.100351277 GAK 0.447900467 17:43543830:T:C_AB*17:43548778:G:C_AB 0.026573 5.256035392 1.260087236 0.298965157 PLEKHM1 0.594378819 17:43548778:G:C_AB*17:43558092:C:T_BB 0.016115 5.144651981 1.256275831 0.303902022 PLEKHM1 0.594378819 17:43548778:G:C_AB*17:43564222:T:G_BB 0.02174 5.144651981 1.256275831 0.303902022 PLEKHM1 0.594378819 4:939087:C:T_AA*4:951179:G:A_BB 0.014799 6.522435183 1.43095898 0.09598405 TMEM175 0.484405966 4:939113:G:A_AB*4:948640:G:A_BB 0.180206 5.177499006 1.367560108 0.097218266 TMEM175 0.484405966 I'm looking forward to hearing from you about the above mentioned questions. Thank you. Linduni

________________________________ From: Chester <notifications@github.com> Sent: Wednesday, August 5, 2020 12:19 AM To: Chester75321/GenEpi <GenEpi@noreply.github.com> Cc: Linduni Rodrigo <undugodage.rodrigo@hdr.qut.edu.au>; Author <author@noreply.github.com> Subject: Re: [Chester75321/GenEpi] Error in step05 (#5) Hi Linduni, Sorry for the late response. The error happened because there were no SNPs selected in step5. Please check the files in the singleGeneResult folder, which are the output of step4. In the *_Result.csv, I guess that the chi-square p-values of the selected features were not significant enough (log10(p-value) < 5) for further step. And, thanks for the feedback, the GenEpi 2.0.10 will send you a warning message for this situation instead of the type error. Best, Chester LinduniR <notifications@github.com> 於 2020年7月13日 週一 下午7:08寫道：

Hi, I successfully run the GenEpi up to step 04 and getting an error in step 05 as below. *Traceback (most recent call last): File "/home/n10398406/PD_Data/GenEpi_PD/Trial_chr21_gen/GenEpiL21/bin/GenEpi", line 8, in sys.exit(main()) File "/home/n10398406/PD_Data/GenEpi_PD/Trial_chr21_gen/GenEpiL21/lib/python3.7/site-packages/genepi/GenEpi.py", line 209, in main float_score_train, float_score_test = CrossGeneEpistasisLogistic(os.path.join(str_outputFilePath, "singleGeneResult"), str_inputFileName_phenotype, int_kOfKFold=int(args.k), int_nJobs=1) TypeError: cannot unpack non-iterable float object* What can I do to get rid of this error? Really appreciated if you could help me. Thank you. Linduni — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5><https://urldefense.com/v3/__https://github.com/Chester75321/GenEpi/issues/5*3E__;JQ!!NVzLfOphnbDXSw!Wbd8ZZ4YXG4EuRInP-8jvXsvrWmQgBg8UBWdq18beY7ds4XJqblE16mdWcVAYfU9aQCK--hJ-rnSMQ$>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADUJNC6XX25TS46S4SHABFLR3LTMBANCNFSM4OYL3LBQ><https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ADUJNC6XX25TS46S4SHABFLR3LTMBANCNFSM4OYL3LBQ*3E__;JQ!!NVzLfOphnbDXSw!Wbd8ZZ4YXG4EuRInP-8jvXsvrWmQgBg8UBWdq18beY7ds4XJqblE16mdWcVAYfU9aQCK--gNfRoGPA$> .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Chester75321/GenEpi/issues/5*issuecomment-668624545__;Iw!!NVzLfOphnbDXSw!Wbd8ZZ4YXG4EuRInP-8jvXsvrWmQgBg8UBWdq18beY7ds4XJqblE16mdWcVAYfU9aQCK--gfVVhbJA$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/APU2PHMCXCRA2M2F6FCVINLR7AKF7ANCNFSM4OYL3LBQ__;!!NVzLfOphnbDXSw!Wbd8ZZ4YXG4EuRInP-8jvXsvrWmQgBg8UBWdq18beY7ds4XJqblE16mdWcVAYfU9aQCK--ho-EzKoQ$>.