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GargGroup / BioDivGenomics

MIT License
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Add assembly logic. #18

Closed junaruga closed 1 year ago

junaruga commented 1 year ago
junaruga commented 1 year ago

The hifiasm command was killed by GitHub Actions, maybe due to the over using memory. We need to limit the memory for the hifiasm.

https://github.com/GargGroup/BioDivGenomics/runs/8303250489?check_suite_focus=true#step:12:1293

 [2022-09-12 10:24:52,61] [info] WorkflowManagerActor: Workflow f404e391-a6dc-4372-97f6-958e8c64b011 failed (during ExecutingWorkflowState): Job assembly.hifiasm:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /tmp/1662978213257-0/cromwell-executions/bio_diversity_genomics/f404e391-a6dc-4372-97f6-958e8c64b011/call-assembly/assembly/a951fe84-6bed-414b-a8f3-c30d16a70180/call-hifiasm/execution/stderr.
 [First 3000 bytes]:/cromwell-executions/bio_diversity_genomics/f404e391-a6dc-4372-97f6-958e8c64b011/call-assembly/assembly/a951fe84-6bed-414b-a8f3-c30d16a70180/call-hifiasm/execution/script: line 30:    18 Killed                  hifiasm -o tmp/hifiasm/asm -t10 -z40 "/cromwell-executions/bio_diversity_genomics/f404e391-a6dc-4372-97f6-958e8c64b011/call-assembly/assembly/a951fe84-6bed-414b-a8f3-c30d16a70180/call-hifiasm/inputs/642380491/hifi_input.fastq"