missing pseudochr.fasta.gz for Leishmania in Public server (is Companion still supported)

[rosshandler]

Dear Companion team,

I would like to use your public server for annotating some assemblies from leishmania that I have generated. However, it seems to me that the server does not actually contain the training sets mentioned in the webpage list. I have use a Leishmania mexicana downloaded from NCBI and the job fails, despite a lot testing of trial and error. The error obtained is the below. I have emailed the contact address given in the website but no one replies. Is it still supported? I appreciate your input.

/www/companion/annot-web/app/workers/hard_worker.rb:34:in add_result_file': required file not present: /www/companion/annot-web/public/jobs/74f8275b60bbaeba61562e29/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'

Many thanks,
Ivan

[janxkoci]

We have the same issue with Lmex too. Have you found any solution?

I'm thinking about disabling pseudochromosome contiguation (in step 5), as that step uses pseudochromosomes, to see if it makes any difference. Have you tried or considered this?

Btw on their twitter they seem to be looking for programmers.

Thanks for any help.