Cannot input fastq.gz, ref genome or genome annotation

[thomchr]

Hi, I really like this software in principal and am trying to get it to work! When I open the software I can load my files - I'd like to do this using gz files though, are fastq.gz files not supported? Second, when I get to specifying reference genome/genome annotation there are no options from the dropdown box - is this related to files or is there a problem with my setup? Where I expect a list of species/genomes there is a blank line. Thanks for any advice!

[alaimos]

Hi, I appreciate your interest in RNAdetector. Regarding your question, ".gz" files are supported by the software. When you select the FASTQ format, RNAdetector can automatically detect if you are using a compressed file or a regular FASTQ file.

For your second issue, did you install any reference genome from our repository (or load a custom genome) before trying analysis? Further details can be found here: https://github.com/alessandrolaferlita/RNAdetector/wiki/Add-reference-and-annotation-files.

[mjm269]

I am having the same problem it gives me an error when I try and upload a reference transcriptome. It does not matter what mapper I chose or if I have the fasta file as .fa .fasta or anything else.

The error is below

Starting job. Error: ErrorException: rename(/rnadetector/ws/storage/app/public/jobs/5//rnadetector/ws/storage/app/public/jobs/5/Eragrostis_tef.ASM97063v1.cdna.all.fasta,/rnadetector/ws/storage/app/references//teff/reference.fa): No such file or directory in /rnadetector/ws/app/Jobs/Types/ReferenceUploadJobType.php:293 Stack trace:

0 [internal function]: Illuminate\Foundation\Bootstrap\HandleExceptions->handleError()

1 /rnadetector/ws/app/Jobs/Types/ReferenceUploadJobType.php(293): rename()

2 /rnadetector/ws/app/Jobs/Request.php(72): App\Jobs\Types\ReferenceUploadJobType->handle()

3 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/BoundMethod.php(36): App\Jobs\Request->handle()

4 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/Util.php(37): Illuminate\Container\BoundMethod::Illuminate\Container{closure}()

5 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/BoundMethod.php(93): Illuminate\Container\Util::unwrapIfClosure()

6 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/BoundMethod.php(37): Illuminate\Container\BoundMethod::callBoundMethod()

7 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/Container.php(590): Illuminate\Container\BoundMethod::call()

8 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Bus/Dispatcher.php(94): Illuminate\Container\Container->call()

9 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php(130): Illuminate\Bus\Dispatcher->Illuminate\Bus{closure}()

10 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php(105): Illuminate\Pipeline\Pipeline->Illuminate\Pipeline{closure}()

11 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Bus/Dispatcher.php(98): Illuminate\Pipeline\Pipeline->then()

12 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/CallQueuedHandler.php(83): Illuminate\Bus\Dispatcher->dispatchNow()

13 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php(130): Illuminate\Queue\CallQueuedHandler->Illuminate\Queue{closure}()

14 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php(105): Illuminate\Pipeline\Pipeline->Illuminate\Pipeline{closure}()

15 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/CallQueuedHandler.php(85): Illuminate\Pipeline\Pipeline->then()

16 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/CallQueuedHandler.php(59): Illuminate\Queue\CallQueuedHandler->dispatchThroughMiddleware()

17 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/Jobs/Job.php(88): Illuminate\Queue\CallQueuedHandler->call()

18 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/Worker.php(368): Illuminate\Queue\Jobs\Job->fire()

19 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/Worker.php(314): Illuminate\Queue\Worker->process()

20 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/Worker.php(134): Illuminate\Queue\Worker->runJob()

21 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/Console/WorkCommand.php(112): Illuminate\Queue\Worker->daemon()

22 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Queue/Console/WorkCommand.php(96): Illuminate\Queue\Console\WorkCommand->runWorker()

23 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/BoundMethod.php(36): Illuminate\Queue\Console\WorkCommand->handle()

24 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/Util.php(37): Illuminate\Container\BoundMethod::Illuminate\Container{closure}()

25 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/BoundMethod.php(93): Illuminate\Container\Util::unwrapIfClosure()

26 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/BoundMethod.php(37): Illuminate\Container\BoundMethod::callBoundMethod()

27 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Container/Container.php(590): Illuminate\Container\BoundMethod::call()

28 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Console/Command.php(134): Illuminate\Container\Container->call()

29 /rnadetector/ws/vendor/symfony/console/Command/Command.php(255): Illuminate\Console\Command->execute()

30 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Console/Command.php(121): Symfony\Component\Console\Command\Command->run()

31 /rnadetector/ws/vendor/symfony/console/Application.php(1009): Illuminate\Console\Command->run()

32 /rnadetector/ws/vendor/symfony/console/Application.php(273): Symfony\Component\Console\Application->doRunCommand()

33 /rnadetector/ws/vendor/symfony/console/Application.php(149): Symfony\Component\Console\Application->doRun()

34 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Console/Application.php(93): Symfony\Component\Console\Application->run()

35 /rnadetector/ws/vendor/laravel/framework/src/Illuminate/Foundation/Console/Kernel.php(131): Illuminate\Console\Application->run()

36 /rnadetector/ws/artisan(37): Illuminate\Foundation\Console\Kernel->handle()

37 {main}