Check your job logs in the Job Details view (using the i-info icon). Is the job failing for memory reasons? Like this topic below?
For your use case, since you are already filtering for the contig length with this Quast parameter setting:
You could try pre-filtering the lengths first to reduce the size of the input data, and maybe avoid this error?
Search the tool panel for: Filter sequences by length
You can run this on the entire collection. If some of the samples are now empty, you might need to then run Filter empty datasets before running Quast.
If you want to share your history, we might be able to suggest more pre-steps or different Quast parameters to try. Thanks!
Ok, thanks for clarifying @Martyn, the memory error was a guess since it is more common.
If the error instead states the job is exceeding runtime resources, that is a bit different for the root cause, but still the same result with similar solutions. The EU server doesn’t apply walltime at all but they will eventually kill runaway jobs.
Hi JennaJ, how do I do it on the EU server. Do i need to submit my Assembly with MEGAHIT on collection to the EU version or do i have to start it all over again?
Instead, you can copy the data you want to move over into a new smaller history on the “from” server, then move that history over to the “to” server. You can also move individual files if you ever need to.
Hi everyone, I have tried subsampling the data on the EU server and I am still getting the same error message. This is really frustrating as i have tried everything now. Is the issue QUAST itself?
What happens if your run a tool like Fasta Statistics on the data? Can that tool understand the data in your collections or does it report a problem? If it runs, does anything else look unexpected in the summary?
I am also curious about what happens if you try to run on just one genome file?
You are welcome to share the EU history back. Please leave the subset and statistics job in there too please. Maybe we can help to recognize what the problem is.
In the job logs (using the i-con), I see the root message.
Text versions of reports and plots for each metric (for all references and assemblies) are saved to /data/jwd06/main/080/801/80801793/working/outputdir/summary/
Icarus (contig browser) is saved to /data/jwd06/main/080/801/80801793/working/outputdir/icarus.html
Drawing interactive Krona plots...
WARNING: Error occurred while build Krona charts, skipping... You can disable drawing Krona (and thus, this warning) with "--no-krona".
Extended version of HTML-report (for all references and assemblies) is saved to /data/jwd06/main/080/801/80801793/working/outputdir/report.html
The tool is having trouble processing one of the output files, specifically the Krona plot. But it also states that the step was skipped. Confusing!
I’m rerunning with that option not selected to see what happens. Maybe the other log files will be informative. This is the link to that history. We can follow up more once it is completed. (some reports are already produced)
I set different output parameters. You can review what I did versus what you did by comparing the job details pages from the different runs (these summarize the parameters used each time).
From that result (HTML report), the underlying problem seems to be that the assembly for some accessions didn’t work very well, resulting in too many contigs for the Krona chart tool to handle. You could leave those out and try running this with just the successful assemblies?
