I have used the Create assembly with Unicycler tool for genome assembly from Illumina paired end sequence reads on Usegalaxy.org. But from yesterday I have been trying to use this tool and the job is waiting to run, it has been more than 24 hours and I dont understand why is it not running. Please help.
The job started on "Created: Mon 03 Sep 2018 05:11:44 AM (UTC)" has finished. It ended with an error because the same dataset was selected for both the forward and reverse input reads (data 233).
You can skip the Fastq Groomer step because the data is already in
fastqsanger format (and assigned that datatype). It looks like the inputs you will want to use instead are data 211 (forward) and 212 (reverse).
I ran a couple of test Unicyler jobs earlier this morning just to make sure the PCS Bridges cluster service was functional and those came back successful. The delay with your prior (now deleted) Unicycler jobs were probably due to Bridges being busy. Also, launching multiple jobs or deleting queued jobs then starting up new rerun jobs can also cause delays.
In almost all cases it is best to allow a queued job to remain queued until complete. The only exception is if you know there a problem and wish to discard that run (wrong inputs or tool settings). Deleting and rerunning does not make a job run quicker, it only adds the job back to the end of the queue, extending wait time (your original queue placement is lost).
- Datasets and how jobs execute
- My job ended with an error. What can I do?
- How to format fastq data for tools that require .fastqsanger format?
Please try a new run with the proper inputs and allow it to run to completion. If there are problems, review your FastQC results and do some QA/QC (if needed), then try again.
- NGS logistics
- How to interpret FastQC module results: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Analysis-specific QA/QC is also included in many of the other Galaxy tutorials, including those from the Galaxy Training Network (GTN). All are linked from the Tutorials home page.
Thanks! Jen, Galaxy team