I have a rails 5 ember 2.17 app that was previously being successfully deployed in production. The deployment is done with ember-cli-rails.
During asset compilation I have the following error :
=================================================================================
ENV Summary:
TIME: Mon Jul 08 2019 15:40:33 GMT+0200 (CEST)
TITLE: ember
ARGV:
- /usr/bin/node
- /srv/production/www/placedemarche/releases/20190708133545/marketadmin/node_modules/ember-cli/bin/ember
- build
- --environment
- production
- --output-path
- /srv/production/www/placedemarche/releases/20190708133545/tmp/ember-cli/apps/marketadmin
EXEC_PATH: /usr/bin/node
TMPDIR: /tmp
SHELL: /bin/bash
PATH:
- /srv/production/www/placedemarche/shared/bundle/ruby/2.4.0/bin
- /home/admin/.rvm/gems/ruby-2.4.1/bin
- /home/admin/.rvm/gems/ruby-2.4.1#global/bin
- /home/admin/.rvm/rubies/ruby-2.4.1/bin
- /home/admin/.rvm/bin
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /sbin
- /bin
- /usr/games
- /usr/local/games
PLATFORM: linux x64
FREEMEM: 1093439488
TOTALMEM: 3149369344
UPTIME: 16758723
LOADAVG: 0.8134765625,0.71240234375,0.56201171875
CPUS:
- Intel(R) Xeon(R) CPU E5-2650 v4 # 2.20GHz - 2200
- Intel(R) Xeon(R) CPU E5-2650 v4 # 2.20GHz - 2200
- Intel(R) Xeon(R) CPU E5-2650 v4 # 2.20GHz - 2200
- Intel(R) Xeon(R) CPU E5-2650 v4 # 2.20GHz - 2200
- Intel(R) Xeon(R) CPU E5-2650 v4 # 2.20GHz - 2200
- Intel(R) Xeon(R) CPU E5-2650 v4 # 2.20GHz - 2200
ENDIANNESS: LE
VERSIONS:
- ares: 1.10.1-DEV
- http_parser: 2.8.0
- icu: 58.2
- modules: 48
- napi: 3
- node: 6.14.3
- openssl: 1.0.2o
- uv: 1.16.1
- v8: 5.1.281.111
- zlib: 1.2.11
ERROR Summary:
- broccoliBuilderErrorStack: [undefined]
- code: [undefined]
- codeFrame: [undefined]
- errorMessage: Unexpected identifier
- errorType: [undefined]
- location:
- column: [undefined]
- file: [undefined]
- line: [undefined]
- message: Unexpected identifier
- name: SyntaxError
- nodeAnnotation: [undefined]
- nodeName: [undefined]
- originalErrorMessage: [undefined]
- stack: /srv/production/www/placedemarche/releases/20190708133545/marketadmin/node_modules/#embroider/core/src/to-broccoli-plugin.js:18
async build() {
^^^^^
SyntaxError: Unexpected identifier
at createScript (vm.js:56:10)
at Object.runInThisContext (vm.js:97:10)
at Module._compile (module.js:549:28)
at Object.Module._extensions..js (module.js:586:10)
at Module.load (module.js:494:32)
at tryModuleLoad (module.js:453:12)
at Function.Module._load (module.js:445:3)
at Module.require (module.js:504:17)
at require (internal/module.js:20:19)
at Object.<anonymous> (/srv/production/www/placedemarche/releases/20190708133545/marketadmin/node_modules/#embroider/core/src/index.js:9:28)
=================================================================================
I am not sure what's the next step to solve this problem.
I could see in the error log that the build used node 6:
ENV Summary:
VERSIONS:
- node: 6.14.3
Node 6 is not supported anymore. It's LTS supported ended at April 30, 2019. The ember ecosystem drops support for it as well.
Embroider is an experimental build tool for Ember. It's only tested against Node 10 so far.
I would recommend upgrading your build environment to a recent version of node.
Related
Can anyone guide me on following error,
at Bundler.transformFile (/Users/mobile-app/node_modules/metro/src/Bundler.js:48:30)
at processTicksAndRejections (node:internal/process/task_queues:96:5)
at async Object.transform (/Users/mobile-app/node_modules/metro/src/lib/transformHelpers.js:101:12)
at async processModule (/Users/mobile-app/node_modules/metro/src/DeltaBundler/traverseDependencies.js:137:18)
at async traverseDependenciesForSingleFile (/Users/mobile-app/node_modules/metro/src/DeltaBundler/traverseDependencies.js:131:3)
at async Promise.all (index 0)
at async DeltaBundler.buildGraph (/Users/mobile-app/node_modules/metro/src/DeltaBundler.js:50:5)
info Fetching system and libraries information...
System:
OS: macOS 12.2.1
CPU: (8) x64 Intel(R) Core(TM) i5-1038NG7 CPU # 2.00GHz
Memory: 557.49 MB / 16.00 GB
Shell: 3.2.57 - /bin/bash
Binaries:
Node: 16.13.0 - ~/.nvm/versions/node/v16.13.0/bin/node
Yarn: Not Found
npm: 8.1.0 - ~/.nvm/versions/node/v16.13.0/bin/npm
Watchman: 2022.02.21.00 - /usr/local/bin/watchman
Managers:
CocoaPods: 1.11.2 - /usr/local/bin/pod
SDKs:
iOS SDK:
Platforms: DriverKit 21.2, iOS 15.2, macOS 12.1, tvOS 15.2, watchOS 8.3
Android SDK:
API Levels: 23, 28, 29, 30, 32
Build Tools: 28.0.3, 29.0.2, 29.0.3, 30.0.2, 30.0.3, 32.0.0, 32.1.0
System Images: android-29 | Intel x86 Atom_64, android-32 | Google APIs Intel x86 Atom_64
Android NDK: Not Found
IDEs:
Android Studio: 2021.1 AI-211.7628.21.2111.8139111
Xcode: 13.2.1/13C100 - /usr/bin/xcodebuild
Languages:
Java: 11.0.8 - /usr/bin/javac
npmPackages:
#react-native-community/cli: Not Found
react: 17.0.2 => 17.0.2
react-native: 0.67.3 => 0.67.3
react-native-macos: Not Found
npmGlobalPackages:
*react-native*: Not Found
Adding #babel/preset-env to the package has finally fixed it. If deleting and re-installing node_modules didn't work, try this.
"devDependencies": {
"#babel/core": "^7.8.4",
"#babel/preset-env": "^7.16.11",
"#babel/runtime": "^7.8.4",
"#react-native-community/eslint-config": "^0.0.7",
"babel-jest": "^25.1.0",
"eslint": "^6.8.0",
"jest": "^25.1.0",
"metro-react-native-babel-preset": "0.69.0",
"react-test-renderer": "16.9.0"
},
Thanks
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.
Started by using expo init app and used bare-minimum typescript template, the app is not building using react-native run-ios, but works if expo start in the Expo-go app.
here is the error code:
info Installing "/Users/mac/Library/Developer/Xcode/DerivedData/myproject-ccluoxcwmsrveqavqitrwaszccss/Build/Products/Debug-iphonesimulator/myproject"
An error was encountered processing the command (domain=IXUserPresentableErrorDomain, code=1):
This app could not be installed at this time.
Could not install at this time.
Failed to chmod /Users/mac/Library/Developer/CoreSimulator/Devices/2D6990A9-04F6-4391-BFA3-BFF2AA6890A5/data/Bundle/Application/2B342978-B520-410C-ABB0-F5961248B7BF/myproject.app/myproject : No such file or directory
Underlying error (domain=MIInstallerErrorDomain, code=4):
Failed to chmod /Users/mac/Library/Developer/CoreSimulator/Devices/2D6990A9-04F6-4391-BFA3-BFF2AA6890A5/data/Bundle/Application/2B342978-B520-410C-ABB0-F5961248B7BF/myproject.app/myproject : No such file or directory
info Launching "org.name.myproject"
error Failed to launch the app on simulator, An error was encountered processing the command (domain=FBSOpenApplicationServiceErrorDomain, code=1):
The request to open "org.name.myproject" failed.
The request was denied by service delegate (SBMainWorkspace) for reason: NotFound ("Application "org.name. myproject" is unknown to FrontBoard").
Underlying error (domain=FBSOpenApplicationErrorDomain, code=4):
The operation couldn’t be completed. Application "org.name.myproject" is unknown to FrontBoard.
Application "org.name.myproject" is unknown to FrontBoard.
When app is launched in Xcode the build is successful but the app don't load on simulator and I get this error message:
the config:
Expo CLI 4.1.6 environment info:
System:
OS: macOS 11.0.1
Shell: 5.8 - /bin/zsh
Binaries:
Node: 14.15.5 - ~/.nvm/versions/node/v14.15.5/bin/node
Yarn: 1.22.0 - /usr/local/bin/yarn
npm: 6.14.11 - ~/.nvm/versions/node/v14.15.5/bin/npm
Watchman: 4.9.0 - /usr/local/bin/watchman
Managers:
CocoaPods: 1.9.3 - /usr/local/bin/pod
SDKs:
iOS SDK:
Platforms: iOS 13.7, DriverKit 19.0, macOS 10.15, tvOS 13.4, watchOS 6.2
Android SDK:
API Levels: 23, 24, 27, 28, 29
Build Tools: 23.0.1, 27.0.3, 28.0.2, 28.0.3, 29.0.2
System Images: android-29 | Google APIs Intel x86 Atom, android-29 | Google Play Intel x86 Atom
IDEs:
Xcode: 11.7/11E801a - /usr/bin/xcodebuild
npmPackages:
expo: ~40.0.0 => 40.0.1
react: 16.13.1 => 16.13.1
react-dom: 16.13.1 => 16.13.1
react-native: ~0.63.4 => 0.63.4
react-native-web: ~0.13.12 => 0.13.18
Expo Workflow: bare
I have an issue with upgrading react-native version from 0.59.10 to 0.61.5. We are using our own native modules and it seems like to be problem with them. This problem I have only on iOS.
ERROR:
Invariant Violation: Native module cannot be null.
React Native version:
System:
OS: macOS 10.15.2
CPU: (8) x64 Intel(R) Core(TM) i5-8259U CPU # 2.30GHz
Memory: 70.44 MB / 8.00 GB
Shell: 3.2.57 - /bin/bash
Binaries:
Node: 11.5.0 - /usr/local/bin/node
Yarn: 1.12.3 - /usr/local/bin/yarn
npm: 6.12.0 - /usr/local/bin/npm
SDKs:
iOS SDK:
Platforms: iOS 13.2, DriverKit 19.0, macOS 10.15, tvOS 13.2, watchOS 6.1
Android SDK:
API Levels: 27, 28, 29
Build Tools: 28.0.3, 29.0.0, 29.0.1, 29.0.2
System Images: android-26 | Google APIs Intel x86 Atom, android-28 | Google APIs Intel x86 Atom
Android NDK: 20.0.5594570
IDEs:
Android Studio: 3.5 AI-191.8026.42.35.5791312
Xcode: 11.3/11C29 - /usr/bin/xcodebuild
npmPackages:
react: 16.9.0 => 16.9.0
react-native: 0.61.5 => 0.61.5
npmGlobalPackages:
react-native-cli: 2.0.1
react-native-git-upgrade: 0.2.7
react-native: 0.61.5
GITHUB: https://github.com/facebook/react-native/issues/27975
How to read binary image file in julia?
imread(file) gives following error:
ERROR: type: Gray: in T, expected T<:Union(FixedPoint,FloatingPoint), got Type{Bool}
in imread at C:\Users\Harsh\.julia\v0.3\Images\src\io.jl:259
in imread at C:\Users\Harsh\.julia\v0.3\Images\src\io.jl:113
Output of versioinfo(true):
julia> versioninfo(true)
Julia Version 0.3.0
Commit 7681878 (2014-08-20 20:43 UTC)
Platform Info:
System: Windows (x86_64-w64-mingw32)
CPU: Intel(R) Core(TM) i7-3632QM CPU # 2.20GHz
WORD_SIZE: 64
Microsoft Windows [Version 6.3.9600]
uname: MINGW32_NT-6.2 1.0.12(0.46/3/2) 2012-07-05 14:56 i686 unknown
Memory: 7.948513031005859 GB (4763.9375 MB free)
Uptime: 111087.5328943 sec
Load Avg: 0.0 0.0 0.0
Intel(R) Core(TM) i7-3632QM CPU # 2.20GHz:
speed user nice sys idle irq ticks
#1 2195 MHz 13078796 0 2444890 22142265 348375 ticks
#2 2195 MHz 10343718 0 1964375 25357578 165765 ticks
#3 2195 MHz 15137796 0 1628015 20899875 89390 ticks
#4 2195 MHz 15702750 0 1140187 20822718 73968 ticks
#5 2195 MHz 12287718 0 1952390 23425562 52781 ticks
#6 2195 MHz 9467671 0 1546562 26651421 49406 ticks
#7 2195 MHz 13431750 0 1668484 22565437 36375 ticks
#8 2195 MHz 12820796 0 1473484 23371359 30500 ticks
BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Sandybridge)
LAPACK: libopenblas
LIBM: libopenlibm
LLVM: libLLVM-3.3
Environment:
ANT_HOME = C:\PROGRA~1\APACHE~1.2
CUDA_BIN_PATH = C:\CUDA\bin64
CUDA_INC_PATH = C:\CUDA\include
CUDA_LIB_PATH = C:\CUDA\lib64
HOMEDRIVE = C:
HOMEPATH = \Users\Harsh
JAVA_HOME = C:\Progra~1\Java\jre6
PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC;.RB;.RBW
Package Directory: C:\Users\Harsh\.julia\v0.3
3 required packages:
- DataFrames 0.5.7
- DecisionTree 0.3.4
- Images 0.4.10
14 additional packages:
- ArrayViews 0.4.6
- BinDeps 0.3.5
- Color 0.3.8
- DataArrays 0.2.1
- FixedPointNumbers 0.0.4
- GZip 0.2.13
- Reexport 0.0.1
- SHA 0.0.3
- SIUnits 0.0.2
- SortingAlgorithms 0.0.1
- StatsBase 0.6.5
- TexExtensions 0.0.2
- URIParser 0.0.2
- Zlib 0.1.7
file is this binary file:
Image Link
Original RGB image is this, (which has been processed to obtain the above file) This does not give error.:
This was a bug, thanks for reporting it. It should be fixed if you do a Pkg.update().