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knowmics-lab / RNAdetector

RNAdetector: a free user-friendly and stand-alone software for RNA-Seq data analysis
https://rnadetector.atlas.dmi.unict.it/index.html
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Unable to upload reference genomes #43

Open nalamvj opened 2 years ago

nalamvj commented 2 years ago

I have been looking for a tool like this for a long time. And I am really looking forward to using it. But when I try to upload a reference genome, I keep getting the following error: Starting job. Error: ErrorException: rename(/rnadetector/ws/storage/app/public/jobs/11//rnadetector/ws/storage/app/public/jobs/11/genome.fa,/rnadetector/ws/storage/app/references//aglycines/reference.fa): No such file or directory in /rnadetector/ws/app/Jobs/Types/ReferenceUploadJobType.php:293

Any help/guidance to help resolve this issue will be greatly appreciated?

alaimos commented 2 years ago

Hi, Thank you for your interest in RNAdetector. Do you have more details about this error? For example, the complete error log, the genome you are using, and the parameters you select in the GUI? These details could help us reproduce the error.

nalamvj commented 1 year ago

Hello @alaimos, did you get my email with the details about the error? Please let me know. Thanks.

amarinderthind commented 1 year ago

I also got error while uploading reference fasta, it ask to select one mapping tool name for indexing. But in log it fails.

Whats is the meaning of this line Choose which alignment algorithms will be available for this sequence, do we suppose to install mapping tool separately?

`Starting job. Error: ErrorException: rename(/rnadetector/ws/storage/app/public/jobs/5//rnadetector/ws/storage/app/public/jobs/5/hg38_GRCh38.p13.fa,/rnadetector/ws/storage/app/references//hg38GRCh38p13/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}`

amarinderthind commented 1 year ago

Reference genome index building works for STAR, but not for other tools.

nalamvj commented 1 year ago

Hello,

Thank for getting back to me. Here are more details about the error.

  1. The complete error log is attached
  2. I am trying to upload the reference genome for soybean aphid (Aphis glycines)
  3. I chose Reference sequences and followed the steps to upload the reference genome. The genome size is around 308 Mb.
  4. I have not proceeded with RNA-seq Analysis because the reference genome is required for this step.

Please let me know if you need any other information.

Thanks,

Vamsi

On Fri, Jul 22, 2022 at 2:09 AM Salvatore Alaimo @.***> wrote:

Thank you for your interest in RNAdetector. Do you have more details about this error? For example, the complete error log, the genome you are using, and the parameters you select in the GUI? These details could help us reproduce the error.

— Reply to this email directly, view it on GitHub https://github.com/alessandrolaferlita/RNAdetector/issues/43#issuecomment-1192303494, or unsubscribe https://github.com/notifications/unsubscribe-auth/AYYXD7S6WCKDMI7DB7Q7ZQ3VVJJMZANCNFSM54BQZXWA . You are receiving this because you authored the thread.Message ID: @.***>

RNAdetector Jobs list Actions Create and index reference Aglycines Reference Upload Failed 32 seconds ago
Create and index reference Aglycines Reference Upload Failed 5 minutes ago
Create and index reference Aglycines Reference Upload Failed 1 day ago
Rows per page:

15 1-3 of 3

Logs of Create and index reference Aglycines Starting job. Error: ErrorException: rename(/rnadetector/ws/storage/app/public/jobs/16//rnadetector/ws/storage/app/public/jobs/16/SBAphid_ref_genome_v6.fa,/rnadetector/ws/storage/app/references//Aglycines/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}

chrysanthemyl commented 1 year ago

Just commenting in case it helps others - I was able to upload a genome in gz format, but not the unzipped fasta.