Closed joyleng closed 7 months ago
nggvs
commented
1 year ago Hi!
Thank you for using the workflow! Just to be sure, what do you mean by this: the fixes suggested ? You can change the rank level using the --taxonomic_rank flag.
I suspect that some input files from the report might be empty. I will try to reproduce the error.
joyleng
commented
1 year ago Hi
Thanks for getting back to me. I thought there were a couple of people who had reported something similar but now I look again the errors are slightly different. I am using the EPI2ME downloaded programme and when I set the taxonomic rank to genus it works fine but when I set it to species it errors at some point when it's trying to make the report.
Joy
nggvs
commented
1 year ago Hi @joyleng , Apologies for the late answer. Could you send me the content of the bracken folder (you can zip it) in the "Outputs" (you'll see that in the app, clicking in the "stopped by error", "Overview" tab, "Outputs")?
Also, what are the resources of the device where you are running the workflow?
joyleng
commented
1 year ago Hi
I have attached the zipped bracken folder below.
In terms of the second question - do you need information on the device that I am running the programme on?
Thanks again Joy
nggvs
commented
8 months ago Hi @joyleng , Could you retry this with the latest release? A 137 error normally is due to there is not enough RAM memory.
nggvs
commented
7 months ago Hi @joyleng , Are you still getting this 137 error? If not, would you mind to close the ticket? If you think you have enough resources, let me know and I could explain you how to override the memory assigned for each process by default using a config file. Thank you very much,
Operating System
Windows 10
Other Linux
No response
Workflow Version
v2.5.0
Workflow Execution
EPI2ME Desktop application
EPI2ME Version
v2.5.0
CLI command run
No response
Workflow Execution - CLI Execution Profile
None
What happened?
Hi
I have seen this error on a couple of issues and tried the fixes suggested but I am still getting the same error. I have amplified the v1-v2 region of the 16S in 59 samples and then sequenced them on the MinION. I am looking to generate bacterial species sequence count data so that I can import it into R for further analyses. However I keep getting the same error but sometimes for 29 samples, sometimes 22. I have tried this with both the 16S and the metagenomics workflows and I am getting the same error, but after a different number of samples every time. I have used the KRAKEN2 option and the NCBI database. The 16s workflow using KRAKEN and NCBI did compete without errors when I set it to run to genus level but I would ideally like to generate data down to species. From the error it seems to me its getting stuck generating one of the plots in the report.
Any help would be much appreciated
Many thanks Joy
Relevant log output
Application activity log entry