How can we deactivate SSL check or add the certificates to the appropriate container?
022-08-26T11:55:28Z ๐ Showing engine logs for 'bigMemCtx'
2022-08-26T11:55:28Z ๐ Getting log stream for workflow run '7ec7d927-bcd3-4530-9991-c30f66b48f50'
Fri, 26 Aug 2022 11:45:02 +0000 === ENVIRONMENT ===
Fri, 26 Aug 2022 11:45:02 +0000 AWS_BATCH_JOB_ATTEMPT=1
Fri, 26 Aug 2022 11:45:02 +0000 NF_WORKDIR=s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/runs
Fri, 26 Aug 2022 11:45:02 +0000 HOSTNAME=ip-10-0-125-245.ec2.internal
Fri, 26 Aug 2022 11:45:02 +0000 AWS_CONTAINER_CREDENTIALS_RELATIVE_URI=/v2/credentials/49964af3-6bc3-4607-aa83-bbd7175e9caf
Fri, 26 Aug 2022 11:45:02 +0000 NF_JOB_QUEUE=arn:aws:batch:us-east-1:336191139269:job-queue/BatchTaskBatchJobQueue15-pqWIkgXIaUvwC6EY
Fri, 26 Aug 2022 11:45:02 +0000 AWS_EXECUTION_ENV=AWS_ECS_EC2
Fri, 26 Aug 2022 11:45:02 +0000 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Fri, 26 Aug 2022 11:45:02 +0000 PWD=/opt/work
Fri, 26 Aug 2022 11:45:02 +0000 JAVA_HOME=/usr/lib/jvm/jre-openjdk/
Fri, 26 Aug 2022 11:45:02 +0000 AWS_METADATA_SERVICE_TIMEOUT=10
Fri, 26 Aug 2022 11:45:02 +0000 AWS_BATCH_JOB_ID=7ec7d927-bcd3-4530-9991-c30f66b48f50
Fri, 26 Aug 2022 11:45:02 +0000 NF_LOGSDIR=s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs
Fri, 26 Aug 2022 11:45:02 +0000 SHLVL=1
Fri, 26 Aug 2022 11:45:02 +0000 HOME=/root
Fri, 26 Aug 2022 11:45:02 +0000 AWS_BATCH_CE_NAME=BatchTaskBatchComputeEnv-TLqMfOSBKUUxVnpX
Fri, 26 Aug 2022 11:45:02 +0000 AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
Fri, 26 Aug 2022 11:45:02 +0000 ECS_CONTAINER_METADATA_URI=http://169.254.170.2/v3/8fe39e21-5c00-4515-99b2-ca67a6f114e3
Fri, 26 Aug 2022 11:45:02 +0000 ECS_CONTAINER_METADATA_URI_V4=http://169.254.170.2/v4/8fe39e21-5c00-4515-99b2-ca67a6f114e3
Fri, 26 Aug 2022 11:45:02 +0000 AWS_BATCH_JQ_NAME=BatchTaskBatchJobQueue15-pqWIkgXIaUvwC6EY
Fri, 26 Aug 2022 11:45:02 +0000 _=/usr/bin/printenv
Fri, 26 Aug 2022 11:45:02 +0000 === RUN COMMAND ===
Fri, 26 Aug 2022 11:45:02 +0000 s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/workflow/proteinfold/workflow.zip
Fri, 26 Aug 2022 11:45:02 +0000 Creating config file: ./nextflow.config
Fri, 26 Aug 2022 11:45:02 +0000 === CONFIGURATION ===
Fri, 26 Aug 2022 11:45:02 +0000 workDir = "s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/runs"
Fri, 26 Aug 2022 11:45:02 +0000 process.executor = "awsbatch"
Fri, 26 Aug 2022 11:45:02 +0000 process.queue = "arn:aws:batch:us-east-1:336191139269:job-queue/BatchTaskBatchJobQueue15-pqWIkgXIaUvwC6EY"
Fri, 26 Aug 2022 11:45:02 +0000 aws.batch.cliPath = "/opt/aws-cli/bin/aws"
Fri, 26 Aug 2022 11:45:02 +0000 == Restoring Session Cache ==
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/000003.log to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/000003.log
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/000005.log to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/000005.log
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/index.agitated_ardinghelli to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/index.agitated_ardinghelli
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/history to .nextflow/history
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/LOCK to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/LOCK
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/META-INF/MANIFEST.MF to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/META-INF/MANIFEST.MF
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/CURRENT to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/CURRENT
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/META-INF/extensions.idx to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/META-INF/extensions.idx
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory$_closure1.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory$_closure1.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonPlugin.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonPlugin.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor$_createExecutorService_closure2.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor$_createExecutorService_closure2.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonPlugin.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonPlugin.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/META-INF/MANIFEST.MF to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/META-INF/MANIFEST.MF
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/MANIFEST-000002 to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/MANIFEST-000002
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory$_closure2.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/AmazonClientFactory$_closure2.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor$_createExecutorService_closure1.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor$_createExecutorService_closure1.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/index.lethal_lamarck to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/index.lethal_lamarck
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor$_createExecutorService_closure3.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor$_createExecutorService_closure3.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/MANIFEST-000004 to .nextflow/cache/a4d22556-64c2-4f0f-b41b-cc8345cebb5f/db/MANIFEST-000004
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper$_closure1.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper$_closure1.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchExecutor.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper$_closure2.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchHelper$_closure2.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchProxy.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchProxy.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchProxy.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchProxy.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchScriptLauncher.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchScriptLauncher.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchScriptLauncher.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchScriptLauncher.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions$_makeVols_closure2.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions$_makeVols_closure2.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler$_findJobDef_closure2.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler$_findJobDef_closure2.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions$_makeVols_closure1.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions$_makeVols_closure1.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler$_terminateJob_closure1.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsBatchTaskHandler$_terminateJob_closure1.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/AwsOptions.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper$_closure2.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper$_closure2.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper$_closure1.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper$_closure1.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/S3Helper.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/S3Helper.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/BatchHelper.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/S3Helper.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/batch/S3Helper.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/util/S3PathSerializer.class to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/util/S3PathSerializer.class
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/util/S3PathSerializer.groovy to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/classes/nextflow/cloud/aws/util/S3PathSerializer.groovy
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-batch-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-batch-1.11.542.jar
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-ecs-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-ecs-1.11.542.jar
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-core-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-core-1.11.542.jar
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-kms-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-kms-1.11.542.jar
Fri, 26 Aug 2022 11:45:03 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/commons-codec-1.10.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/commons-codec-1.10.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-s3-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-s3-1.11.542.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/commons-logging-1.2.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/commons-logging-1.2.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/httpcore-4.4.9.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/httpcore-4.4.9.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-iam-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-iam-1.11.542.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-ec2-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/aws-java-sdk-ec2-1.11.542.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/httpclient-4.5.5.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/httpclient-4.5.5.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jmespath-java-1.11.542.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jmespath-java-1.11.542.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-annotations-2.6.0.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-annotations-2.6.0.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/nxf-s3fs-1.1.0.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/nxf-s3fs-1.1.0.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/joda-time-2.8.1.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/joda-time-2.8.1.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-dataformat-cbor-2.6.7.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-dataformat-cbor-2.6.7.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-core-2.6.7.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-core-2.6.7.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/ion-java-1.0.2.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/ion-java-1.0.2.jar
Fri, 26 Aug 2022 11:45:04 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/logs/.nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-databind-2.6.7.2.jar to .nextflow/plr/87881143a005e0d03979c7dc22790185/nf-amazon-1.0.5/lib/jackson-databind-2.6.7.2.jar
Fri, 26 Aug 2022 11:45:04 +0000 == Staging S3 Project ==
Fri, 26 Aug 2022 11:45:05 +0000 download: s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/workflow/proteinfold/workflow.zip to project/workflow.zip
Fri, 26 Aug 2022 11:45:05 +0000 Archive: ./workflow.zip
Fri, 26 Aug 2022 11:45:05 +0000 inflating: .ipynb_checkpoints/MANIFEST-checkpoint.json
Fri, 26 Aug 2022 11:45:05 +0000 inflating: .ipynb_checkpoints/Readme-checkpoint.txt
Fri, 26 Aug 2022 11:45:05 +0000 inflating: .ipynb_checkpoints/inputs-checkpoint.json
Fri, 26 Aug 2022 11:45:05 +0000 inflating: .ipynb_checkpoints/nextflow-checkpoint.config
Fri, 26 Aug 2022 11:45:05 +0000 inflating: .ipynb_checkpoints/samplesheet-checkpoint.csv
Fri, 26 Aug 2022 11:45:05 +0000 inflating: MANIFEST.json
Fri, 26 Aug 2022 11:45:05 +0000 inflating: Readme.txt
Fri, 26 Aug 2022 11:45:05 +0000 inflating: inputs.json
Fri, 26 Aug 2022 11:45:05 +0000 inflating: nextflow.config
Fri, 26 Aug 2022 11:45:05 +0000 inflating: samplesheet.csv
Fri, 26 Aug 2022 11:45:05 +0000 total 0
Fri, 26 Aug 2022 11:45:05 +0000 -rw-r--r-- 1 root root 161 Dec 31 1979 MANIFEST.json
Fri, 26 Aug 2022 11:45:05 +0000 -rw-r--r-- 1 root root 709 Dec 31 1979 Readme.txt
Fri, 26 Aug 2022 11:45:05 +0000 -rw-r--r-- 1 root root 234 Dec 31 1979 inputs.json
Fri, 26 Aug 2022 11:45:05 +0000 -rw-r--r-- 1 root root 147 Dec 31 1979 nextflow.config
Fri, 26 Aug 2022 11:45:05 +0000 -rw-r--r-- 1 root root 224 Dec 31 1979 samplesheet.csv
Fri, 26 Aug 2022 11:45:05 +0000 -rw-r--r-- 1 root root 3293 Aug 26 11:42 workflow.zip
Fri, 26 Aug 2022 11:45:05 +0000 cat ./project/MANIFEST.json
Fri, 26 Aug 2022 11:45:05 +0000 {
Fri, 26 Aug 2022 11:45:05 +0000 "mainWorkflowURL": "https://github.com/ArlindNocaj/proteinfold.git",
Fri, 26 Aug 2022 11:45:05 +0000 "inputFileURLs": [
Fri, 26 Aug 2022 11:45:05 +0000 "inputs.json"
Fri, 26 Aug 2022 11:45:05 +0000 ],
Fri, 26 Aug 2022 11:45:05 +0000 "engineOptions": "-resume -r dev"
Fri, 26 Aug 2022 11:45:05 +0000
Fri, 26 Aug 2022 11:45:05 +0000 }
Fri, 26 Aug 2022 11:45:05 +0000 cat ./project/inputs.json
Fri, 26 Aug 2022 11:45:05 +0000 {"af2_db":"s3://alphafold2-agc/af2_db","full_dbs":false,"input":"s3://alphafold2-agc/input/samplesheet.csv","mode":"AF2","model_preset":"monomer","outdir":"s3://alphafold2-agc/results_samplesheet","skip_download":false,"use_gpu":true}== Running Workflow ==
Fri, 26 Aug 2022 11:45:05 +0000 nextflow run https://github.com/ArlindNocaj/proteinfold.git -resume -r dev -params-file ./project/inputs.json
Fri, 26 Aug 2022 11:45:05 +0000 nextflow pid: 54
Fri, 26 Aug 2022 11:45:05 +0000 [1]+ Running nextflow run $NEXTFLOW_PROJECT $NEXTFLOW_PARAMS &
Fri, 26 Aug 2022 11:45:05 +0000 waiting ..
Fri, 26 Aug 2022 11:45:10 +0000 N E X T F L O W ~ version 21.04.3
Fri, 26 Aug 2022 11:45:10 +0000 Pulling ArlindNocaj/proteinfold ...
Fri, 26 Aug 2022 11:45:15 +0000 downloaded from https://github.com/ArlindNocaj/proteinfold.git
Fri, 26 Aug 2022 11:45:15 +0000 Launching `ArlindNocaj/proteinfold` [silly_meucci] - revision: 01fbbca6fb [dev]
Fri, 26 Aug 2022 11:45:22 +0000 ------------------------------------------------------
Fri, 26 Aug 2022 11:45:22 +0000 ,--./,-.
Fri, 26 Aug 2022 11:45:22 +0000 ___ __ __ __ ___ /,-._.--~'
Fri, 26 Aug 2022 11:45:22 +0000 |\ | |__ __ / ` / \ |__) |__ } {
Fri, 26 Aug 2022 11:45:22 +0000 | \| | \__, \__/ | \ |___ \`-._,-`-,
Fri, 26 Aug 2022 11:45:22 +0000 `._,._,'
Fri, 26 Aug 2022 11:45:22 +0000 nf-core/proteinfold v1.0dev
Fri, 26 Aug 2022 11:45:22 +0000 ------------------------------------------------------
Fri, 26 Aug 2022 11:45:22 +0000 Core Nextflow options
Fri, 26 Aug 2022 11:45:22 +0000 revision : dev
Fri, 26 Aug 2022 11:45:22 +0000 runName : silly_meucci
Fri, 26 Aug 2022 11:45:22 +0000 launchDir : /opt/work/7ec7d927-bcd3-4530-9991-c30f66b48f50/1
Fri, 26 Aug 2022 11:45:22 +0000 workDir : /agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/runs
Fri, 26 Aug 2022 11:45:22 +0000 projectDir : /root/.nextflow/assets/ArlindNocaj/proteinfold
Fri, 26 Aug 2022 11:45:22 +0000 userName : root
Fri, 26 Aug 2022 11:45:22 +0000 profile : standard
Fri, 26 Aug 2022 11:45:22 +0000 configFiles : /root/.nextflow/assets/ArlindNocaj/proteinfold/nextflow.config, /opt/work/7ec7d927-bcd3-4530-9991-c30f66b48f50/1/nextflow.config
Fri, 26 Aug 2022 11:45:22 +0000 Global options
Fri, 26 Aug 2022 11:45:22 +0000 input : s3://alphafold2-agc/input/samplesheet.csv
Fri, 26 Aug 2022 11:45:22 +0000 outdir : s3://alphafold2-agc/results_samplesheet
Fri, 26 Aug 2022 11:45:22 +0000 use_gpu : true
Fri, 26 Aug 2022 11:45:22 +0000 skip_download: false
Fri, 26 Aug 2022 11:45:22 +0000 Alphafold2 options
Fri, 26 Aug 2022 11:45:22 +0000 af2_db : s3://alphafold2-agc/af2_db
Fri, 26 Aug 2022 11:45:22 +0000 full_dbs : false
Fri, 26 Aug 2022 11:45:22 +0000 Colabfold options
Fri, 26 Aug 2022 11:45:22 +0000 colabfold_db : /nfs/users/cn/abaltzis/db/colabfold
Fri, 26 Aug 2022 11:45:22 +0000 !! Only displaying parameters that differ from the pipeline defaults !!
Fri, 26 Aug 2022 11:45:22 +0000 ------------------------------------------------------
Fri, 26 Aug 2022 11:45:22 +0000 If you use nf-core/proteinfold for your analysis please cite:
Fri, 26 Aug 2022 11:45:22 +0000 * The nf-core framework
Fri, 26 Aug 2022 11:45:22 +0000 https://doi.org/10.1038/s41587-020-0439-x
Fri, 26 Aug 2022 11:45:22 +0000 * Software dependencies
Fri, 26 Aug 2022 11:45:22 +0000 https://github.com/nf-core/proteinfold/blob/master/CITATIONS.md
Fri, 26 Aug 2022 11:45:22 +0000 ------------------------------------------------------
Fri, 26 Aug 2022 11:45:24 +0000 Uploading local `bin` scripts folder to s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/runs/tmp/31/edaebf4ca50c97c8dcd5b7bd2c2893/bin
Fri, 26 Aug 2022 11:45:28 +0000 [5e/0e0094] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_UNIPROT
Fri, 26 Aug 2022 11:45:28 +0000 [16/a3f66f] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)
Fri, 26 Aug 2022 11:45:28 +0000 [b5/b5c245] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_UNICLUST30
Fri, 26 Aug 2022 11:45:28 +0000 [7f/f044fe] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_SMALL_BFD
Fri, 26 Aug 2022 11:45:28 +0000 [5d/3e4746] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_PDB_MMCIF
Fri, 26 Aug 2022 11:45:28 +0000 [79/94c128] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_UNIREF90
Fri, 26 Aug 2022 11:45:28 +0000 [24/4620f1] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_AF2_PARAMS
Fri, 26 Aug 2022 11:45:28 +0000 [75/ce3948] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_PDB70
Fri, 26 Aug 2022 11:45:28 +0000 [69/2b3890] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_MGNIFY
Fri, 26 Aug 2022 11:45:29 +0000 [5d/ddf6b6] Submitted process > NFCORE_PROTEINFOLD:ALPHAFOLD2:MULTIQC
Fri, 26 Aug 2022 11:49:55 +0000 Error executing process > 'NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_PDB70'
Fri, 26 Aug 2022 11:49:55 +0000 Caused by:
Fri, 26 Aug 2022 11:49:55 +0000 Process `NFCORE_PROTEINFOLD:ALPHAFOLD2:DOWNLOAD_AF2_DBS_AND_PARAMS:DOWNLOAD_PDB70` terminated with an error exit status (1)
Fri, 26 Aug 2022 11:49:55 +0000 Command executed:
Fri, 26 Aug 2022 11:49:55 +0000 download_pdb70.sh $PWD
Fri, 26 Aug 2022 11:49:55 +0000 Command exit status:
Fri, 26 Aug 2022 11:49:55 +0000 1
Fri, 26 Aug 2022 11:49:55 +0000 Command output:
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:44 [NOTICE] Downloading 1 item(s)
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:44 [NOTICE] CUID#7 - Redirecting to https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:45 [ERROR] CUID#7 - Download aborted. URI=http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000 Exception: [AbstractCommand.cc:351] errorCode=1 URI=https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000 -> [SocketCore.cc:1018] errorCode=1 SSL/TLS handshake failure: `not signed by known authorities or invalid' `issuer is not known'
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:45 [NOTICE] Download GID#9ac1e320f6fad7af not complete:
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 Download Results:
Fri, 26 Aug 2022 11:49:55 +0000 gid |stat|avg speed |path/URI
Fri, 26 Aug 2022 11:49:55 +0000 ======+====+===========+=======================================================
Fri, 26 Aug 2022 11:49:55 +0000 9ac1e3|ERR | 0B/s|http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 Status Legend:
Fri, 26 Aug 2022 11:49:55 +0000 (ERR):error occurred.
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 aria2 will resume download if the transfer is restarted.
Fri, 26 Aug 2022 11:49:55 +0000 If there are any errors, then see the log file. See '-l' option in help/man page for details.
Fri, 26 Aug 2022 11:49:55 +0000 Command wrapper:
Fri, 26 Aug 2022 11:49:55 +0000 nxf-scratch-dir ip-10-0-97-116.ec2.internal:/tmp/nxf.ad23fp3kFc
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:44 [NOTICE] Downloading 1 item(s)
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:44 [NOTICE] CUID#7 - Redirecting to https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:45 [ERROR] CUID#7 - Download aborted. URI=http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000 Exception: [AbstractCommand.cc:351] errorCode=1 URI=https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000 -> [SocketCore.cc:1018] errorCode=1 SSL/TLS handshake failure: `not signed by known authorities or invalid' `issuer is not known'
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 08/26 11:49:45 [NOTICE] Download GID#9ac1e320f6fad7af not complete:
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 Download Results:
Fri, 26 Aug 2022 11:49:55 +0000 gid |stat|avg speed |path/URI
Fri, 26 Aug 2022 11:49:55 +0000 ======+====+===========+=======================================================
Fri, 26 Aug 2022 11:49:55 +0000 9ac1e3|ERR | 0B/s|http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 Status Legend:
Fri, 26 Aug 2022 11:49:55 +0000 (ERR):error occurred.
Fri, 26 Aug 2022 11:49:55 +0000
Fri, 26 Aug 2022 11:49:55 +0000 aria2 will resume download if the transfer is restarted.
Fri, 26 Aug 2022 11:49:55 +0000 If there are any errors, then see the log file. See '-l' option in help/man page for details.
Fri, 26 Aug 2022 11:49:55 +0000 Work dir:
Fri, 26 Aug 2022 11:49:55 +0000 s3://agc-336191139269-us-east-1/project/NFCorePopular/userid/arlnocaj4nFMjG/context/bigMemCtx/nextflow-execution/runs/75/ce3948acad2e7ce3671579bc01c4f5
Fri, 26 Aug 2022 11:49:55 +0000 Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Fri, 26 Aug 2022 11:49:55 +0000 Execution cancelled -- Finishing pending tasks before exit
Fri, 26 Aug 2022 11:54:45 +0000 WARN: Cannot use mode `symlink` to publish files to path: /alphafold2-agc/af2_db -- Using mode `copy` instead