ErrorException in S2GController.php line 317

[parveen...@gmail.com]

Hello,

After uploading my data in .tsv format, i get this type of error. Kindly help me to resolving this out.

 ######################################

ErrorException in S2GController.php line 317:

implode(): Invalid arguments passed

in S2GController.php line 317

at HandleExceptions->handleError('2', 'implode(): Invalid arguments passed', '/var/www/fuma/app/Http/Controllers/S2GController.php', '317', array('request' => object(Request), 'date' => '2020-06-02 12:25:35', 'jobID' => '83263', 'filedir' => '/data/fuma/jobs/83263', 'email' => 'parveen...@gmail.com', 'type' => 'text/plain', 'jobtitle' => 'None', 'submitJob' => object(SubmitJob), 'leadSNPs' => 'input.lead', 'GWAS' => 'input.gwas', 'regions' => 'input.regions', 'leadSNPsfileup' => '0', 'GWASfileup' => '1', 'regionsfileup' => '0', 'addleadSNPs' => '1', 'chrcol' => 'NA', 'poscol' => 'NA', 'rsIDcol' => 'NA', 'pcol' => 'NA', 'eacol' => 'NA', 'neacol' => 'NA', 'orcol' => 'NA', 'becol' => 'NA', 'secol' => 'NA', 'exMHC' => '0', 'MHCopt' => 'NA', 'extMHC' => 'NA', 'ensembl' => null))

at implode(':', null) in S2GController.php line 317

at S2GController->newJob(object(Request))

at call_user_func_array(array(object(S2GController), 'newJob'), array(object(Request))) in Controller.php line 80

at Controller->callAction('newJob', array(object(Request))) in ControllerDispatcher.php line 146

at ControllerDispatcher->call(object(S2GController), object(Route), 'newJob') in ControllerDispatcher.php line 94

at ControllerDispatcher->Illuminate\Routing\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 52

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in Authenticate.php line 28

at Authenticate->handle(object(Request), object(Closure))

at call_user_func_array(array(object(Authenticate), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 103

at Pipeline->then(object(Closure)) in ControllerDispatcher.php line 96

at ControllerDispatcher->callWithinStack(object(S2GController), object(Route), object(Request), 'newJob') in ControllerDispatcher.php line 54

at ControllerDispatcher->dispatch(object(Route), object(Request), 'fuma\Http\Controllers\S2GController', 'newJob') in Route.php line 174

at Route->runController(object(Request)) in Route.php line 140

at Route->run(object(Request)) in Router.php line 724

at Router->Illuminate\Routing\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 52

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in Authenticate.php line 28

at Authenticate->handle(object(Request), object(Closure))

at call_user_func_array(array(object(Authenticate), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in VerifyCsrfToken.php line 64

at VerifyCsrfToken->handle(object(Request), object(Closure))

at call_user_func_array(array(object(VerifyCsrfToken), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in ShareErrorsFromSession.php line 49

at ShareErrorsFromSession->handle(object(Request), object(Closure))

at call_user_func_array(array(object(ShareErrorsFromSession), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in StartSession.php line 64

at StartSession->handle(object(Request), object(Closure))

at call_user_func_array(array(object(StartSession), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in AddQueuedCookiesToResponse.php line 37

at AddQueuedCookiesToResponse->handle(object(Request), object(Closure))

at call_user_func_array(array(object(AddQueuedCookiesToResponse), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in EncryptCookies.php line 59

at EncryptCookies->handle(object(Request), object(Closure))

at call_user_func_array(array(object(EncryptCookies), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 103

at Pipeline->then(object(Closure)) in Router.php line 726

at Router->runRouteWithinStack(object(Route), object(Request)) in Router.php line 699

at Router->dispatchToRoute(object(Request)) in Router.php line 675

at Router->dispatch(object(Request)) in Kernel.php line 246

at Kernel->Illuminate\Foundation\Http\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 52

at Pipeline->Illuminate\Routing\{closure}(object(Request)) in CheckForMaintenanceMode.php line 44

at CheckForMaintenanceMode->handle(object(Request), object(Closure))

at call_user_func_array(array(object(CheckForMaintenanceMode), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136

at Pipeline->Illuminate\Pipeline\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32

at Pipeline->Illuminate\Routing\{closure}(object(Request))

at call_user_func(object(Closure), object(Request)) in Pipeline.php line 103

at Pipeline->then(object(Closure)) in Kernel.php line 132

at Kernel->sendRequestThroughRouter(object(Request)) in Kernel.php line 99

at Kernel->handle(object(Request)) in index.php line 54

##############################################

Thanks and regards

Kayenat Parveen

Email : parveen...@gmail.com

[parveen...@gmail.com]

Sorry my email is parveen...@gmail.com

[DP Wightman]

Hi Kayenat,

It seems to have a problem when combining gene type options into a string. Do you know what option you chose for gene type? Did you input column names?

Cheers,

Doug

[kayenat parveen]

Hello,

Thank you for your reply. I am not understanding the gene type. Actually, i am working on Psychiatric disorders, so the diseases of my interest are Parkinsons, Alzheimer, Depression etc. I am uploading the file in .tsv as well as .txt format and using the default format of fuma but SNP2GEN is not working. I am sending you the overview of my input file, please have a look and tell me what is wrong with this. It is really urgent.

chrom pos pvalue 

1 100021041 0.005306

1 100035028 0.01316

1 100037608 0.01316

1 100038236 0.01316

1 100039072 0.01883

1 100040904 0.01316

1 100042142 0.01883

1 100042988 0.01316

1 100043983 0.01316

1 100045961 0.03493

1 100047895 0.01316

1 100047942 0.01883

1 100048184 0.03493

Best Regards

Kayenat Parveen

[DP Wightman]

I don't see any problem with your input file format. From the error it appears that many input parameters were not specified or there is a problem with parsing the parameters.

To see if it is the first problem, please try using a different browser and specifying the input parameters (selecting 'All' in the gene type box of the gene types section on the submission page or giving a specific column name in section 1 of the submission page).

If you have specified parameters and still get the same error, where all of these are NA or null:

'jobtitle' => 'None', 'chrcol' => 'NA', 'poscol' => 'NA', 'rsIDcol' => 'NA', 'pcol' => 'NA', 'eacol' => 'NA', 'neacol' => 'NA', 'orcol' => 'NA', 'becol' => 'NA', 'secol' => 'NA', 'MHCopt' => 'NA', 'extMHC' => 'NA', 'ensembl' => null

then it is likely that something is going wrong with the submission process.

Cheers,

Doug

[kayenat parveen]

Hello,

Thank you for your reply. Yes there is the problem with submission process because i use another web server (which is Microsoft edge) and the problem is same.

#################

ErrorException in S2GController.php line 317:

implode(): Invalid arguments passed

in S2GController.php line 317

at HandleExceptions->handleError('2', 'implode(): Invalid arguments passed', '/var/www/fuma/app/Http/Controllers/S2GController.php', '317', array('request' => object(Request), 'date' => '2020-06-03 15:28:44', 'jobID' => '83554', 'filedir' => '/data/fuma/jobs/83554', 'email' => 's4ka...@uni-bonn.de', 'type' => 'text/plain', 'jobtitle' => 'None', 'submitJob' => object(SubmitJob), 'leadSNPs' => 'input.lead', 'GWAS' => 'input.gwas', 'regions' => 'input.regions', 'leadSNPsfileup' => '0', 'GWASfileup' => '1', 'regionsfileup' => '0', 'addleadSNPs' => '1', 'chrcol' => 'NA', 'poscol' => 'NA', 'rsIDcol' => 'NA', 'pcol' => 'NA', 'eacol' => 'NA', 'neacol' => 'NA', 'orcol' => 'NA', 'becol' => 'NA', 'secol' => 'NA', 'exMHC' => '0', 'MHCopt' => 'NA', 'extMHC' => 'NA', 'ensembl' => null))

#################

So how it will be resolve. Please help me in this regard.

Thanks and regards

Kayenat Parveen

PhD scholar

University Hospital Bonn, Germany

[Ming-Ju Tsai]

Hi,

I also received the same error message when trying to upload the summary statistics file.
I have checked S2GController.php line 317 that is $genetype = implode(":", $request -> input('genetype'));

I did choose the Protein coding for the gene type.

Could you help me figure out where the problem is?

Thanks,

Ming-Ju

[Kyoko Watanabe]

Hi Ming-Ju,

I'm sorry about the error, I've been getting similar reports several times but I'm having trouble figuring out what is exactly causing this problem since I cannot replicate the same error.

Could you share below information?

Your browser

Your OS

All parameters you set (you can skip default parameters)

Best regards,

Kyoko