-
Notifications
You must be signed in to change notification settings - Fork 0
/
.nextflow.log
86 lines (78 loc) · 6.92 KB
/
.nextflow.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
Oct-05 16:40:22.388 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pipeline.nf -with-singularity 'snpEff:5.0.sif'
Oct-05 16:40:22.595 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.10.7
Oct-05 16:40:22.626 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/guest/.nextflow/plugins; core-plugins: nf-amazon@1.11.4,nf-azure@0.14.2,nf-codecommit@0.1.2,nf-console@1.0.4,nf-ga4gh@1.0.4,nf-google@1.4.5,nf-tower@1.5.6,nf-wave@0.5.4
Oct-05 16:40:22.642 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-05 16:40:22.643 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-05 16:40:22.647 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-05 16:40:22.661 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Oct-05 16:40:22.746 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by command-line option `-with-singularity null`
Oct-05 16:40:22.771 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Oct-05 16:40:22.793 [main] INFO nextflow.cli.CmdRun - Launching `pipeline.nf` [big_yonath] DSL2 - revision: 5581c87249
Oct-05 16:40:22.794 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-05 16:40:22.794 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-05 16:40:22.807 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/guest/.nextflow/secrets/store.json
Oct-05 16:40:22.811 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@7c2327fa] - activable => nextflow.secret.LocalSecretsProvider@7c2327fa
Oct-05 16:40:22.901 [main] DEBUG nextflow.Session - Session UUID: 1872e6b1-1583-4f88-ac19-8d3f362df438
Oct-05 16:40:22.902 [main] DEBUG nextflow.Session - Run name: big_yonath
Oct-05 16:40:22.902 [main] DEBUG nextflow.Session - Executor pool size: 6
Oct-05 16:40:22.916 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=18; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-05 16:40:22.949 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.10.7 build 5853
Created: 18-02-2023 20:32 UTC (21:32 CEST)
System: Linux 6.2.11-100.fc36.x86_64
Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.6+10
Encoding: UTF-8 (UTF-8)
Process: 328923@fedora [10.0.2.15]
CPUs: 6 - Mem: 7.7 GB (1009.2 MB) - Swap: 7.7 GB (5.3 GB)
Oct-05 16:40:22.994 [main] DEBUG nextflow.Session - Work-dir: /home/guest/snpEff/PIPE/work [btrfs]
Oct-05 16:40:22.994 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/guest/snpEff/PIPE/bin
Oct-05 16:40:23.008 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-05 16:40:23.020 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-05 16:40:23.052 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-05 16:40:23.065 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 7; maxThreads: 1000
Oct-05 16:40:23.179 [main] DEBUG nextflow.Session - Session start
Oct-05 16:40:24.028 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-05 16:40:24.150 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-05 16:40:24.150 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-05 16:40:24.159 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-05 16:40:24.164 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=6; memory=7.7 GB; capacity=6; pollInterval=100ms; dumpInterval=5m
Oct-05 16:40:24.324 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: snpEff
Oct-05 16:40:24.324 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Oct-05 16:40:24.324 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snpEff
Oct-05 16:40:24.325 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Oct-05 16:40:24.325 [main] DEBUG nextflow.Session - Session await
Oct-05 16:40:24.563 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-05 16:40:24.566 [Task submitter] INFO nextflow.Session - [df/923aad] Submitted process > snpEff
Oct-05 16:40:27.091 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: snpEff; status: COMPLETED; exit: 255; error: -; workDir: /home/guest/snpEff/PIPE/work/df/923aad29f2e723f9a19a2e3d563b1a]
Oct-05 16:40:27.112 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'snpEff'
Caused by:
Process `snpEff` terminated with an error exit status (255)
Command executed:
cd /home/guest/snpEff/PIPE
java -jar /usr/local/share/snpeff-5.0-0/snpEff.jar -i vcf -o vcf -fastaProt out.fa ~/snpEff/data/hg38 00_INPUT/in.vcf
Command exit status:
255
Command output:
(empty)
Command error:
WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
java.lang.RuntimeException: Property: '/home/guest/snpEff/data/hg38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:104)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:456)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:938)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:922)
at org.snpeff.SnpEff.run(SnpEff.java:1194)
at org.snpeff.SnpEff.main(SnpEff.java:167)
Work dir:
/home/guest/snpEff/PIPE/work/df/923aad29f2e723f9a19a2e3d563b1a
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Oct-05 16:40:27.121 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-05 16:40:27.125 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `snpEff` terminated with an error exit status (255)
Oct-05 16:40:27.145 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-05 16:40:27.172 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=2.5s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Oct-05 16:40:27.345 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-05 16:40:27.368 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye