Could anyone help identify an issue I am experiencing lunching nextflow on google cloud batch?
[20/0b29e9] process > get_ref_pos (1) [ 0%] 0 of 1
[d6/530adb] process > parse_gvcf (1) [ 0%] 0 of 1
[- ] process > cnv_indel_sv -
[b4/17a2df] process > generate_patient_data2 (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > generate_gene_scores -
[- ] process > generate_overall_risk -
[- ] process > report_input_generator -
[- ] process > report_generator_azure -
Error executing process > 'generate_patient_data2 (1)'
Caused by:
Process generate_patient_data2 (1) terminated with an error exit status (null)
Command executed:
generate_patient_data2.R 11_patient_data1.tab
Command exit status:
null
Command output:
(empty)
Work dir:
gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
WARN: Killing running tasks (2)
root@742c961c8b28:/genome_to_report# cat nextflo^C
root@742c961c8b28:/genome_to_report# cat .nextflow.log
May-01 18:06:26.706 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -c nextflow_genome_to_report_cgosdevuk.config genome_to_report_v2.nf -w 'gs://data/nextflow-logs' -with-docker 'europe-west2-docker.pkg.dev/cgos-dev-uk/gcr-cgos-dev-uk/genome-tools@sha256:d5132031363042588a11de231bba6d68b26745b3272624e9c644bec08c6877d4' --id 11 --base_dir 'gs://data/' --template_id 75 --data_dir patient-data --barcode GFX
May-01 18:06:26.855 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.10.0
May-01 18:06:26.877 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@1.11.0,nf-azure@0.14.2,nf-codecommit@0.1.2,nf-console@1.0.4,nf-ga4gh@1.0.4,nf-google@1.4.4,nf-tower@1.5.5,nf-wave@0.5.2
May-01 18:06:26.888 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-01 18:06:26.889 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-01 18:06:26.893 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
May-01 18:06:26.905 [main] INFO org.pf4j.AbstractPluginManager - No plugins
May-01 18:06:26.932 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /genome_to_report/nextflow_genome_to_report_cgosdevuk.config
May-01 18:06:26.933 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /genome_to_report/nextflow_genome_to_report_cgosdevuk.config
May-01 18:06:26.964 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
May-01 18:06:27.654 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Docker container as requested by command-line option -with-docker europe-west2-docker.pkg.dev/cgos-dev-uk/gcr-cgos-dev-uk/genome-tools@sha256:d5132031363042588a11de231bba6d68b26745b3272624e9c644bec08c6877d4
May-01 18:06:27.670 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=1 by probing script field
May-01 18:06:27.695 [main] INFO nextflow.cli.CmdRun - Launching genome_to_report_v2.nf [infallible_shockley] DSL1 - revision: aaf83627a1
May-01 18:06:27.696 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-google@1.4.4]
May-01 18:06:27.697 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[nf-google@1.4.4]
May-01 18:06:27.697 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-google@1.4.4]
May-01 18:06:27.697 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-google version: 1.4.4
May-01 18:06:27.702 [main] INFO nextflow.plugin.PluginUpdater - Downloading plugin nf-google@1.4.4
May-01 18:06:32.831 [main] INFO org.pf4j.util.FileUtils - Expanded plugin zip 'nf-google-1.4.4.zip' in 'nf-google-1.4.4'
May-01 18:06:32.846 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-google@1.4.4' resolved
May-01 18:06:32.846 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-google@1.4.4'
May-01 18:06:32.878 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-google@1.4.4
May-01 18:06:32.892 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
May-01 18:06:32.896 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@50eb4a2c] - activable => nextflow.secret.LocalSecretsProvider@50eb4a2c
May-01 18:06:32.966 [main] DEBUG nextflow.Session - Session UUID: a6196fd6-a79b-4fd4-bfe3-fa6d2e1db64c
May-01 18:06:32.966 [main] DEBUG nextflow.Session - Run name: infallible_shockley
May-01 18:06:32.967 [main] DEBUG nextflow.Session - Executor pool size: 6
May-01 18:06:33.143 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=18; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-01 18:06:33.167 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.10.0 build 5826
Created: 13-10-2022 05:44 UTC
System: Linux 5.15.49-linuxkit-pr
Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.10+7-Ubuntu-120.04.1
Encoding: UTF-8 (UTF-8)
Process: 3404@742c961c8b28 [172.17.0.3]
CPUs: 6 - Mem: 19.5 GB (516.6 MB) - Swap: 1.5 GB (1.5 GB)
May-01 18:06:33.221 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): gs://data/nextflow-logs
May-01 18:06:33.221 [main] DEBUG nextflow.Session - Work-dir: gs://data/nextflow-logs [null]
May-01 18:06:33.254 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, GoogleBatchExecutor]
May-01 18:06:33.267 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-01 18:06:33.313 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-01 18:06:33.326 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 7; maxThreads: 1000
May-01 18:06:33.400 [main] DEBUG nextflow.Session - Session start
May-01 18:06:34.630 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-01 18:06:34.658 [main] INFO nextflow.Nextflow - G E N O M E TO R E P O R T - N F P I P E L I N E
Genome version : hg38
reference genome : gs://data/pipeline-data/fixed-input/hg38.fa
SNP panel : gs://data/pipeline-data/templates/75/panel-data/SNPpanel*hg38.samtools.txt
patient data : gs:/data/patient-data/11/input/casemanagement-data/11_patient_data1.tab
Caused by:
Process generate_patient_data2 (1) terminated with an error exit status (null)
Command executed:
generate_patient_data2.R 11_patient_data1.tab
Command exit status:
null
Command output:
(empty)
Work dir:
gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
May-01 18:27:52.831 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process generate_patient_data2 (1) terminated with an error exit status (null)
May-01 18:27:52.857 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] generate_gene_scores
status=ACTIVE
port 0: (value) bound ; channel: base_dir
port 1: (queue) OPEN ; channel: snp_picker_data
port 2: (queue) OPEN ; channel: snp_panel_risk
port 3: (queue) OPEN ; channel: patient_data
port 4: (queue) OPEN ; channel: ethnicity
port 5: (queue) OPEN ; channel: refpos
port 6: (value) bound ; channel: patient_id
port 7: (value) bound ; channel: panel_id
port 8: (value) bound ; channel: genome_id
port 9: (value) bound ; channel: template_id
port 10: (cntrl) - ; channel: $
[process] generate_overall_risk
status=ACTIVE
port 0: (value) bound ; channel: base_dir
port 1: (queue) OPEN ; channel: snp_scores
port 2: (queue) OPEN ; channel: qrisk2_output
port 3: (queue) OPEN ; channel: formulas_1
port 4: (value) bound ; channel: patient_id
port 5: (value) bound ; channel: panel_id
port 6: (value) bound ; channel: genome_id
port 7: (value) bound ; channel: template_id
port 8: (cntrl) - ; channel: $
Hello,
Could anyone help identify an issue I am experiencing lunching nextflow on google cloud batch?
[20/0b29e9] process > get_ref_pos (1) [ 0%] 0 of 1 [d6/530adb] process > parse_gvcf (1) [ 0%] 0 of 1 [- ] process > cnv_indel_sv - [b4/17a2df] process > generate_patient_data2 (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > generate_gene_scores - [- ] process > generate_overall_risk - [- ] process > report_input_generator - [- ] process > report_generator_azure - Error executing process > 'generate_patient_data2 (1)'
Caused by: Process
generate_patient_data2 (1)terminated with an error exit status (null)Command executed:
generate_patient_data2.R 11_patient_data1.tab
Command exit status: null
Command output: (empty)
Work dir: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.outWARN: Killing running tasks (2)
root@742c961c8b28:/genome_to_report# cat nextflo^C root@742c961c8b28:/genome_to_report# cat .nextflow.log May-01 18:06:26.706 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -c nextflow_genome_to_report_cgosdevuk.config genome_to_report_v2.nf -w 'gs://data/nextflow-logs' -with-docker 'europe-west2-docker.pkg.dev/cgos-dev-uk/gcr-cgos-dev-uk/genome-tools@sha256:d5132031363042588a11de231bba6d68b26745b3272624e9c644bec08c6877d4' --id 11 --base_dir 'gs://data/' --template_id 75 --data_dir patient-data --barcode GFX May-01 18:06:26.855 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.10.0 May-01 18:06:26.877 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@1.11.0,nf-azure@0.14.2,nf-codecommit@0.1.2,nf-console@1.0.4,nf-ga4gh@1.0.4,nf-google@1.4.4,nf-tower@1.5.5,nf-wave@0.5.2 May-01 18:06:26.888 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-01 18:06:26.889 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-01 18:06:26.893 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-01 18:06:26.905 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-01 18:06:26.932 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /genome_to_report/nextflow_genome_to_report_cgosdevuk.config May-01 18:06:26.933 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /genome_to_report/nextflow_genome_to_report_cgosdevuk.config May-01 18:06:26.964 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:
standardMay-01 18:06:27.654 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Docker container as requested by command-line option-with-docker europe-west2-docker.pkg.dev/cgos-dev-uk/gcr-cgos-dev-uk/genome-tools@sha256:d5132031363042588a11de231bba6d68b26745b3272624e9c644bec08c6877d4May-01 18:06:27.670 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=1 by probing script field May-01 18:06:27.695 [main] INFO nextflow.cli.CmdRun - Launchinggenome_to_report_v2.nf[infallible_shockley] DSL1 - revision: aaf83627a1 May-01 18:06:27.696 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-google@1.4.4] May-01 18:06:27.697 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[nf-google@1.4.4] May-01 18:06:27.697 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-google@1.4.4] May-01 18:06:27.697 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-google version: 1.4.4 May-01 18:06:27.702 [main] INFO nextflow.plugin.PluginUpdater - Downloading plugin nf-google@1.4.4 May-01 18:06:32.831 [main] INFO org.pf4j.util.FileUtils - Expanded plugin zip 'nf-google-1.4.4.zip' in 'nf-google-1.4.4' May-01 18:06:32.846 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-google@1.4.4' resolved May-01 18:06:32.846 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-google@1.4.4' May-01 18:06:32.878 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-google@1.4.4 May-01 18:06:32.892 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json May-01 18:06:32.896 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@50eb4a2c] - activable => nextflow.secret.LocalSecretsProvider@50eb4a2c May-01 18:06:32.966 [main] DEBUG nextflow.Session - Session UUID: a6196fd6-a79b-4fd4-bfe3-fa6d2e1db64c May-01 18:06:32.966 [main] DEBUG nextflow.Session - Run name: infallible_shockley May-01 18:06:32.967 [main] DEBUG nextflow.Session - Executor pool size: 6 May-01 18:06:33.143 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=18; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-01 18:06:33.167 [main] DEBUG nextflow.cli.CmdRun - Version: 22.10.0 build 5826 Created: 13-10-2022 05:44 UTC System: Linux 5.15.49-linuxkit-pr Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.10+7-Ubuntu-120.04.1 Encoding: UTF-8 (UTF-8) Process: 3404@742c961c8b28 [172.17.0.3] CPUs: 6 - Mem: 19.5 GB (516.6 MB) - Swap: 1.5 GB (1.5 GB) May-01 18:06:33.221 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): gs://data/nextflow-logsMay-01 18:06:33.221 [main] DEBUG nextflow.Session - Work-dir: gs://data/nextflow-logs [null] May-01 18:06:33.254 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, GoogleBatchExecutor] May-01 18:06:33.267 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-01 18:06:33.313 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-01 18:06:33.326 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 7; maxThreads: 1000 May-01 18:06:33.400 [main] DEBUG nextflow.Session - Session start May-01 18:06:34.630 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-01 18:06:34.658 [main] INFO nextflow.Nextflow - G E N O M E TO R E P O R T - N F P I P E L I N E
Genome version : hg38 reference genome : gs://data/pipeline-data/fixed-input/hg38.fa
input gvcf files : gs://data/patient-data/11/input/hg38/variant_calling/haplotypecaller/GFX/*.haplotypecaller.vcf.gz
SNP panel : gs://data/pipeline-data/templates/75/panel-data/SNPpanel*hg38.samtools.txt patient data : gs:/data/patient-data/11/input/casemanagement-data/11_patient_data1.tab
cnv_indel_sv process inputs cnv file : gs://data/patient-data/11/input/hg38/CNVs.final.gff gene panel file : gs://data/pipeline-data/templates/75/panel-data/_gene_panel.tab indel file : gs://data/patient-data/11/input/hg38/indelxls sv file : gs://data/patient-data/11/input/hg38/dellyxls snp annotation : gs://data/patient-data/11/input/hg38/snpxls
intermediate output : gs://data/patient-data/11/output/intermediate final output : gs://data/patient-data/11/output/final
May-01 18:06:34.696 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/patient-data/11/input/hg38/variant_calling/haplotypecaller/GFX/; pattern: .haplotypecaller.vcf.gz; options: [:] May-01 18:06:34.703 [PathVisitor-2] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/patient-data/11/input/hg38/variant_calling/haplotypecaller/GFX/; pattern: .haplotypecaller.vcf.gz.tbi; options: [:] May-01 18:06:34.706 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/pipeline-data/templates/75/panel-data/; pattern: SNPpanelhg38.samtools.txt; options: [:] May-01 18:06:34.758 [PathVisitor-4] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/patient-data/11/input/hg38/; pattern: CNVs.final.gff; options: [:] May-01 18:06:34.759 [PathVisitor-5] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/pipeline-data/templates/75/panel-data/; pattern: _gene_panel.tab; options: [:] May-01 18:06:34.761 [PathVisitor-6] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/patient-data/11/input/hg38/; pattern: indelxls; options: [:] May-01 18:06:34.763 [PathVisitor-7] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/patient-data/11/input/hg38/; pattern: dellyxls; options: [:] May-01 18:06:34.764 [PathVisitor-8] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/patient-data/11/input/hg38/; pattern: snpxls; options: [:] May-01 18:06:34.769 [PathVisitor-11] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/pipeline-data/templates/75/; pattern: report_generator.Rmd; options: [:] May-01 18:06:34.788 [PathVisitor-9] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/pipeline-data/templates/75/annotation-data/; pattern: *hg38_panel_risk_coeff.tab; options: [:] May-01 18:06:34.841 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:34.841 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:34.843 [main] DEBUG nextflow.executor.Executor - [warm up] executor > google-batch May-01 18:06:34.850 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'google-batch' > capacity: 1000; pollInterval: 10s; dumpInterval: 5m May-01 18:06:34.869 [main] DEBUG nextflow.cloud.google.GoogleOpts - Google auth via application credentials file: /cgos-dev-uk-7f453a0d8565_app-user_30Apr24.json May-01 18:06:34.874 [main] DEBUG n.c.google.batch.GoogleBatchExecutor - [GOOGLE BATCH] Executor config=BatchConfig[googleOpts=GoogleOpts(projectId:cgos-dev-uk, credsFile:/cgos-dev-uk-7f453a0d8565_app-user_30Apr24.json, location:europe-west2, enableRequesterPaysBuckets:false, credentials:ServiceAccountCredentials{clientId=£££££££5195046123, clientEmail=app@dev-uk.iam.gserviceaccount.com, privateKeyId=£££££££££9e60c828, transportFactoryClassName=com.google.auth.oauth2.OAuth2Utils$DefaultHttpTransportFactory, tokenServerUri=https://oauth2.googleapis.com/token, scopes=[https://www.googleapis.com/auth/cloud-platform], defaultScopes=[], serviceAccountUser=null, quotaProjectId=null, lifetime=3600, useJwtAccessWithScope=false, defaultRetriesEnabled=true}) May-01 18:06:37.689 [main] INFO n.c.google.batch.GoogleBatchExecutor - Uploading local
binscripts folder to gs://data/nextflow-logs/tmp/66/dbac6923cd65f3d7470cfaa57c116b/bin May-01 18:06:52.421 [main] DEBUG n.c.google.batch.client.BatchClient - [GOOGLE BATCH] Creating service client with config credentials May-01 18:06:53.151 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:53.151 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:53.170 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:53.170 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:53.187 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:53.187 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:53.198 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:53.199 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:53.215 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:53.216 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:53.237 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:53.237 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:53.253 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: google-batch May-01 18:06:53.253 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'google-batch' May-01 18:06:53.268 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: generate_patient_data2, get_ref_pos, cnv_indel_sv, parse_gvcf, generate_overall_risk, report_generator_azure, report_input_generator, generate_gene_scores May-01 18:06:53.269 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination May-01 18:06:53.269 [main] DEBUG nextflow.Session - Session await May-01 18:06:58.206 [Task submitter] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] submitted > job=nf-200b29e9-1714586814696; uid=nf-200b29e9-171458-121fef56-712b-471e0; work-dir=gs://data/nextflow-logs/20/0b29e99351bd730431e4bc57613ff2 May-01 18:06:58.207 [Task submitter] INFO nextflow.Session - [20/0b29e9] Submitted process > get_ref_pos (1) May-01 18:07:00.311 [Task submitter] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] submitted > job=nf-b417a2df-1714586815112; uid=nf-b417a2df-171458-30f42ecb-e212-43af0; work-dir=gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6 May-01 18:07:00.311 [Task submitter] INFO nextflow.Session - [b4/17a2df] Submitted process > generate_patient_data2 (1) May-01 18:07:02.159 [Task submitter] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] submitted > job=nf-d6530adb-1714586815865; uid=nf-d6530adb-171458-852fca65-0459-4e3b0; work-dir=gs://data/nextflow-logs/d6/530adb07d726798b4c2bc459cd6b35 May-01 18:07:02.160 [Task submitter] INFO nextflow.Session - [d6/530adb] Submitted process > parse_gvcf (1) May-01 18:11:44.875 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor google-batch > tasks to be completed: 3 -- submitted tasks are shown below ~> TaskHandler[id: 1; name: get_ref_pos (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/20/0b29e99351bd730431e4bc57613ff2] ~> TaskHandler[id: 3; name: generate_patient_data2 (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6] ~> TaskHandler[id: 2; name: parse_gvcf (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/d6/530adb07d726798b4c2bc459cd6b35] May-01 18:16:44.893 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor google-batch > tasks to be completed: 3 -- submitted tasks are shown below ~> TaskHandler[id: 1; name: get_ref_pos (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/20/0b29e99351bd730431e4bc57613ff2] ~> TaskHandler[id: 3; name: generate_patient_data2 (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6] ~> TaskHandler[id: 2; name: parse_gvcf (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/d6/530adb07d726798b4c2bc459cd6b35] May-01 18:21:44.913 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor google-batch > tasks to be completed: 3 -- submitted tasks are shown below ~> TaskHandler[id: 1; name: get_ref_pos (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/20/0b29e99351bd730431e4bc57613ff2] ~> TaskHandler[id: 3; name: generate_patient_data2 (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6] ~> TaskHandler[id: 2; name: parse_gvcf (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/d6/530adb07d726798b4c2bc459cd6b35] May-01 18:26:44.930 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor google-batch > tasks to be completed: 3 -- submitted tasks are shown below ~> TaskHandler[id: 1; name: get_ref_pos (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/20/0b29e99351bd730431e4bc57613ff2] ~> TaskHandler[id: 3; name: generate_patient_data2 (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6] ~> TaskHandler[id: 2; name: parse_gvcf (1); status: SUBMITTED; exit: -; error: -; workDir: gs://data/nextflow-logs/d6/530adb07d726798b4c2bc459cd6b35] May-01 18:27:45.807 [Task monitor] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] Terminated job=nf-b417a2df-1714586815112; state=FAILED May-01 18:27:46.990 [Task monitor] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] Cannot read exitstatus for task:generate_patient_data2 (1)| gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.exitcode May-01 18:27:51.304 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: generate_patient_data2 (1); status: COMPLETED; exit: null; error: -; workDir: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6] May-01 18:27:51.561 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'null' -- Cause: java.nio.file.NoSuchFileException: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.command.out May-01 18:27:52.079 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.command.err May-01 18:27:52.328 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.command.log May-01 18:27:52.330 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'generate_patient_data2 (1)'Caused by: Process
generate_patient_data2 (1)terminated with an error exit status (null)Command executed:
generate_patient_data2.R 11_patient_data1.tab
Command exit status: null
Command output: (empty)
Work dir: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.outMay-01 18:27:52.831 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Processgenerate_patient_data2 (1)terminated with an error exit status (null) May-01 18:27:52.857 [Task monitor] DEBUG nextflow.Session - The following nodes are still active: [process] generate_gene_scores status=ACTIVE port 0: (value) bound ; channel: base_dir port 1: (queue) OPEN ; channel: snp_picker_data port 2: (queue) OPEN ; channel: snp_panel_risk port 3: (queue) OPEN ; channel: patient_data port 4: (queue) OPEN ; channel: ethnicity port 5: (queue) OPEN ; channel: refpos port 6: (value) bound ; channel: patient_id port 7: (value) bound ; channel: panel_id port 8: (value) bound ; channel: genome_id port 9: (value) bound ; channel: template_id port 10: (cntrl) - ; channel: $[process] generate_overall_risk status=ACTIVE port 0: (value) bound ; channel: base_dir port 1: (queue) OPEN ; channel: snp_scores port 2: (queue) OPEN ; channel: qrisk2_output port 3: (queue) OPEN ; channel: formulas_1 port 4: (value) bound ; channel: patient_id port 5: (value) bound ; channel: panel_id port 6: (value) bound ; channel: genome_id port 7: (value) bound ; channel: template_id port 8: (cntrl) - ; channel: $
May-01 18:27:53.094 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.command.err May-01 18:27:53.620 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'null' -- Cause: java.nio.file.NoSuchFileException: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.command.out May-01 18:27:53.622 [main] DEBUG nextflow.Session - Session await > all processes finished May-01 18:27:53.622 [main] DEBUG nextflow.Session - Session await > all barriers passed May-01 18:27:53.862 [main] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.command.err May-01 18:27:53.869 [Task monitor] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] Terminated job=nf-d6530adb-1714586815865; state=FAILED May-01 18:27:54.376 [main] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'null' -- Cause: java.nio.file.NoSuchFileException: gs://data/nextflow-logs/b4/17a2df4adfa1bc2d4954ff66e47ac6/.command.out May-01 18:27:54.381 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (2) May-01 18:27:54.391 [main] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] Oops.. invalid delete action May-01 18:27:54.393 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=1; runningCount=-1; retriesCount=0; abortedCount=2; succeedDuration=0ms; failedDuration=5.5s; cachedDuration=0ms;loadCpus=-1; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ] May-01 18:27:54.403 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-01 18:27:54.403 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-google@1.4.4' May-01 18:27:54.403 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-google May-01 18:27:54.428 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye