I’m quite new at running galaxy from local (but used galaxy.org and galaxy.eu for years) so I might be unaware of some basics.
It seems that there are different issues although the prompt does not yield Error messages.
- I run a workflow (Fasta Split, Bowtie2, ivar variants, … VCF combine) on a dataset collection of 10000 fasta files (one sequence of 4kb each file). It seemed to work fine for three days up to tonight that got stuck before the last step VCFCombine.
- The entire workflow was tested on a collection on 20 files and worked perfectly.
- Approximately at the same time my computer got its wifi connection broken but now has been repaired (I don’t know if it is connected to Galaxy issue).
- My history (450 Mb used) shows the last step (VCV combine) paused, and the two previous steps finished in green.
- I have Galaxy installed in a Virtual machine (VirtualBox) 20 GB RAM and 23 GB memory left.
- Every time I load the localhost:8080 interface and click any button to stuck for a while
- I tried to download a whole dataset collection from the interface but did not produce anything
- When I look at the local folder database/jobs_directory/ there are several folders but ALL empty
- When I resume the paused job from the history menu, the prompt says:
“was paused before the job started, Input dataset ‘Variants (VCF)’ was paused before the job started, Input dataset ‘Variants (VCF)’ was paused before the job started. To resume this job fix the input dataset(s).”
How could I resume the last job or fix the input dataset?
I also would like to download the dataset collection just in case I have to do the last step using command line. Anything that saves the work done.
I would appreciate very much any help and advice.