You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Using nf-aggregate with run IDs greater than 20 sometimes encounters a connection timeout. I tried to trace the API calls, but they don't seem to be consistently directed only to a specific endpoint.
Aug-01 13:29:26.497 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=36; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-01 13:31:29.957 [Actor Thread 8] WARN nextflow.Nextflow -
Could not get workflow details for workflow 1FJPW8FdT638Ek in workspace Mark/mark-private:
↳ Status code null returned from request to https://api.cloud.seqera.io/orgs (authentication headers excluded)
Aug-01 13:31:29.960 [Actor Thread 8] ERROR nextflow.Nextflow - Exception: Connection timed out
wslite.rest.RESTClientException: Connection timed out
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
Command used and terminal output
1. Create a runids.csv input file with 50 or more run ids.2. Run the following locally or on Platform.nextflow run seqeralabs/nf-aggregate --input runids1.csv --outdir ./results -profile docker -w ./work/
### Relevant files
_No response_
### System information
Aug-01 13:29:15.059 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.04.2 build 5914
Created: 29-05-2024 06:19 UTC (02:19 EDT)
System: Linux 5.15.153.1-microsoft-standard-WSL2
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.6+10
Encoding: UTF-8 (UTF-8)
Process: 501537@LAPTOP-CURHNF2E [127.0.1.1]
CPUs: 12 - Mem: 15.5 GB (13.6 GB) - Swap: 4 GB (4 GB)
It happens on both local executor and AWS Batch.
The text was updated successfully, but these errors were encountered:
Description of the bug
Using nf-aggregate with run IDs greater than 20 sometimes encounters a connection timeout. I tried to trace the API calls, but they don't seem to be consistently directed only to a specific endpoint.
Command used and terminal output
Aug-01 13:29:15.059 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.04.2 build 5914
Created: 29-05-2024 06:19 UTC (02:19 EDT)
System: Linux 5.15.153.1-microsoft-standard-WSL2
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.6+10
Encoding: UTF-8 (UTF-8)
Process: 501537@LAPTOP-CURHNF2E [127.0.1.1]
CPUs: 12 - Mem: 15.5 GB (13.6 GB) - Swap: 4 GB (4 GB)
The text was updated successfully, but these errors were encountered: