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sanger-pathogens / annot-web

This repository has been archived, currently maintained version is at https://github.com/iii-companion/annot-web
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missing pseudochr.fasta.gz for Leishmania in Public server #34

Open janxkoci opened 3 years ago

janxkoci commented 3 years ago

Multiple users have problem running Companion with Leishmania mexicana. I have found the issue has been first reported in the repo for standalone version, so I wanted to also bring it to attention here.

I see the same error as the user who reported the original issue, I include the error below for completeness:

/www/companion/annot-web/app/workers/hard_worker.rb:34:in `add_result_file': required file not present: /www/companion/annot-web/public/jobs/9dbbee2d4a721d45b3ef72bd/pseudochr.fasta.gz (RuntimeError)
    /www/companion/annot-web/app/workers/hard_worker.rb:142:in `perform'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:150:in `execute_job'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:132:in `block (2 levels) in process'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:127:in `block in invoke'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-status-0.6.0/lib/sidekiq-status/server_middleware.rb:37:in `call'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/active_record.rb:6:in `call'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/retry_jobs.rb:74:in `call'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/logging.rb:11:in `block in call'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/logging.rb:30:in `with_context'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/logging.rb:7:in `call'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:132:in `invoke'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:127:in `block in process'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:166:in `stats'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:126:in `process'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:79:in `process_one'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:67:in `run'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/util.rb:16:in `watchdog'
    /www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/util.rb:24:in `block in safe_thread'
asgiraldoc commented 3 years ago

Hey, did they give you an answer? I have the same issue for Plasmodium falciparum

janxkoci commented 3 years ago

Nope.