-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path.nextflow.log.8
126 lines (116 loc) · 10.3 KB
/
.nextflow.log.8
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
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
Oct-05 03:01:02.405 [main] DEBUG nextflow.cli.Launcher - $> nextflow run part1.nf -with-singularity 'snpEff:5.0.sif'
Oct-05 03:01:02.503 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.10.7
Oct-05 03:01:02.525 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/guest/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Oct-05 03:01:02.537 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-05 03:01:02.539 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-05 03:01:02.543 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-05 03:01:02.555 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Oct-05 03:01:02.605 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by command-line option `-with-singularity null`
Oct-05 03:01:02.623 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Oct-05 03:01:02.642 [main] INFO nextflow.cli.CmdRun - Launching `part1.nf` [big_shannon] DSL2 - revision: da1ac6a0d8
Oct-05 03:01:02.642 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-05 03:01:02.643 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-05 03:01:02.653 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/guest/.nextflow/secrets/store.json
Oct-05 03:01:02.657 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3d7fa3ae] - activable => nextflow.secret.LocalSecretsProvider@3d7fa3ae
Oct-05 03:01:02.733 [main] DEBUG nextflow.Session - Session UUID: f9daea4d-ee02-4380-85f3-f1427ea04e94
Oct-05 03:01:02.733 [main] DEBUG nextflow.Session - Run name: big_shannon
Oct-05 03:01:02.734 [main] DEBUG nextflow.Session - Executor pool size: 6
Oct-05 03:01:02.746 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=18; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-05 03:01:02.776 [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: 307393@fedora [10.0.2.15]
CPUs: 6 - Mem: 7.7 GB (782.3 MB) - Swap: 7.7 GB (5.5 GB)
Oct-05 03:01:02.799 [main] DEBUG nextflow.Session - Work-dir: /home/guest/snpEff/PIPE/work [btrfs]
Oct-05 03:01:02.799 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/guest/snpEff/PIPE/bin
Oct-05 03:01:02.809 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-05 03:01:02.821 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-05 03:01:02.845 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-05 03:01:02.855 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 7; maxThreads: 1000
Oct-05 03:01:02.948 [main] DEBUG nextflow.Session - Session start
Oct-05 03:01:03.653 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-05 03:01:03.763 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-05 03:01:03.763 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-05 03:01:03.771 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-05 03:01:03.776 [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 03:01:03.895 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: singularityProcess
Oct-05 03:01:03.896 [main] DEBUG nextflow.Session - Igniting dataflow network (2)
Oct-05 03:01:03.902 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > singularityProcess
Oct-05 03:01:03.903 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Oct-05 03:01:03.904 [main] DEBUG nextflow.Session - Session await
Oct-05 03:01:04.087 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-05 03:01:04.089 [Task submitter] INFO nextflow.Session - [9f/dfd4e1] Submitted process > singularityProcess (1)
Oct-05 03:01:04.748 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: singularityProcess (1); status: COMPLETED; exit: 255; error: -; workDir: /home/guest/snpEff/PIPE/work/9f/dfd4e1dd34bd55d137ee239b3ec79e]
Oct-05 03:01:04.766 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'singularityProcess (1)'
Caused by:
Process `singularityProcess (1)` terminated with an error exit status (255)
Command executed:
#!/bin/bash
singularity exec -B ~/snpEff/PIPE/00_INPUT/:/input snpEff:5.0.sif
ls -l /input
java -jar /usr/local/share/snpeff-5.0-0/snpEff.jar -i vcf -o vcf -fastaProt out.fa hg38 /input/in.vcf > out.vcf
Command exit status:
255
Command output:
(empty)
Command error:
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: false
-hgvs : Use HGVS annotations for amino acid sub-field. Default: true
-hgvsOld : Use old HGVS notation. Default: false
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false
-hgvsTrId : Use transcript ID in HGVS notation. Default: false
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof : Do not add LOF and NMD annotations.
-noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end).
-oicr : Add OICR tag in VCF file. Default: false
-sequenceOntology : Use Sequence Ontology terms. Default: true
Generic options:
-c , -config : Specify config file
-configOption name=value : Override a config file option
-d , -debug : Debug mode (very verbose).
-dataDir <path> : Override data_dir parameter from config file.
-download : Download a SnpEff database, if not available locally. Default: true
-nodownload : Do not download a SnpEff database, if not available locally.
-h , -help : Show this help and exit
-noLog : Do not report usage statistics to server
-q , -quiet : Quiet mode (do not show any messages or errors)
-v , -verbose : Verbose mode
-version : Show version number and exit
Database options:
-canon : Only use canonical transcripts.
-canonList <file> : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in <file>.
-interaction : Annotate using inteactions (requires interaciton database). Default: true
-interval <file> : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
-maxTSL <TSL_number> : Only use transcripts having Transcript Support Level lower than <TSL_number>.
-motif : Annotate using motifs (requires Motif database). Default: true
-nextProt : Annotate using NextProt (requires NextProt database).
-noGenome : Do not load any genomic database (e.g. annotate using custom files).
-noExpandIUB : Disable IUB code expansion in input variants
-noInteraction : Disable inteaction annotations
-noMotif : Disable motif annotations.
-noNextProt : Disable NextProt annotations.
-onlyReg : Only use regulation tracks.
-onlyProtein : Only use protein coding transcripts. Default: false
-onlyTr <file.txt> : Only use the transcripts in this file. Format: One transcript ID per line.
-reg <name> : Regulation track to use (this option can be used add several times).
-ss , -spliceSiteSize <int> : Set size for splice sites (donor and acceptor) in bases. Default: 2
-spliceRegionExonSize <int> : Set size for splice site region within exons. Default: 3 bases
-spliceRegionIntronMin <int> : Set minimum number of bases for splice site region within intron. Default: 3 bases
-spliceRegionIntronMax <int> : Set maximum number of bases for splice site region within intron. Default: 8 bases
-strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false
-ud , -upDownStreamLen <int> : Set upstream downstream interval length (in bases)
Work dir:
/home/guest/snpEff/PIPE/work/9f/dfd4e1dd34bd55d137ee239b3ec79e
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Oct-05 03:01:04.774 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-05 03:01:04.781 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `singularityProcess (1)` terminated with an error exit status (255)
Oct-05 03:01:04.799 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-05 03:01:04.805 [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=561ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Oct-05 03:01:04.993 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-05 03:01:05.010 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye