Open nikhil777shingte opened 1 year ago
Hi,
Based on the error message, the resource allocated for canu isn't enough for it to run. You can adjust the WDL accordingly when running the pipeline.
That being said, canu is resource hungry and the mouse genome is large. So the assembly could run for weeks for your data (it could be really really expensive). The workflow is really written for the assembly of small genomes. I'd advise planning your analysis strategy accordingly before running this pipeline.
Regards, Steve
Hi Steve, thanks for your response. I was actually able to run this successfully with relatively inexpensive cost ( less than 10$ )
I should provide more context.
Sequencing Data I have is coming ONT sequencer with adaptive sampling. Due to this, I have to run few more steps in addition to the this pipeline to select region of interest for which I have the reads. I have forked repository and made changes so that I am able to pass Canu parameter of estimated size given my adaptive sampling reads.
Earlier, mouse genome size used by Canu was incorrect in my case since my data is from adaptive sampling.
You can find more details here :
https://github.com/nikhil777shingte/long-read-pipelines/tree/test-long-read-canu-assembly
I still have changes made for the Canu resources here [ when it was using mouse genome size ] but with workflow changes I have done, dont think Canu will be resource intensive and able to finish the pipeline within couple of hours.
Link to dockstore published workflow : https://dockstore.org/workflows/github.com/nikhil777shingte/long-read-pipelines/ONTAssembleWithCanuAdaptiveSampling:test-long-read-canu-assembly
Terra details :
ONTAssembleWithCanuAdaptiveSampling ID: 9aadab80-9ca6-4b89-b29b-459295d9097a
workspace-id: 88614ae6-5245-4a6e-ab14-5c3fc9d007a2 submission-id: 4c630f67-bdbe-4521-b415-4205c5828429
I am not sure if you have adaptive sampling support already in current pipeline or have that in your backlog, but would be good to hear your thoughts.
Thanks Nikhil
I am trying to run a long read pipeline with ONT long reads data for mouse models using Terra platform.
I was able to run https://github.com/broadinstitute/long-read-pipelines/blob/kvg_guppy_cpu/wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl successfully using my fast5 files.
When I am trying to run https://github.com/broadinstitute/long-read-pipelines/blob/3.0.1/wdl/ONTAssembleWithCanu.wdl , I am running into the below issue. Can you please advise.