positional mapping

[kayenat parveen]

Hello,

Whenever i am performing positional mapping it always shows error. Please help me in this regard. The glipmse of my file is below:

CHR BP non_effect_allele effect_allele pval

chr1 662613 G A 0.758458211403948

chr1 662622 G A 0.537557518016488

chr1 668394 AG A 0.939594709486159

chr1 676118 C T 0.962571834242852

THE ERROR IS BELOW:

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' => '2020-07-30 22:35:04', 'jobID' => '91615', 'filedir' => '/data/fuma/jobs/91615', '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

[Kyoko Watanabe]

Hi,

It looks like Ensembl version and gene types are not selected.

Could you check both ensembl version and genetype are selected under section "4. Gene type" on the submission page?

Could you also tell me exactly what you did to get this error? It's probably a minor bug, I'll try to fix it.

Did you load the previous parameter set or did you manually set?

If you did load the previous parameter, what is the jobID of that?

Best,

Kyoko