Why is my singularity pull failing in my nextflow script? - docker

I have looked hard for an answer, but haven't managed to find one, so I'm hoping someone here can help me understand this error and what is happening during the singularity pull command.
Here is the error:
Error executing process > 'QC_TRIM_READS (1)'
Caused by:
Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-sickle-trim-1.33--2.img.pulling.1632264509884 docker://quay.io/biocontainers/sickle-trim:1.33--2 > /dev/null
status : 127
message:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
/usr/bin/env: ‘python’: No such file or directory
ERROR: pulling container failed!
Here is the script (excuse the mess, I am just getting used to nextflow)
#!/usr/bin/env Nextflow
nextflow.enable.dsl=2
params.ref_genome = "./data/GmaxFiskeby_678_v1.0.fa"
params.ref_annotation = "./data/GmaxFiskeby_678_v1.1.gene_exons.gff3"
params.intermediate_dir = "$workDir/intermediate/"
workflow {
ref_genome_ch = Channel.fromPath("$params.ref_genome")
ref_annotation_ch = Channel.fromPath("$params.ref_annotation")
input_fastq_ch = Channel.fromPath("./data/*.fastq")
ref_genome_ch.view()
QC_TRIM_READS(input_fastq_ch)
STAR_INDEX_GENOME(ref_genome_ch, ref_annotation_ch)
}
process GZIP_VERSION {
echo true
script:
"""
gzip --version
"""
}
process UNZIP {
publishDir "intermediate/"
input:
path file
output:
path "${file.baseName}"
script:
"""
gzip -dfk ${file}
"""
}
process QC_TRIM_READS {
publishDir "intermediate/"
container 'quay.io/biocontainers/sickle-trim:1.33--2'
input:
path fastqFile
output:
path "${fastqFile.baseName}_trimmed.${fastqFile.getExtension()}"
script:
"""
sickle se \\
-f $fastqFile \\
-t sanger \\
-o ${fastqFile.baseName}_trimmed.${fastqFile.getExtension()} \\
-q 35 \\
-l 45
"""
}
process STAR_INDEX_GENOME {
publishDir "intermediate/indexedGenome/"
/*if (worflow.containerEngine == 'singularity'){
container "https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0"
} else {*/
container "quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0" //'quay.io/biocontainers/star:2.6.1d--0'
//}
input:
path genome
path gtf
output:
path "star" , emit: index
script:
"""
STAR \\
--runMode genomeGenerate \\
--genomeDir star/ \\
--genomeFastaFiles ${genome}\\
--sjdbGTFfile ${gtf} \\
--sjdbGTFtagExonParentTranscript Parent \\
--sjdbOverhang 100 \\
--runThreadN 2
"""
}
Here is my configuration file:
//docker.enabled = false
singularity.enabled = true
singularity.autoMounts = true
I built my environment as a conda environment, here is the yml file:
name: nf-core
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=4.5=1_gnu
- attrs=21.2.0=pyhd3eb1b0_0
- brotlipy=0.7.0=py38h27cfd23_1003
- bzip2=1.0.8=h7b6447c_0
- c-ares=1.17.1=h27cfd23_0
- ca-certificates=2021.7.5=h06a4308_1
- cairo=1.14.12=h7636065_2
- cattrs=1.7.1=pyhd3eb1b0_0
- certifi=2021.5.30=py38h06a4308_0
- cffi=1.14.6=py38h400218f_0
- charset-normalizer=2.0.4=pyhd3eb1b0_0
- click=8.0.1=pyhd3eb1b0_0
- colorama=0.4.4=pyhd3eb1b0_0
- commonmark=0.9.1=pyhd3eb1b0_0
- coreutils=8.32=h7b6447c_0
- cryptography=3.4.7=py38hd23ed53_0
- curl=7.78.0=h1ccaba5_0
- expat=2.4.1=h2531618_2
- fontconfig=2.12.6=h49f89f6_0
- freetype=2.8=hab7d2ae_1
- fribidi=1.0.10=h7b6447c_0
- future=0.18.2=py38_1
- gettext=0.21.0=hf68c758_0
- git=2.32.0=pl5262hc120c5b_1
- gitdb=4.0.7=pyhd3eb1b0_0
- gitpython=3.1.18=pyhd3eb1b0_1
- glib=2.69.1=h5202010_0
- graphite2=1.3.14=h23475e2_0
- graphviz=2.40.1=h25d223c_0
- harfbuzz=1.7.6=h5f0a787_1
- hdf5=1.10.6=hb1b8bf9_0
- icu=58.2=he6710b0_3
- idna=3.2=pyhd3eb1b0_0
- importlib-metadata=4.8.1=py38h06a4308_0
- importlib_metadata=4.8.1=hd3eb1b0_0
- itsdangerous=2.0.1=pyhd3eb1b0_0
- jinja2=3.0.1=pyhd3eb1b0_0
- jpeg=9d=h7f8727e_0
- jsonschema=3.2.0=pyhd3eb1b0_2
- krb5=1.19.2=hac12032_0
- ld_impl_linux-64=2.35.1=h7274673_9
- libcurl=7.78.0=h0b77cf5_0
- libedit=3.1.20210714=h7f8727e_0
- libev=4.33=h7b6447c_0
- libffi=3.3=he6710b0_2
- libgcc-ng=9.3.0=h5101ec6_17
- libgfortran-ng=7.5.0=ha8ba4b0_17
- libgfortran4=7.5.0=ha8ba4b0_17
- libgomp=9.3.0=h5101ec6_17
- libiconv=1.15=h63c8f33_5
- libnghttp2=1.41.0=hf8bcb03_2
- libpng=1.6.37=hbc83047_0
- libssh2=1.9.0=h1ba5d50_1
- libstdcxx-ng=9.3.0=hd4cf53a_17
- libtiff=4.2.0=h85742a9_0
- libtool=2.4.6=h7b6447c_1005
- libwebp-base=1.2.0=h27cfd23_0
- libxcb=1.14=h7b6447c_0
- libxml2=2.9.12=h03d6c58_0
- lz4-c=1.9.3=h295c915_1
- markupsafe=2.0.1=py38h27cfd23_0
- ncbi-ngs-sdk=2.10.4=hdf6179e_0
- ncurses=6.2=he6710b0_1
- nextflow=21.04.0=h4a94de4_0
- nf-core=2.1=pyh5e36f6f_0
- openjdk=8.0.152=h7b6447c_3
- openssl=1.1.1l=h7f8727e_0
- ossuuid=1.6.2=hf484d3e_1000
- packaging=21.0=pyhd3eb1b0_0
- pango=1.42.0=h377f3fa_0
- pcre=8.45=h295c915_0
- pcre2=10.35=h14c3975_1
- perl=5.26.2=h14c3975_0
- perl-app-cpanminus=1.7044=pl526_1
- perl-business-isbn=3.004=pl526_0
- perl-business-isbn-data=20140910.003=pl526_0
- perl-carp=1.38=pl526_3
- perl-constant=1.33=pl526_1
- perl-data-dumper=2.173=pl526_0
- perl-encode=2.88=pl526_1
- perl-exporter=5.72=pl526_1
- perl-extutils-makemaker=7.36=pl526_1
- perl-file-path=2.16=pl526_0
- perl-file-temp=0.2304=pl526_2
- perl-mime-base64=3.15=pl526_1
- perl-parent=0.236=pl526_1
- perl-uri=1.76=pl526_0
- perl-xml-libxml=2.0132=pl526h7ec2d77_1
- perl-xml-namespacesupport=1.12=pl526_0
- perl-xml-sax=1.02=pl526_0
- perl-xml-sax-base=1.09=pl526_0
- perl-xsloader=0.24=pl526_0
- pip=21.2.2=py38h06a4308_0
- pixman=0.40.0=h7b6447c_0
- prompt-toolkit=3.0.17=pyhca03da5_0
- prompt_toolkit=3.0.17=hd3eb1b0_0
- pycparser=2.20=py_2
- pygments=2.10.0=pyhd3eb1b0_0
- pyopenssl=20.0.1=pyhd3eb1b0_1
- pyparsing=2.4.7=pyhd3eb1b0_0
- pyrsistent=0.17.3=py38h7b6447c_0
- pysocks=1.7.1=py38h06a4308_0
- python=3.8.11=h12debd9_0_cpython
- python_abi=3.8=2_cp38
- pyyaml=5.4.1=py38h27cfd23_1
- questionary=1.10.0=pyhd8ed1ab_0
- readline=8.1=h27cfd23_0
- requests=2.26.0=pyhd3eb1b0_0
- requests-cache=0.7.4=pyhd8ed1ab_0
- rich=10.10.0=py38h578d9bd_0
- setuptools=58.0.4=py38h06a4308_0
- singularity=2.4.2=0
- six=1.16.0=pyhd3eb1b0_0
- smmap=4.0.0=pyhd3eb1b0_0
- sqlite=3.36.0=hc218d9a_0
- sra-tools=2.11.0=pl5262h314213e_0
- tabulate=0.8.9=py38h06a4308_0
- tk=8.6.10=hbc83047_0
- typing-extensions=3.10.0.2=hd3eb1b0_0
- typing_extensions=3.10.0.2=pyh06a4308_0
- url-normalize=1.4.3=pyhd8ed1ab_0
- urllib3=1.26.6=pyhd3eb1b0_1
- wcwidth=0.2.5=pyhd3eb1b0_0
- wheel=0.37.0=pyhd3eb1b0_1
- xz=5.2.5=h7b6447c_0
- yaml=0.2.5=h7b6447c_0
- zipp=3.5.0=pyhd3eb1b0_0
- zlib=1.2.11=h7b6447c_3
- zstd=1.4.9=haebb681_0
prefix: /home/mkozubov/miniconda3/envs/nf-core
Here is the log file:
Sep-21 16:00:49.076 [main] DEBUG nextflow.cli.Launcher - $> nextflow run rnaseq.nf
Sep-21 16:00:49.318 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.0
Sep-21 16:00:49.367 [main] INFO nextflow.cli.CmdRun - Launching `rnaseq.nf` [reverent_jepsen] - revision: 0fc00d31fc
Sep-21 16:00:49.414 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/nextflow.config
Sep-21 16:00:49.418 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/nextflow.config
Sep-21 16:00:49.506 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Sep-21 16:00:50.238 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/mkozubov/.nextflow/plugins
Sep-21 16:00:50.240 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Sep-21 16:00:50.242 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty
Sep-21 16:00:50.258 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Sep-21 16:00:50.262 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Sep-21 16:00:50.266 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Sep-21 16:00:50.289 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Sep-21 16:00:50.366 [main] DEBUG nextflow.Session - Session uuid: 22a13149-e9f8-47cc-8f09-98a6b000a83a
Sep-21 16:00:50.367 [main] DEBUG nextflow.Session - Run name: reverent_jepsen
Sep-21 16:00:50.372 [main] DEBUG nextflow.Session - Executor pool size: 5
Sep-21 16:00:50.418 [main] DEBUG nextflow.cli.CmdRun -
Version: 21.04.0 build 5552
Created: 02-05-2021 16:22 UTC (09:22 PDT)
System: Linux 5.10.16.3-microsoft-standard-WSL2
Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12
Encoding: UTF-8 (UTF-8)
Process: 10590#DESKTOP-UJ90D1J [127.0.1.1]
CPUs: 5 - Mem: 1.9 GB (311.8 MB) - Swap: 1 GB (783.4 MB)
Sep-21 16:00:50.539 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/work
v9fs
Sep-21 16:00:50.541 [main] DEBUG nextflow.Session - Work-dir: /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/work [null]
Sep-21 16:00:50.545 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/bin
Sep-21 16:00:50.585 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Sep-21 16:00:50.616 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Sep-21 16:00:50.999 [main] DEBUG nextflow.Session - Session start invoked
Sep-21 16:00:51.461 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Sep-21 16:00:51.511 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: QC_TRIM_READS, UNZIP, STAR_INDEX_GENOME, GZIP_VERSION
Sep-21 16:00:51.643 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Sep-21 16:00:51.643 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Sep-21 16:00:51.651 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Sep-21 16:00:51.656 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=5; memory=1.9 GB; capacity=5; pollInterval=100ms; dumpInterval=5m
Sep-21 16:00:51.868 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Sep-21 16:00:51.869 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Sep-21 16:00:51.904 [main] DEBUG nextflow.Session - Ignite dataflow network (5)
Sep-21 16:00:51.963 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > QC_TRIM_READS
Sep-21 16:00:51.965 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > STAR_INDEX_GENOME
Sep-21 16:00:51.966 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Sep-21 16:00:51.968 [main] DEBUG nextflow.Session - Session await
Sep-21 16:00:51.969 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: ./data/; pattern: *.fastq; options: [:]
Sep-21 16:00:52.300 [Actor Thread 8] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Sep-21 16:00:52.300 [Actor Thread 8] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://quay.io/biocontainers/sickle-trim:1.33--2 [cache /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/work/singularity/quay.io-biocontainers-sickle-trim-1.33--2.img]
Sep-21 16:00:52.300 [Actor Thread 7] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0 [cache /mnt/c/Users/mkozubov/Desktop/nextflow_tutorial/rnaseq/work/singularity/quay.io-biocontainers-mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2-59cdd445419f14abac76b31dd0d71217994cbcc9-0.img]
Sep-21 16:00:52.433 [Actor Thread 5] ERROR nextflow.processor.TaskProcessor - Error executing process > 'QC_TRIM_READS (1)'
Caused by:
Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-sickle-trim-1.33--2.img.pulling.1632265252300 docker://quay.io/biocontainers/sickle-trim:1.33--2 > /dev/null
status : 127
message:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
/usr/bin/env: ‘python’: No such file or directory
ERROR: pulling container failed!
java.lang.IllegalStateException: java.lang.IllegalStateException: Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-sickle-trim-1.33--2.img.pulling.1632265252300 docker://quay.io/biocontainers/sickle-trim:1.33--2 > /dev/null
status : 127
message:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
/usr/bin/env: ‘python’: No such file or directory
ERROR: pulling container failed!
at nextflow.container.SingularityCache.getCachePathFor(SingularityCache.groovy:304)
at nextflow.container.SingularityCache$getCachePathFor.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at nextflow.container.ContainerHandler.createSingularityCache(ContainerHandler.groovy:85)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
at nextflow.container.ContainerHandler.normalizeImageName(ContainerHandler.groovy:68)
at nextflow.container.ContainerHandler$normalizeImageName.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at nextflow.processor.TaskRun.getContainer(TaskRun.groovy:587)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.MethodMetaProperty$GetBeanMethodMetaProperty.getProperty(MethodMetaProperty.java:76)
at org.codehaus.groovy.runtime.callsite.GetEffectivePogoPropertySite.getProperty(GetEffectivePogoPropertySite.java:85)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:341)
at nextflow.processor.TaskProcessor.createTaskHashKey(TaskProcessor.groovy:1939)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
at nextflow.processor.TaskProcessor.invokeTask(TaskProcessor.groovy:591)
at nextflow.processor.InvokeTaskAdapter.call(InvokeTaskAdapter.groovy:59)
at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.access$001(ForkingDataflowOperatorActor.java:35)
at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor$1.run(ForkingDataflowOperatorActor.java:58)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-sickle-trim-1.33--2.img.pulling.1632265252300 docker://quay.io/biocontainers/sickle-trim:1.33--2 > /dev/null
status : 127
message:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
/usr/bin/env: ‘python’: No such file or directory
ERROR: pulling container failed!
at nextflow.container.SingularityCache.runCommand(SingularityCache.groovy:256)
at nextflow.container.SingularityCache.downloadSingularityImage0(SingularityCache.groovy:223)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1029)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1012)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:101)
at nextflow.container.SingularityCache$_downloadSingularityImage_closure1.doCall(SingularityCache.groovy:191)
at nextflow.container.SingularityCache$_downloadSingularityImage_closure1.call(SingularityCache.groovy)
at nextflow.file.FileMutex.lock(FileMutex.groovy:107)
at nextflow.container.SingularityCache.downloadSingularityImage(SingularityCache.groovy:191)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1029)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1012)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:101)
at nextflow.container.SingularityCache$_getLazyImagePath_closure2.doCall(SingularityCache.groovy:281)
at nextflow.container.SingularityCache$_getLazyImagePath_closure2.call(SingularityCache.groovy)
at groovyx.gpars.dataflow.LazyDataflowVariable$1.run(LazyDataflowVariable.java:70)
... 3 common frames omitted
Sep-21 16:00:52.443 [Actor Thread 5] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.IllegalStateException: Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-sickle-trim-1.33--2.img.pulling.1632265252300 docker://quay.io/biocontainers/sickle-trim:1.33--2 > /dev/null
status : 127
message:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
/usr/bin/env: ‘python’: No such file or directory
ERROR: pulling container failed!
Sep-21 16:00:52.494 [Actor Thread 5] DEBUG nextflow.Session - The following nodes are still active:
[process] QC_TRIM_READS
status=ACTIVE
port 0: (queue) closed; channel: fastqFile
port 1: (cntrl) - ; channel: $
Sep-21 16:00:52.507 [main] DEBUG nextflow.Session - Session await > all process finished
Sep-21 16:00:52.510 [main] DEBUG nextflow.Session - Session await > all barriers passed
Sep-21 16:00:52.521 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Sep-21 16:00:52.685 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Sep-21 16:00:52.752 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
I have been using nf-core's rnaseq pipeline to guide me a bit: https://github.com/nf-core/rnaseq
If it helps, here is the pipeline I am trying to automate: https://bioinformatics.uconn.edu/resources-and-events/tutorials-2/rna-seq-tutorial-with-reference-genome/#
My computer has a Windows 10 operating system, and I have enabled WSL2 and got Ubuntu.
I am fairly new to Docker, Singularity, and Nextflow so I am hoping someone can explain the error. I don't even understand why python is being mentioned. Is the issue that singularity cannot pull from Quay.io? I am a bit lost and would appreciate a nudge in the right direction.
Also the reason I am trying to get singularity to work is STAR immediately gives me a Segmentation fault error on my local machine (i'm assuming I run out of memory), and I would like to test this pipeline on our HPC (but I don't have root privileges).

You can ignore the Singularity warnings, but not the errors. The problem looks to be that you're missing python in your environment:
/usr/bin/env: ‘python’: No such file or directory
ERROR: pulling container failed!
You need to make sure you have Python 3 installed. If you have, you should be able to see it here with:
/usr/bin/python --version
You didn't mention the version of Ubuntu you are using, but if you have Ubuntu 20.04 then you should already have Python 3 pre-installed. If this is the case, and you have Python 3 already installed (i.e. you find that /usr/bin/python3 --version works, note the '3') but the above doesn't, try:
sudo apt-get install python-is-python3
This will install a symlink to point the /usr/bin/python interpreter at the current default python3.

Related

Issue with Docker container deployment via elastic beanstalk : basex 9.3.1

I have this Dockerfile :
FROM basex/basexhttp:9.3.1
I deploy it on Elasticbeanstalk but i get the following error :
[main] INFO org.eclipse.jetty.util.log - Logging initialized #549ms to
org.eclipse.jetty.util.log.Slf4jLog [main] INFO
org.eclipse.jetty.server.Server - jetty-9.4.24.v20191120; built:
2019-11-20T21:37:49.771Z; git:
363d5f2df3a8a28de40604320230664b9c793c16; jvm 1.8.0_212-b04 [main]
WARN org.eclipse.jetty.webapp.WebAppContext - Failed startup of
context
o.e.j.w.WebAppContext#31a5c39e{/,null,UNAVAILABLE}{/srv/basex/webapp}
java.lang.IllegalStateException: Parent for temp dir not configured
correctly: writeable=false
at org.eclipse.jetty.webapp.WebInfConfiguration.makeTempDirectory(WebInfConfiguration.java:499)
at org.eclipse.jetty.webapp.WebInfConfiguration.resolveTempDirectory(WebInfConfiguration.java:468)
at org.eclipse.jetty.webapp.WebInfConfiguration.preConfigure(WebInfConfiguration.java:138)
at org.eclipse.jetty.webapp.WebAppContext.preConfigure(WebAppContext.java:488)
at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:523)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:72)
at org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:169)
at org.eclipse.jetty.server.Server.start(Server.java:407)
at org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:110)
at org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:100)
at org.eclipse.jetty.server.Server.doStart(Server.java:371)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:72)
at org.basex.BaseXHTTP.(BaseXHTTP.java:129)
at org.basex.BaseXHTTP.main(BaseXHTTP.java:53) [main] INFO org.eclipse.jetty.server.AbstractConnector - Started
ServerConnector#48eff760{HTTP/1.1,[http/1.1]}{0.0.0.0:8984} [main]
INFO org.eclipse.jetty.server.Server - Started #936ms
java.lang.NullPointerException
and then container stops.
Now i tried to use the same image and run it via the root user and it starts and works perfectly fine. Following is the command :
docker run -d b58e4a50371d
Any suggestions/help appreciated.

Jenkins windows slave offline

I have Jenkins 2.164.3 on a CentOS 7 server.
I have a Windows Server 2003 slave with Java version 1.8.0.
I have 3 x linux slaves working successfully.
The windows service on the slave is installed and running.
The windows slave is setup with the following with Launch Method "Let jenkins control this Windows salve as a Windows server"
This Jenkins server is a new server that replaced an older jenkins server (debian wheezy from turnkey linux ~3 years ago). This windows slave used to connect to that old server. To remove the connection on this slave to the old server, I did the following:
1. sc delete
2. deleted the files in folder c:\jenkins
3. rebooted server
4. from new jenkins server, launched slave which copied files to c:\jenkins folder and installed service.
On my new jenkins server, I setup the windows slave and when I connect, the log has the following:
[2019-05-27 12:24:07] [windows-slaves] Connecting to 192.168.1.152
Checking if Java exists
java -version returned 1.8.0.
[2019-05-27 12:24:16] [windows-slaves] Copying jenkins-slave.xml
[2019-05-27 12:24:16] [windows-slaves] Copying slave.jar
[2019-05-27 12:24:16] [windows-slaves] Starting the service
[2019-05-27 12:24:16] [windows-slaves] Waiting for the service to become ready
ERROR: [2019-05-27 12:24:52] [windows-slaves] The service did not respond. Perhaps it failed to launch?
[2019-05-27 12:36:00] [windows-slaves] Connecting to 192.168.1.152
Checking if Java exists
java -version returned 1.8.0.
[2019-05-27 12:36:08] [windows-slaves] Copying jenkins-slave.xml
[2019-05-27 12:36:08] [windows-slaves] Copying slave.jar
[2019-05-27 12:36:08] [windows-slaves] Starting the service
ERROR: Unexpected error in launching an agent. This is probably a bug in Jenkins
org.jinterop.dcom.common.JIException: Service Already Running
at org.jvnet.hudson.wmi.Win32Service$Implementation.start(Win32Service.java:149)
Caused: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.kohsuke.jinterop.JInteropInvocationHandler.invoke(JInteropInvocationHandler.java:140)
Caused: java.lang.reflect.UndeclaredThrowableException
at com.sun.proxy.$Proxy90.start(Unknown Source)
at hudson.os.windows.ManagedWindowsServiceLauncher.launch(ManagedWindowsServiceLauncher.java:342)
at hudson.slaves.SlaveComputer$1.call(SlaveComputer.java:294)
at jenkins.util.ContextResettingExecutorService$2.call(ContextResettingExecutorService.java:46)
at jenkins.security.ImpersonatingExecutorService$2.call(ImpersonatingExecutorService.java:71)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
The windows slave is Windows Server 2003, the service is installed and running.
In the log file C:\Jenkins\jenkins-slave.wrapper.log, it has the following:
2019-05-27 12:19:32,644 INFO - Starting ServiceWrapper in the service mode
2019-05-27 12:19:32,659 INFO - Starting javaw.exe -Xrs -jar "C:\Jenkins\slave.jar" -tcp "C:\Jenkins\port.txt"
2019-05-27 12:19:32,675 INFO - Extension loaded: killOnStartup
2019-05-27 12:19:32,675 DEBUG - Checking the potentially runaway process with PID=1408
2019-05-27 12:19:32,675 DEBUG - No runaway process with PID=1408. The process has been already stopped.
2019-05-27 12:19:32,675 INFO - Starting javaw.exe -Xrs -jar "C:\Jenkins\slave.jar" -tcp "C:\Jenkins\port.txt"
2019-05-27 12:19:32,691 INFO - Started process 4084
2019-05-27 12:19:32,691 DEBUG - Forwarding logs of the process System.Diagnostics.Process (javaw) to winsw.SizeBasedRollingLogAppender
2019-05-27 12:19:32,691 INFO - Recording PID of the started process:4084. PID file destination is C:\Jenkins\jenkins_agent.pid
2019-05-27 12:23:56,529 INFO - Stopping jenkinsslave-C__Jenkins
2019-05-27 12:23:56,529 DEBUG - ProcessKill 4084
2019-05-27 12:23:56,561 INFO - Stopping process 4084
2019-05-27 12:23:56,561 INFO - Send SIGINT 4084
2019-05-27 12:23:56,561 WARN - SIGINT to 4084 failed - Killing as fallback
2019-05-27 12:23:56,561 INFO - Finished jenkinsslave-C__Jenkins
2019-05-27 12:23:56,561 DEBUG - Completed. Exit code is 0
2019-05-27 12:24:16,374 INFO - Starting ServiceWrapper in the service mode
2019-05-27 12:24:16,390 INFO - Starting javaw.exe -Xrs -jar "C:\Jenkins\slave.jar" -tcp "C:\Jenkins\port.txt"
2019-05-27 12:24:16,405 INFO - Extension loaded: killOnStartup
2019-05-27 12:24:16,405 DEBUG - Checking the potentially runaway process with PID=4084
2019-05-27 12:24:16,405 DEBUG - No runaway process with PID=4084. The process has been already stopped.
2019-05-27 12:24:16,405 INFO - Starting javaw.exe -Xrs -jar "C:\Jenkins\slave.jar" -tcp "C:\Jenkins\port.txt"
2019-05-27 12:24:16,421 INFO - Started process 364
2019-05-27 12:24:16,421 DEBUG - Forwarding logs of the process System.Diagnostics.Process (javaw) to winsw.SizeBasedRollingLogAppender
2019-05-27 12:24:16,421 INFO - Recording PID of the started process:364. PID file destination is C:\Jenkins\jenkins_agent.pid
The error on the jenkins server shows the service is not running. On the windows slave machine, the service is running. What is the problem and how do I fix?
Thanks.
Very old question, but if you end up here because you are getting this error, find the jenkins_agent.pid file and delete it. It should be in the same folder the rest of your jenkins slave files. The service should start again normally after that.
I know this question is old and you've long moved on but maybe this will help someone. I ran into a similar problem with a Windows slave, specifically I was seeing it go through a cycle of restarts much like you were:
2019-05-27 12:24:16,405 DEBUG - Checking the potentially runaway process with PID=4084
2019-05-27 12:24:16,405 DEBUG - No runaway process with PID=4084. The process has been already stopped.
2019-05-27 12:24:16,405 INFO - Starting javaw.exe -Xrs -jar "C:\Jenkins\slave.jar" -tcp "C:\Jenkins\port.txt"
2019-05-27 12:24:16,421 INFO - Started process 364
To solve the problem I checked the following:
See if the Windows service is running, cycle it
In addition to checking the C:\<path to jenkins>\jenkins-slave.wrapper.log also have a look at C:\<path to jenkins>\jenkins-slave.err.log
The err log is where I found my problem, I had an issue with a cert unable to find valid certificate
Edit the C:\<path to jenkins>\jenkins-slave.xml file and fix whatever startup parameter is causing you a problem. Make sure to check the java path and version.
In my certificate error case, I needed to add a -noCertificateCheck to my arguments so I could move on
Another potential downfall maybe that the executable setting in the jenkins-slave.xml config file no longer points to a valid java.exe.
This may happen after a Java update

Caused by: java.lang.IllegalStateException: The folder 'test' does not exist for

I will need your help please.
This is the context, I'm trying to set up a Continous Integration plateform, for specifc needs, and this is my Configuration, all in the same machine(Windows 7 ):
SonarQube 5.1 (I tried both internal and external databases)
SonarQube runner 2.4
PHP plugin for Sonar
Jenkins 1.6
SonarQube plugin for Jenkins (I'have already done all of the Sonarqube config in Jenkins)
I created a specific Job for PHP (Which is a local folder in my file system)(I configured the build section of Jenkins bu adding Standalone SonarQube Analysis, with the specific Path to projeetc proporties which point to my sonar-project.properties behind )
sonar.projectKey=my:project
sonar.projectName=PHP project analyzed with the SonarQube Runner reusing PHPUnit reports
sonar.projectVersion=1.0
sonar.sources=userthing,test sonar.tests=test sonar.language=php sonar.sourceEncoding=UTF-8 # Reusing PHPUnit reports #sonar.php.coverage.reportPath=reports/phpunit.coverage.xml #sonar.php.tests.reportPath=reports/phpunit.xml
When I launch a build from Jenkins I have this error :
NFO: Work directory: C:\Users\user\.jenkins\jobs\test projet\workspace\.sonar
INFO: SonarQube Server 5.1.2
14:13:10.295 INFO - Load global repositories
14:13:10.372 INFO - Load global repositories (done) | time=78ms
14:13:10.374 INFO - Server id: 20151028133512
14:13:10.374 INFO - User cache: C:\Users\user\.sonar\cache
14:13:10.379 INFO - Install plugins
14:13:10.706 INFO - Install JDBC driver
14:13:10.710 INFO - Create JDBC datasource for jdbc:h2:tcp://localhost/sonar
14:13:11.247 INFO - Initializing Hibernate
14:13:12.106 ERROR - Invalid value of sonar.tests for my:project
INFO: ------------------------------------------------------------------------
INFO: EXECUTION FAILURE
INFO: ------------------------------------------------------------------------
Total time: 2.131s
Final Memory: 6M/20M
INFO: ------------------------------------------------------------------------
ERROR: Error during Sonar runner execution
org.sonar.runner.impl.RunnerException: Unable to execute Sonar
at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:91)
at org.sonar.runner.impl.BatchLauncher$1.run(BatchLauncher.java:75)
at java.security.AccessController.doPrivileged(Native Method)
at org.sonar.runner.impl.BatchLauncher.doExecute(BatchLauncher.java:69)
at org.sonar.runner.impl.BatchLauncher.execute(BatchLauncher.java:50)
at org.sonar.runner.api.EmbeddedRunner.doExecute(EmbeddedRunner.java:102)
at org.sonar.runner.api.Runner.execute(Runner.java:100)
at org.sonar.runner.Main.executeTask(Main.java:70)
at org.sonar.runner.Main.execute(Main.java:59)
at org.sonar.runner.Main.main(Main.java:53)
Caused by: java.lang.IllegalStateException: The folder 'test' does not exist for 'my:project' (base directory = C:\Users\user\.jenkins\jobs\test projet\workspace)
at org.sonar.batch.scan.ProjectReactorBuilder.checkExistenceOfPaths(ProjectReactorBuilder.java:427)
at org.sonar.batch.scan.ProjectReactorBuilder.validateDirectories(ProjectReactorBuilder.java:334)
at org.sonar.batch.scan.ProjectReactorBuilder.defineRootProject(ProjectReactorBuilder.java:163)
at org.sonar.batch.scan.ProjectReactorBuilder.execute(ProjectReactorBuilder.java:116)
at org.sonar.batch.scan.ProjectScanContainer.projectBootstrap(ProjectScanContainer.java:110)
at org.sonar.batch.scan.ProjectScanContainer.doBeforeStart(ProjectScanContainer.java:86)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:90)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
at org.sonar.batch.scan.ScanTask.scan(ScanTask.java:57)
at org.sonar.batch.scan.ScanTask.execute(ScanTask.java:45)
at org.sonar.batch.bootstrap.TaskContainer.doAfterStart(TaskContainer.java:135)
at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
at org.sonar.batch.bootstrap.GlobalContainer.executeTask(GlobalContainer.java:158)
at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:95)
at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:67)
at org.sonar.runner.batch.IsolatedLauncher.execute(IsolatedLauncher.java:48)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:87)
... 9 more
ERROR:
ERROR: Re-run SonarQube Runner using the -X switch to enable full debug logging.
Build step 'Lancer une analyse SonarQube autonome' marked build as failure
Finished: FAILURE
I follow those steps to identify the root concern:
I created manually sonar-project.properties.
Lunch sonar-runner.bat directly from my php folder, => then it works perfectly I have all the metric.
I'm sure that the root cause is Jenkins, but I don't know exactly what I'm missing.
Even if some times everything seems to work fine, I got this message from stacktrace
0 file indexed
:
INFO: Error stacktraces are turned on.
INFO: Runner configuration file: C:\DevTools\sonar-runner-2.4\conf\sonar-runner.properties
INFO: Project configuration file: C:\Users\user\Desktop\Exemple de projet PHPUNIT\sonar-project.properties
INFO: Default locale: "fr_FR", source code encoding: "UTF-8"
INFO: Work directory: C:\Users\user\.jenkins\jobs\projet\workspace\.sonar
INFO: SonarQube Server 5.1.2
14:55:20.977 INFO - Load global repositories
14:55:21.040 INFO - Load global repositories (done) | time=63ms
14:55:21.040 INFO - Server id: 20151028133512
14:55:21.040 INFO - User cache: C:\Users\user\.sonar\cache
14:55:21.040 INFO - Install plugins
14:55:21.390 INFO - Install JDBC driver
14:55:21.390 INFO - Create JDBC datasource for jdbc:h2:tcp://localhost/sonar
14:55:21.918 INFO - Initializing Hibernate
14:55:22.858 INFO - Load project repositories
14:55:23.030 INFO - Load project repositories (done) | time=172ms
14:55:23.030 INFO - Load project settings
14:55:23.326 INFO - Load technical debt model
14:55:23.358 INFO - Apply project exclusions
14:55:23.498 WARN - SCM provider autodetection failed. No SCM provider claims to support this project. Please use sonar.scm.provider to define SCM of your project.
14:55:23.498 INFO - ------------- Scan My Sonar Analyses for PHP project
14:55:23.498 INFO - Load module settings
14:55:23.576 INFO - Language is forced to php
14:55:23.576 INFO - Load rules
14:55:23.864 INFO - Base dir: C:\Users\user\.jenkins\jobs\projet\workspace
14:55:23.864 INFO - Working dir: C:\Users\user\.jenkins\jobs\projet\workspace\.sonar
14:55:23.864 INFO - Source paths: .
14:55:23.864 INFO - Source encoding: UTF-8, default locale: fr_FR
14:55:23.864 INFO - Index files
14:55:23.866 INFO - **0 files indexed******************************
14:55:23.866 INFO - Quality profile for php: Sonar way
14:55:24.095 INFO - Sensor Lines Sensor
14:55:24.095 INFO - Sensor Lines Sensor (done) | time=0ms
14:55:24.095 INFO - Sensor QProfileSensor
14:55:24.105 INFO - Sensor QProfileSensor (done) | time=10ms
14:55:24.105 INFO - Sensor InitialOpenIssuesSensor
14:55:24.120 INFO - Sensor InitialOpenIssuesSensor (done) | time=15ms
14:55:24.120 INFO - Sensor ProjectLinksSensor
14:55:24.128 INFO - Sensor ProjectLinksSensor (done) | time=8ms
14:55:24.128 INFO - Sensor VersionEventsSensor
14:55:24.133 INFO - Sensor VersionEventsSensor (done) | time=5ms
14:55:24.133 INFO - Sensor SCM Sensor
14:55:24.133 INFO - No SCM system was detected. You can use the 'sonar.scm.provider' property to explicitly specify it.
14:55:24.133 INFO - Sensor SCM Sensor (done) | time=0ms
14:55:24.133 INFO - Sensor CPD Sensor
14:55:24.133 INFO - DefaultCpdEngine is used for php
14:55:24.133 INFO - Sensor CPD Sensor (done) | time=0ms
14:55:24.133 INFO - No quality gate is configured.
14:55:24.163 INFO - Compare to previous analysis (2015-10-28)
14:55:24.165 INFO - Compare over 30 days (2015-09-28, analysis of Wed Oct 28 14:39:55 CET 2015)
14:55:24.267 INFO - Execute decorators...
14:55:24.372 INFO - Store results in database
14:55:24.425 INFO - Analysis reports generated in 35ms, dir size=2 KB
14:55:24.435 INFO - Analysis reports compressed in 10ms, zip size=2 KB
14:55:24.459 INFO - Analysis reports sent to server in 23ms
14:55:24.460 INFO - ANALYSIS SUCCESSFUL, you can browse http://localhost:9000/dashboard/index/projet
14:55:24.460 INFO - Note that you will be able to access the updated dashboard once the server has processed the submitted analysis report.
INFO: ------------------------------------------------------------------------
INFO: EXECUTION SUCCESS
INFO: ------------------------------------------------------------------------
Total time: 3.851s
Final Memory: 13M/113M
INFO: ------------------------------------------------------------------------
Finished: SUCCESS
It seems like his enable to index files that I have in my php folder.
Thanks in advance for your help!
I found the root cause, as I suggested in my last comment Jenkis is the root concern, because, I wasn't aware how Jenkins, build non source Controle Projects.
In fact you have to follow those steps in order to copy your projet into Jenkis workspace:
Build the Project at least once, (it will fail), but Jenkins will
create the structure jenkins/workspace/PROJECTNAME/
Copy the project files to jenkins/workspace/PROJECTNAME/
Build again and configure appropriately
For more information in the subject, I will suggest that you look jenkins docs:Builds for Non-Source Control Projects

Neo4j server not starting up:

I am using Neo4j 2.3.0-M03 community version. I have created a database using neo4j import tool. Now when I am going to start the neo4j server, its failing. Any advice? Thanks in advance!
Starting Neo4j Server...WARNING: not changing user
process [21597]... waiting for server to be ready......... Failed to start within 120 seconds.
Neo4j Server may have failed to start, please check the logs.
The log is as follows:
2015-10-14 14:55:35.438-0400 INFO No SSL certificate found, generating a self-signed certificate..
14:55:35.936 [main] DEBUG i.n.u.i.l.InternalLoggerFactory - Using SLF4J as the default logging framework
14:55:36.105 [main] DEBUG i.n.util.internal.PlatformDependent0 - java.nio.Buffer.address: available
14:55:36.106 [main] DEBUG i.n.util.internal.PlatformDependent0 - sun.misc.Unsafe.theUnsafe: available
14:55:36.107 [main] DEBUG i.n.util.internal.PlatformDependent0 - sun.misc.Unsafe.copyMemory: available
14:55:36.107 [main] DEBUG i.n.util.internal.PlatformDependent0 - java.nio.Bits.unaligned: true
14:55:36.108 [main] DEBUG i.n.util.internal.PlatformDependent - Java version: 7
14:55:36.108 [main] DEBUG i.n.util.internal.PlatformDependent - -Dio.netty.noUnsafe: false
14:55:36.109 [main] DEBUG i.n.util.internal.PlatformDependent - sun.misc.Unsafe: available
14:55:36.109 [main] DEBUG i.n.util.internal.PlatformDependent - -Dio.netty.noJavassist: false
14:55:36.110 [main] DEBUG i.n.util.internal.PlatformDependent - Javassist: unavailable
14:55:36.110 [main] DEBUG i.n.util.internal.PlatformDependent - You don't have Javassist in your class path or you don't have enough permission to load dynamically generated classes. Please check the configuration for better performance.
14:55:36.110 [main] DEBUG i.n.util.internal.PlatformDependent - -Dio.netty.tmpdir: /tmp (java.io.tmpdir)
14:55:36.110 [main] DEBUG i.n.util.internal.PlatformDependent - -Dio.netty.bitMode: 64 (sun.arch.data.model)
14:55:36.110 [main] DEBUG i.n.util.internal.PlatformDependent - -Dio.netty.noPreferDirect: false
14:55:36.119 [main] DEBUG io.netty.util.ResourceLeakDetector - -Dio.netty.leakDetectionLevel: simple
14:55:36.135 [main] DEBUG io.netty.buffer.ByteBufUtil - -Dio.netty.allocator.type: unpooled
14:55:36.135 [main] DEBUG io.netty.buffer.ByteBufUtil - -Dio.netty.threadLocalDirectBufferSize: 65536
2015-10-14 14:55:41.341-0400 INFO Successfully started database
2015-10-14 14:55:41.405-0400 INFO Starting HTTP on port 7474 (32 threads available)
2015-10-14 14:55:41.659-0400 INFO Successfully shutdown Neo4j Server
2015-10-14 14:55:42.224-0400 INFO Successfully stopped database
2015-10-14 14:55:42.227-0400 ERROR Failed to start Neo4j: Starting Neo4j failed: tried to access field org.neo4j.server.rest.repr.RepresentationFormat.mediaType from class org.neo4j.server.rest.repr.RepresentationFormatRepository Starting Neo4j failed: tried to access field org.neo4j.server.rest.repr.RepresentationFormat.mediaType from class org.neo4j.server.rest.repr.RepresentationFormatRepository
org.neo4j.server.ServerStartupException: Starting Neo4j failed: tried to access field org.neo4j.server.rest.repr.RepresentationFormat.mediaType from class org.neo4j.server.rest.repr.RepresentationFormatRepository
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:67)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:234)
at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:96)
at org.neo4j.server.CommunityBootstrapper.start(CommunityBootstrapper.java:48)
at org.neo4j.server.CommunityBootstrapper.main(CommunityBootstrapper.java:35)
Caused by: java.lang.IllegalAccessError: tried to access field org.neo4j.server.rest.repr.RepresentationFormat.mediaType from class org.neo4j.server.rest.repr.RepresentationFormatRepository
at org.neo4j.server.rest.repr.RepresentationFormatRepository.<init>(RepresentationFormatRepository.java:46)
at org.neo4j.server.AbstractNeoServer.createDefaultInjectables(AbstractNeoServer.java:641)
at org.neo4j.server.AbstractNeoServer.configureWebServer(AbstractNeoServer.java:360)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:216)
... 3 more
Seems like some permission issue on the lib folder of the Neo4j installation directory.
Try to give full permission to the neo4j installation folder.
Would also suggest to use stable version and not the milestone version.
I could fix it. There was some problem with my embedded database. I tried to run the server with its default graph.db and it run successfully. Now I have to identify what's wrong with the embedded database with I created using import tool.

Error with bulk-loading in cassandra

Good Morning,
I'm trying to implement the massive data dump cassandra example using the bulk-loading (http://www.datastax.com/dev/blog/bulk-loading) as a guide.
In the example resolve dependencies with the script (http://www.datastax.com/wp-content/uploads/2011/08/DataImport) but I find that the dependencies to be covered with cassandra libraries not located in the directories listed here because the version I'm working with dse with cassandra 2.0. Well then trying to cover such dependencies get the following script.
#!/bin/sh
# paths to the cassandra source tree, cassandra jar and java
CASSANDRA_HOME="/usr/share/dse/cassandra"
# CASSANDRA_JAR="./apache-cassandra-2.0.10.jar"
JAVA=`which java`
# Java classpath. Must include:
# - directory of DataImportExample
# - directory with cassandra/log4j config files
# - cassandra jar
# - cassandra depencies jar
CLASSPATH=".:/usr/share/dse/dse.jar:./slf4j-1.7.7/slf4-nop-1.7.7.jar:./slf4j-1.7.7/slf4j-simple-1.7.7.jar:/etc/dse/cassandra"
for jar in $CASSANDRA_HOME/lib/*.jar; do
CLASSPATH=$CLASSPATH:$jar
done
$JAVA -ea -cp $CLASSPATH -Xmx256M \
-Dlog4j.configuration=log4j-tools.properties \
CassandraDataBulk "$#"
CASSANDRA_JAR is commented and I use "cassandra-all-2.0.8.39.jar" located in the folder "/ usr / share / dse / cassandra / lib" and is already included.
I solve slf4j dependencies downloading that in 1.7.7 version.
Due to the difference of cassandra version also I had to accustom SSTableSimpleUnsortedWriter builder.
IPartitioner partitioner = new RandomPartitioner();
SSTableSimpleUnsortedWriter sourcesWriter = new SSTableSimpleUnsortedWriter(
directory,
partitioner,
keyspace,
table,
AsciiType.instance,
null,
64
);
It seems that the problem today is that there are still dependencies.
Under, the trace error I get.
There is a dependency but it seems that being "org.apache.commons.configuration.ConfigurationRuntimeException" the real problem could be another, Could have a bad configuration "cassandra.yaml"?
Thanks,
A greeting!
[dmdb#vm-dmdb01 ~]$ ./init_env.sh export.csv
[main] ERROR org.apache.cassandra.cql3.QueryProcessor - Unable to initialize MemoryMeter (jamm not specified as javaagent). This means Cassandra will be unable to measure object sizes accurately and may consequently OOM.
[main] INFO org.apache.cassandra.config.YamlConfigurationLoader - Loading settings from file:/etc/dse/cassandra/cassandra.yaml
[main] INFO org.apache.cassandra.config.DatabaseDescriptor - Data files directories: [/data01, /data02]
[main] INFO org.apache.cassandra.config.DatabaseDescriptor - Commit log directory: /datatmp/commitlog
[main] INFO org.apache.cassandra.config.DatabaseDescriptor - DiskAccessMode 'auto' determined to be mmap, indexAccessMode is mmap
[main] INFO org.apache.cassandra.config.DatabaseDescriptor - disk_failure_policy is stop
[main] INFO org.apache.cassandra.config.DatabaseDescriptor - commit_failure_policy is stop
[main] INFO org.apache.cassandra.config.DatabaseDescriptor - Global memtable threshold is enabled at 61MB
[main] INFO com.datastax.bdp.snitch.Workload - Setting my workload to Cassandra
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/configuration/ConfigurationRuntimeException
at com.datastax.bdp.config.ConfigUtil.defaultValue(ConfigUtil.java:18)
at com.datastax.bdp.config.DseConfig.<clinit>(DseConfig.java:51)
at com.datastax.bdp.snitch.DseDelegateSnitch.<init>(DseDelegateSnitch.java:42)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at java.lang.Class.newInstance(Class.java:374)
at org.apache.cassandra.utils.FBUtilities.construct(FBUtilities.java:488)
at org.apache.cassandra.config.DatabaseDescriptor.createEndpointSnitch(DatabaseDescriptor.java:508)
at org.apache.cassandra.config.DatabaseDescriptor.applyConfig(DatabaseDescriptor.java:341)
at org.apache.cassandra.config.DatabaseDescriptor.<clinit>(DatabaseDescriptor.java:111)
at org.apache.cassandra.io.sstable.AbstractSSTableSimpleWriter.<init>(AbstractSSTableSimpleWriter.java:50)
at org.apache.cassandra.io.sstable.SSTableSimpleUnsortedWriter.<init>(SSTableSimpleUnsortedWriter.java:96)
at org.apache.cassandra.io.sstable.SSTableSimpleUnsortedWriter.<init>(SSTableSimpleUnsortedWriter.java:80)
at org.apache.cassandra.io.sstable.SSTableSimpleUnsortedWriter.<init>(SSTableSimpleUnsortedWriter.java:91)
at CassandraDataBulk.main(CassandraDataBulk.java:35)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.configuration.ConfigurationRuntimeException
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 17 more
You are missing a "javaagent" parameter in your java call. Add the following:
-javaagent:$CASSANDRA_HOME/lib/jamm-0.2.5.jar
Your final call should look like:
$JAVA -ea -cp $CLASSPATH -Xmx256M \
-Dlog4j.configuration=log4j-tools.properties \
-javaagent:$CASSANDRA_HOME/lib/jamm-0.2.5.jar
CassandraDataBulk "$#"
NOTE: Adjust the path to jamm.jar as necessary
Reference
As for the runtime configuration error, download apache commons 'lang' library and include it to your classpath.
Download here
If you receive NEW exceptions after implementing the fix, download google-common.jar and guava-16.0.1.jar and include them as well to your classpath. These are all of the JARs that my own bulk loader required so far.

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