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Gibbons-Lab / medi

Metagenomic Estimation of Dietary Intake and Content.
Apache License 2.0
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Curl error connection download_sequences #11

Open MarwanMaj opened 2 months ago

MarwanMaj commented 2 months ago

Hi i am trying to setuo Medi on my HPC and i am coming across the following error during the setup process, I have tried to update curl to the latest version but still won't resolve the issue

thanks Marwan

command used

nextflow run -resume database.nf

error producing

June-12 18:06:16.428 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -resume database.nf June-12 18:06:16.681 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1 June-12 18:06:16.756 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/z3192995/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1 June-12 18:06:16.795 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] June-12 18:06:16.796 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] June-12 18:06:16.798 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode June-12 18:06:16.809 [main] INFO org.pf4j.AbstractPluginManager - No plugins June-12 18:06:16.894 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion June-12 18:06:16.925 [main] INFO nextflow.cli.CmdRun - Launching database.nf [clever_hypatia] DSL2 - revision: 8044d4acb7 June-12 18:06:16.926 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] June-12 18:06:16.926 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] June-12 18:06:16.936 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/z3192995/.nextflow/secrets/store.json June-12 18:06:16.944 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@68809cc7] - activable => nextflow.secret.LocalSecretsProvider@68809cc7 June-12 18:06:17.014 [main] DEBUG nextflow.Session - Session UUID: eabe9d30-83f3-4638-b130-74f765362dd6 June-12 18:06:17.014 [main] DEBUG nextflow.Session - Run name: clever_hypatia June-12 18:06:17.015 [main] DEBUG nextflow.Session - Executor pool size: 8 June-12 18:06:17.022 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null June-12 18:06:17.049 [main] DEBUG nextflow.cli.CmdRun - Version: 23.10.1 build 5891 Created: 12-01-2024 22:01 UTC (13-01-2024 08:01 GMT+10:00) System: Linux 4.18.0-513.24.1.el8_9.x86_64 Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 21-internal-adhoc.conda.src Encoding: UTF-8 (UTF-8) Process: 1505130@k073 [10.197.40.73] CPUs: 8 - Mem: 90 GB (89.5 GB) - Swap: 0 (0) - Virtual threads ON June-12 18:06:17.144 [main] DEBUG nextflow.Session - Work-dir: /srv/scratch/z3192995/Softwares/medi/work [nfs] June-12 18:06:17.205 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] June-12 18:06:17.216 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory June-12 18:06:17.234 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory June-12 18:06:17.250 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool June-12 18:06:17.642 [main] DEBUG nextflow.Session - Session start June-12 18:06:18.334 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution June-12 18:06:18.419 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.420 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.424 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local June-12 18:06:18.430 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=90 GB; capacity=8; pollInterval=100ms; dumpInterval=5m June-12 18:06:18.432 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) June-12 18:06:18.543 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.544 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.547 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.547 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.570 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.570 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.574 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.574 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.577 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.577 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.589 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.589 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.597 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.598 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.601 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null June-12 18:06:18.601 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' June-12 18:06:18.603 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: download, get_taxids, match_taxids, download_sequences, food_mappings, get_lineage, sketch, ANI, download_taxa_dbs June-12 18:06:18.603 [main] DEBUG nextflow.Session - Igniting dataflow network (9) June-12 18:06:18.604 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > download June-12 18:06:18.604 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > get_taxids June-12 18:06:18.604 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > download_taxa_dbs June-12 18:06:18.604 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > get_lineage June-12 18:06:18.605 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > match_taxids June-12 18:06:18.605 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > download_sequences June-12 18:06:18.605 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > sketch June-12 18:06:18.605 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > ANI June-12 18:06:18.606 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > food_mappings June-12 18:06:18.607 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_bcbe01597a2ee0f6: /srv/scratch/z3192995/Softwares/medi/database.nf June-12 18:06:18.607 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination June-12 18:06:18.607 [main] DEBUG nextflow.Session - Session await June-12 18:06:18.825 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [f0/cf1d26] Cached process > download June-12 18:06:18.876 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [63/8f2f8e] Cached process > download_taxa_dbs June-12 18:06:18.914 [Actor Thread 24] INFO nextflow.processor.TaskProcessor - [87/c9f25c] Cached process > get_taxids June-12 18:06:19.020 [Actor Thread 34] INFO nextflow.processor.TaskProcessor - [e2/9fc06e] Cached process > get_lineage (1) June-12 18:06:19.097 [Actor Thread 42] INFO nextflow.processor.TaskProcessor - [30/266d5a] Cached process > match_taxids (1) June-12 18:06:19.227 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run June-12 18:06:19.228 [Task submitter] INFO nextflow.Session - [9b/895cec] Submitted process > download_sequences (1) June-12 18:11:18.587 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:11:19.279 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:16:18.614 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:16:19.313 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:21:18.640 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:21:19.345 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:26:18.659 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:26:19.431 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:31:18.682 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:31:19.461 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:36:18.704 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:36:19.495 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:41:18.727 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:41:19.527 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:46:18.734 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 7; name: download_sequences (1); status: RUNNING; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:46:19.553 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 6; name: food_mappings (1); status: NEW; exit: -; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/5b/a8454baf2991a84bfc9301f66f6dcd] June-12 18:47:27.114 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: download_sequences (1); status: COMPLETED; exit: 1; error: -; workDir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151] June-12 18:47:27.141 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=download_sequences (1); work-dir=/srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151 error [nextflow.exception.ProcessFailedException]: Process download_sequences (1) terminated with an error exit status (1) June-12 18:47:27.172 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run June-12 18:47:27.172 [Task submitter] INFO nextflow.Session - [5b/a8454b] Submitted process > food_mappings (1) June-12 18:47:27.208 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'download_sequences (1)'

Caused by: Process download_sequences (1) terminated with an error exit status (1)

Command executed:

download.R matches.csv 8 sequences

Command exit status: 1

Command output: INFO [2024-06-12 18:11:16] Downloading sequences for taxon 375272... INFO [2024-06-12 18:11:23] Downloading sequences for taxon 8204... INFO [2024-06-12 18:11:31] Downloading sequences for taxon 75034... INFO [2024-06-12 18:11:37] Downloading sequences for taxon 27602... INFO [2024-06-12 18:11:47] Downloading sequences for taxon 186965... INFO [2024-06-12 18:11:56] Downloading sequences for taxon 183653... INFO [2024-06-12 18:12:02] Downloading sequences for taxon 403101... INFO [2024-06-12 18:12:09] Downloading sequences for taxon 40888... INFO [2024-06-12 18:12:17] Downloading sequences for taxon 59166... INFO [2024-06-12 18:12:24] Downloading sequences for taxon 29154... INFO [2024-06-12 18:12:30] Downloading sequences for taxon 34814... INFO [2024-06-12 18:12:36] Downloading sequences for taxon 225389... INFO [2024-06-12 18:12:42] Downloading sequences for taxon 3589... INFO [2024-06-12 18:12:49] Downloading sequences for taxon 58228... INFO [2024-06-12 18:12:57] Downloading sequences for taxon 338184... INFO [2024-06-12 18:13:14] Downloading sequences for taxon 8199... INFO [2024-06-12 18:13:20] Downloading sequences for taxon 1041245... INFO [2024-06-12 18:13:27] Downloading sequences for taxon 3527... INFO [2024-06-12 18:13:39] Downloading sequences for taxon 458363... INFO [2024-06-12 18:13:45] Downloading sequences for taxon 3741... INFO [2024-06-12 18:13:52] Downloading sequences for taxon 28381... INFO [2024-06-12 18:13:58] Downloading sequences for taxon 35579... INFO [2024-06-12 18:14:04] Downloading sequences for taxon 39304... INFO [2024-06-12 18:14:10] Downloading sequences for taxon 59296... INFO [2024-06-12 18:14:16] Downloading sequences for taxon 8226... INFO [2024-06-12 18:14:23] Downloading sequences for taxon 304130... INFO [2024-06-12 18:14:31] Downloading sequences for taxon 28478... INFO [2024-06-12 18:14:38] Downloading sequences for taxon 125586... INFO [2024-06-12 18:14:45] Downloading sequences for taxon 260130... INFO [2024-06-12 18:14:51] Downloading sequences for taxon 3277... INFO [2024-06-12 18:14:59] Downloading sequences for taxon 59837... INFO [2024-06-12 18:15:05] Downloading sequences for taxon 224708... INFO [2024-06-12 18:15:11] Downloading sequences for taxon 106175... INFO [2024-06-12 18:15:17] Downloading sequences for taxon 6829... INFO [2024-06-12 18:15:23] Downloading sequences for taxon 145700... INFO [2024-06-12 18:15:30] Downloading sequences for taxon 4270... INFO [2024-06-12 18:15:37] Downloading sequences for taxon 32219... INFO [2024-06-12 18:15:44] Downloading sequences for taxon 105887... INFO [2024-06-12 18:15:51] Downloading sequences for taxon 39174... INFO [2024-06-12 18:15:58] Downloading sequences for taxon 40958... INFO [2024-06-12 18:16:21] Downloading sequences for taxon 49986... INFO [2024-06-12 18:16:29] Downloading sequences for taxon 3801... INFO [2024-06-12 18:16:40] Downloading sequences for taxon 17047... INFO [2024-06-12 18:16:46] Downloading sequences for taxon 31444... INFO [2024-06-12 18:16:53] Downloading sequences for taxon 4450... INFO [2024-06-12 18:17:01] Downloading sequences for taxon 16300... INFO [2024-06-12 18:17:07] Downloading sequences for taxon 4204... ERROR [2024-06-12 18:47:26] Failed downloading 4204. UIDs=2450339909 , ) :( Object of class ‘epost’ [1] "CurlError: Connection died, tried 5 times before giving up"

Command error: INFO [2024-06-12 18:13:45] Downloading sequences for taxon 3741... INFO [2024-06-12 18:13:52] Downloading sequences for taxon 28381... INFO [2024-06-12 18:13:58] Downloading sequences for taxon 35579... INFO [2024-06-12 18:14:04] Downloading sequences for taxon 39304... INFO [2024-06-12 18:14:10] Downloading sequences for taxon 59296... INFO [2024-06-12 18:14:16] Downloading sequences for taxon 8226... INFO [2024-06-12 18:14:23] Downloading sequences for taxon 304130... INFO [2024-06-12 18:14:31] Downloading sequences for taxon 28478... INFO [2024-06-12 18:14:38] Downloading sequences for taxon 125586... INFO [2024-06-12 18:14:45] Downloading sequences for taxon 260130... INFO [2024-06-12 18:14:51] Downloading sequences for taxon 3277... INFO [2024-06-12 18:14:59] Downloading sequences for taxon 59837... INFO [2024-06-12 18:15:05] Downloading sequences for taxon 224708... INFO [2024-06-12 18:15:11] Downloading sequences for taxon 106175... INFO [2024-06-12 18:15:17] Downloading sequences for taxon 6829... INFO [2024-06-12 18:15:23] Downloading sequences for taxon 145700... INFO [2024-06-12 18:15:30] Downloading sequences for taxon 4270... INFO [2024-06-12 18:15:37] Downloading sequences for taxon 32219... INFO [2024-06-12 18:15:44] Downloading sequences for taxon 105887... INFO [2024-06-12 18:15:51] Downloading sequences for taxon 39174... INFO [2024-06-12 18:15:58] Downloading sequences for taxon 40958... INFO [2024-06-12 18:16:21] Downloading sequences for taxon 49986... INFO [2024-06-12 18:16:29] Downloading sequences for taxon 3801... INFO [2024-06-12 18:16:40] Downloading sequences for taxon 17047... INFO [2024-06-12 18:16:46] Downloading sequences for taxon 31444... INFO [2024-06-12 18:16:53] Downloading sequences for taxon 4450... INFO [2024-06-12 18:17:01] Downloading sequences for taxon 16300... INFO [2024-06-12 18:17:07] Downloading sequences for taxon 4204... Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; Warning: CurlError: Connection died, tried 5 times before giving up Warning: HTTP error: Status 400; ERROR [2024-06-12 18:47:26] Failed downloading 4204. UIDs=2450339909 , ) :( Object of class ‘epost’ [1] "CurlError: Connection died, tried 5 times before giving up" Error in download_sequences(.SD, matched_taxid[1]) : Calls: [ -> [.data.table -> download_sequences Execution halted

Work dir: /srv/scratch/z3192995/Softwares/medi/work/9b/895cec996cd514953a60475e9d6151

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out June-12 18:47:27.214 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process download_sequences (1) terminated with an error exit status (1) June-12 18:47:27.223 [main] DEBUG nextflow.Session - Session await > all processes finished June-12 18:47:27.223 [main] DEBUG nextflow.Session - Session await > all barriers passed June-12 18:47:27.224 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop June-12 18:47:27.227 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (1) June-12 18:47:27.239 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=5; pendingCount=0; submittedCount=1; runningCount=-1; retriesCount=0; abortedCount=1; succeedDuration=0ms; failedDuration=5h 29m 2s; cachedDuration=12m 17s;loadCpus=-1; loadMemory=0; peakRunning=1; peakCpus=8; peakMemory=64 GB; ] June-12 18:47:27.669 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done June-12 18:47:27.700 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

cdiener commented 2 months ago

Hi. Unfortunately the connections to NCBI are a bit unstable. The servers go offline quite often and sometimmes there are files in the manifests that haven't been uploaded yet. In most cases this is solved by rerunning the download at another time. You might also have to rerun without the -resume option to force an update of the manifest.