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Unable to upload reference genomes #43

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nalamvj opened this issue Jul 19, 2022 · 6 comments
Open

Unable to upload reference genomes #43

nalamvj opened this issue Jul 19, 2022 · 6 comments

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@nalamvj
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nalamvj commented Jul 19, 2022

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
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alaimos commented Jul 22, 2022

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
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nalamvj commented Aug 2, 2022

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

@amarinderthind
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amarinderthind commented Aug 17, 2022

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

@nalamvj
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nalamvj commented Oct 11, 2022 via email

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

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