Problem gathering output collection after Datatype class not found for extension 'mzML'

[sneumann]

I used a recent PhenoMeNal installation, data of MTBLS36 was downloaded with Metabolights downloader "Import public and private MetaboLights studies (Galaxy Version 3.1.0)" mtbls-dwnld&version=3.1.0 and then I wanted to extract with "ISA to mzML Extract mzML files from an ISA dataset and output a collection of mzML dataset. (Galaxy Version 1.1.0)" tool_id=isa2mzml&version=1.1.0.

The mzML collection in Galaxy turned yellow, and remained yellow even after the container had exited. The Galaxy logs show

galaxy.tools.parameters.output_collect DEBUG 2018-05-31 08:52:20,816 (3) Created dynamic collection dataset for path [/opt/galaxy_data/database/job_working_directory/000/3/working/mzML/neg_20100924_14_TomQC.mzML] with element identifier [neg_20100924_14_TomQC] for output [mzML] (19801.079 ms)
galaxy.model WARNING 2018-05-31 08:52:20,846 Datatype class not found for extension 'mzML'
galaxy.model WARNING 2018-05-31 08:52:20,847 Datatype class not found for extension 'mzML'
galaxy.model WARNING 2018-05-31 08:52:20,847 Datatype class not found for extension 'mzML'
galaxy.tools.parameters.output_collect ERROR 2018-05-31 08:52:20,874 Problem gathering output collection.
galaxy.jobs INFO 2018-05-31 08:52:27,298 Collecting metrics for Job 3
galaxy.jobs DEBUG 2018-05-31 08:52:27,881 job 3 ended (finish() executed in (3235299.488 ms))

I retried today with the same result, so at least its reproducible ...

The following is the screenshot of the "workflow": Download works, ISA to W4M works, but the ISA to mzML hangs.

Yours, Steffen

[djcomlab]

@pkrog @sneumann is this still broken?

[pkrog]

I didn't test it. It's quite a big study. I've tried on publicdev, but it takes too long, I canceled the job. @sneumann ?