Error running eQTL mapping and 3D Chromatin Interaction mapping

[Olesya Ajnakina]

Good morning. 

I have been trying to run the Gene Mapping (eQTL mapping) and Gene Mapping (3D Chromatin Interaction mapping) but I keep getting the error below, which remains regardless of the type f the file I upload (txt, gz file zipped). I will be grateful for any helpful. Thank you!

MY DATA: 

  rsID chromosome position allele1 allele2 Beta SE P HWE_pval N MAF

rs114608975 1 86028 C T 0.0556691 0.0850667 0.512887 1 3453 0.0205618

rs6702460 1 91536 T G 0.011155 0.0268511 0.677845 0.866501 3453 0.281929

rs8179466 1 234313 T C 0.0546386 0.107033 0.609746 1 3453 0.0130321

rs6680723 1 534192 T C -0.0356115 0.0480621 0.458776 0.68143 3453 0.0668983

rs12025928 1 546697 A G -0.0348476 0.0695039 0.616138 0.775329 3453 0.031422

THE ERROR IS BELOW:

ErrorException in S2GController.php line 317:implode(): Invalid arguments passed

1. in S2GController.php line 317
2. at HandleExceptions->handleError('2', 'implode(): Invalid arguments passed', '/var/www/fuma/app/Http/Controllers/S2GController.php', '317', array('request' => object(Request), 'date' => '2020-08-09 08:36:42', 'jobID' => '92752', 'filedir' => '/data/fuma/jobs/92752', 'email' => 'x...@xxx.ac.uk', 'type' => 'application/x-gzip', 'jobtitle' => 'None', 'submitJob' => object(SubmitJob), 'leadSNPs' => 'input.lead', 'GWAS' => 'input.gwas', 'regions' => 'input.regions', 'leadSNPsfileup' => '0', 'GWASfileup' => '1', 'regionsfileup' => '0', 'f' => 'snptest_elsa_imputed_fps0_final.txt.gz', 'addleadSNPs' => '1', 'chrcol' => 'chromosome', 'poscol' => 'position', 'rsIDcol' => 'rsID', 'pcol' => 'P', 'eacol' => 'allele1', 'neacol' => 'allele2', 'orcol' => 'NA', 'becol' => 'Beta', 'secol' => 'SE', 'exMHC' => '0', 'MHCopt' => 'NA', 'extMHC' => 'NA', 'ensembl' => null))
3. at implode(':', null) in S2GController.php line 317
4. at S2GController->newJob(object(Request))
5. at call_user_func_array(array(object(S2GController), 'newJob'), array(object(Request))) in Controller.php line 80
6. at Controller->callAction('newJob', array(object(Request))) in ControllerDispatcher.php line 146
7. at ControllerDispatcher->call(object(S2GController), object(Route), 'newJob') in ControllerDispatcher.php line 94
8. at ControllerDispatcher->Illuminate\Routing\{closure}(object(Request))
9. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 52
10. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in Authenticate.php line 28
11. at Authenticate->handle(object(Request), object(Closure))
12. at call_user_func_array(array(object(Authenticate), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
13. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
14. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
15. at Pipeline->Illuminate\Routing\{closure}(object(Request))
16. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 103
17. at Pipeline->then(object(Closure)) in ControllerDispatcher.php line 96
18. at ControllerDispatcher->callWithinStack(object(S2GController), object(Route), object(Request), 'newJob') in ControllerDispatcher.php line 54
19. at ControllerDispatcher->dispatch(object(Route), object(Request), 'fuma\Http\Controllers\S2GController', 'newJob') in Route.php line 174
20. at Route->runController(object(Request)) in Route.php line 140
21. at Route->run(object(Request)) in Router.php line 724
22. at Router->Illuminate\Routing\{closure}(object(Request))
23. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 52
24. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in Authenticate.php line 28
25. at Authenticate->handle(object(Request), object(Closure))
26. at call_user_func_array(array(object(Authenticate), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
27. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
28. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
29. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in VerifyCsrfToken.php line 64
30. at VerifyCsrfToken->handle(object(Request), object(Closure))
31. at call_user_func_array(array(object(VerifyCsrfToken), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
32. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
33. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
34. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in ShareErrorsFromSession.php line 49
35. at ShareErrorsFromSession->handle(object(Request), object(Closure))
36. at call_user_func_array(array(object(ShareErrorsFromSession), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
37. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
38. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
39. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in StartSession.php line 64
40. at StartSession->handle(object(Request), object(Closure))
41. at call_user_func_array(array(object(StartSession), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
42. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
43. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
44. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in AddQueuedCookiesToResponse.php line 37
45. at AddQueuedCookiesToResponse->handle(object(Request), object(Closure))
46. at call_user_func_array(array(object(AddQueuedCookiesToResponse), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
47. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
48. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
49. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in EncryptCookies.php line 59
50. at EncryptCookies->handle(object(Request), object(Closure))
51. at call_user_func_array(array(object(EncryptCookies), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
52. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
53. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
54. at Pipeline->Illuminate\Routing\{closure}(object(Request))
55. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 103
56. at Pipeline->then(object(Closure)) in Router.php line 726
57. at Router->runRouteWithinStack(object(Route), object(Request)) in Router.php line 699
58. at Router->dispatchToRoute(object(Request)) in Router.php line 675
59. at Router->dispatch(object(Request)) in Kernel.php line 246
60. at Kernel->Illuminate\Foundation\Http\{closure}(object(Request))
61. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 52
62. at Pipeline->Illuminate\Routing\{closure}(object(Request)) in CheckForMaintenanceMode.php line 44
63. at CheckForMaintenanceMode->handle(object(Request), object(Closure))
64. at call_user_func_array(array(object(CheckForMaintenanceMode), 'handle'), array(object(Request), object(Closure))) in Pipeline.php line 136
65. at Pipeline->Illuminate\Pipeline\{closure}(object(Request))
66. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 32
67. at Pipeline->Illuminate\Routing\{closure}(object(Request))
68. at call_user_func(object(Closure), object(Request)) in Pipeline.php line 103
69. at Pipeline->then(object(Closure)) in Kernel.php line 132
70. at Kernel->sendRequestThroughRouter(object(Request)) in Kernel.php line 99
71. at Kernel->handle(object(Request)) in index.php line 54

[Kyoko Watanabe]

Hi,

It looks like ensembl version and gene type were not selected correctly.

Could you check if any option is selected under "4. Gene types" on the SNP2GENE submission page?

 

I've been getting the same question a lot lately, I'm not sure in which scenario this error occurs.

I'd love to fix this bug but I can't replicate the error.

Could you tell me bit about what you did to get this error?

Also, which browser do you use?

Best,

Kyoko