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问为什么我的奇点拉取在我的nextflow脚本中失败了？
EN

Stack Overflow用户

提问于 2021-09-21 23:17:20

回答 1查看 313关注 0票数 1

我一直在努力寻找答案，但没有找到答案，所以我希望这里有人能帮助我理解这个错误以及在奇点拉命令过程中发生了什么。

下面是错误：

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!

下面是脚本(请原谅这里的混乱，我刚刚习惯了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
  """
}

下面是我的配置文件：

//docker.enabled = false
singularity.enabled = true
singularity.autoMounts = true

我将我的环境构建为conda环境，以下是yml文件：

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

以下是日志文件：

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

我一直在使用nf-core的rnaseq流水线来指导我：https://github.com/nf-core/rnaseq

如果有帮助，下面是我正在尝试自动化的管道：https://bioinformatics.uconn.edu/resources-and-events/tutorials-2/rna-seq-tutorial-with-reference-genome/#

我的电脑使用的是Windows10操作系统，并且我已经启用了WSL2并安装了Ubuntu。

我对Docker、Singularity和Nextflow都是新手，所以我希望有人能解释一下这个错误。我甚至不明白为什么要提到python。奇点是不能从Quay.io中拉出来的问题吗？我有点迷茫，希望能在正确的方向上有所作为。

另外，我尝试让奇点工作的原因是STAR会立即在我的本地机器上给我一个分段错误(我假设我的内存用完了)，我想在我们的HPC上测试这个管道(但我没有root权限)。

docker

containers

bioinformatics

singularity-container

nextflow

回答 1

Stack Overflow用户

发布于 2021-09-22 00:28:16

您可以忽略奇点警告，但不能忽略错误。问题看起来是您的环境中缺少python：

/usr/bin/env: ‘python’: No such file or directory
ERROR: pulling container failed!

您需要确保安装了Python3。如果你有，你应该能够在这里看到它：

/usr/bin/python --version

你没有提到你正在使用的Ubuntu版本，但是如果你有Ubuntu 20.04，那么你应该已经预装了Python3。如果是这种情况，并且您已经安装了Python3(即，您发现/usr/bin/python3 --version可以工作，请注意'3')，但上面的代码不能工作，请尝试：

sudo apt-get install python-is-python3

这将安装一个符号链接，使/usr/bin/python解释器指向当前的默认python3。

票数 0

页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持

原文链接：

https://stackoverflow.com/questions/69276516

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