docker - Nextflow+Singularity : No such file or directory, 即使文件存在

Question

我正在尝试运行此 pipeline ，它使用 Nextflow 实现并使用 Docker 容器。不幸的是，我不能使用 Docker，因为它不兼容 HPC(没有 sudo)，所以我使用 Singularity 而不是 Docker。但是，似乎路径未正确安装，因为我收到此错误:

Error executing process > 'truncate_input_headers'

Caused by:
  Process `truncate_input_headers` terminated with an error exit status (1)

Command executed:

  truncate_header.lua < phased.1_scaffolds_FINAL.fasta > truncated.fasta

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 2: phased.1_scaffolds_FINAL.fasta: No such file or directory

Work dir:
  /work/project/ladsie_002/work/77/1854982bdacdd60fbe447554ab153b

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

但是，当我查看路径时，该文件确实存在:

$ ll /work/project/ladsie_002/work/77/1854982bdacdd60fbe447554ab153b
total 1
lrwxrwxrwx 1 bbrink users 76 30. Aug 13:44 phased.1_scaffolds_FINAL.fasta -> /work/project/ladsie_002/companion/input/pleo/phased.1_scaffolds_FINAL.fasta

这是我的配置:

env {
    GT_RETAINIDS = "yes"
    AUGUSTUS_CONFIG_PATH = "/opt/data/augustus"
    FILTER_SHORT_PARTIALS_RULE = "/opt/data/filters/filter_short_partials.lua"
    PFAM = "/opt/pfam/Pfam-A.hmm"
    PFAM2GO = "/opt/data/pfam2go/pfam2go.txt"
    RATT_CONFIG = "/opt/RATT/RATT.config_euk_NoPseudo_SpliceSite"
}

params.GO_OBO = "/opt/go.obo"
params.NCRNA_MODELS = "/opt/data/cm/rnas.cm"
params.CIRCOS_CONFIG_FILE = "/opt/data/circos/circos.debian.conf"
params.CIRCOS_BIN_CONFIG_FILE = "/opt/data/circos/circos.bin.debian.conf"
params.SPECFILE = "/opt/data/speck/output_check.lua"
params.AUGUSTUS_EXTRINSIC_CFG = "/opt/data/augustus/extrinsic.cfg"

process {
    container = 'sangerpathogens/companion:latest'
}

singularity {
    enabled = true
//    autoMounts = true
}

executor {
    name = 'local'
    queueSize = 2
    pollInterval = '3sec'
}

我试图为此找到解决方案，我唯一能找到的是 autoMounts = true选项(上面注释掉)，这会导致管道在启用时甚至找不到它自己的 lua 脚本:

Error executing process > 'truncate_input_headers'

Caused by:
  Process `truncate_input_headers` terminated with an error exit status (127)

Command executed:

  truncate_header.lua < phased.1_scaffolds_FINAL.fasta > truncated.fasta

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: truncate_header.lua: command not found

Work dir:
  /work/project/ladsie_002/work/95/f03b31ed18a84f331b83cad0232bd5

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

编辑1:
我听从了 tsnowlan 的建议并添加了 --debug至 singularity.engineOptions .但是，有问题的路径似乎已安装:

Error executing process > 'truncate_input_headers'

Caused by:
  Process `truncate_input_headers` terminated with an error exit status (1)

Command executed:

  truncate_header.lua < phased.1_scaffolds_FINAL.fasta > truncated.fasta

Command exit status:
  1

Command output:
  (empty)

Command error:
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting tmpfs to /var/singularity/mnt/session
  DEBUG   [U=1038,P=29509]   mountImage()                  Mounting loop device /dev/loop0 to /var/singularity/mnt/session/rootfs
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting overlay to /var/singularity/mnt/session/final
  DEBUG   [U=1038,P=29509]   setPropagationMount()         Set RPC mount propagation flag to SLAVE
  VERBOSE [U=1038,P=29509]   Passwd()                      Checking for template passwd file: /var/singularity/mnt/session/rootfs/etc/passwd
  VERBOSE [U=1038,P=29509]   Passwd()                      Creating passwd content
  VERBOSE [U=1038,P=29509]   Passwd()                      Creating template passwd file and appending user data: /var/singularity/mnt/session/rootfs/etc/passwd
  DEBUG   [U=1038,P=29509]   addIdentityMount()            Adding /etc/passwd to mount list
  VERBOSE [U=1038,P=29509]   addIdentityMount()            Default mount: /etc/passwd:/etc/passwd
  VERBOSE [U=1038,P=29509]   Group()                       Checking for template group file: /var/singularity/mnt/session/rootfs/etc/group
  VERBOSE [U=1038,P=29509]   Group()                       Creating group content
  DEBUG   [U=1038,P=29509]   addIdentityMount()            Adding /etc/group to mount list
  VERBOSE [U=1038,P=29509]   addIdentityMount()            Default mount: /etc/group:/etc/group
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/final
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /dev to /var/singularity/mnt/session/final/dev
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /etc/localtime to /var/singularity/mnt/session/final/usr/share/zoneinfo/UTC
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /etc/hosts to /var/singularity/mnt/session/final/etc/hosts
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /etc/singularity/actions to /var/singularity/mnt/session/final/.singularity.d/actions
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/final/.singularity.d/actions
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /proc to /var/singularity/mnt/session/final/proc
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/final/proc
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting sysfs to /var/singularity/mnt/session/final/sys
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /home/bbrink to /var/singularity/mnt/session/home/bbrink
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/home/bbrink
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /var/singularity/mnt/session/home/bbrink to /var/singularity/mnt/session/final/home/bbrink
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/final/home/bbrink
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /tmp to /var/singularity/mnt/session/final/tmp
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/final/tmp
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /var/tmp to /var/singularity/mnt/session/final/var/tmp
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/final/var/tmp
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /work/project/ladsie_002/work/de/74a8bbd8bd11ad1524800fb7e71556 to /var/singularity/mnt/session/final/work/project/ladsie_002/work/de/74a8bbd8bd11ad1524800fb7e71556
  DEBUG   [U=1038,P=29509]   mountGeneric()                Remounting /var/singularity/mnt/session/final/work/project/ladsie_002/work/de/74a8bbd8bd11ad1524800fb7e71556
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /var/singularity/mnt/session/etc/resolv.conf to /var/singularity/mnt/session/final/etc/resolv.conf
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /var/singularity/mnt/session/etc/passwd to /var/singularity/mnt/session/final/etc/passwd
  DEBUG   [U=1038,P=29509]   mountGeneric()                Mounting /var/singularity/mnt/session/etc/group to /var/singularity/mnt/session/final/etc/group
  DEBUG   [U=1038,P=29509]   create()                      Chroot into /var/singularity/mnt/session/final
  DEBUG   [U=0,P=29543]      Chroot()                      Change current directory to /var/singularity/mnt/session/final
  DEBUG   [U=0,P=29543]      Chroot()                      Hold reference to host / directory
  DEBUG   [U=0,P=29543]      Chroot()                      Called pivot_root on /var/singularity/mnt/session/final
  DEBUG   [U=0,P=29543]      Chroot()                      Change current directory to host / directory
  DEBUG   [U=0,P=29543]      Chroot()                      Apply slave mount propagation for host / directory
  DEBUG   [U=0,P=29543]      Chroot()                      Called unmount(/, syscall.MNT_DETACH)
  DEBUG   [U=0,P=29543]      Chroot()                      Changing directory to / to avoid getpwd issues
  DEBUG   [U=1038,P=29509]   create()                      Chdir into / to avoid errors
  VERBOSE [U=1038,P=29542]   startup()                     Execute stage 2
  DEBUG   [U=1038,P=29542]   Stage()                       Entering stage 2
  DEBUG   [U=1038,P=29509]   PostStartProcess()            Post start process
  .command.sh: line 2: phased.1_scaffolds_FINAL.fasta: No such file or directory
  DEBUG   [U=1038,P=29509]   CleanupContainer()            Cleanup container
  DEBUG   [U=1038,P=29509]   Master()                      Child exited with exit status 1

Work dir:
  /work/project/ladsie_002/work/de/74a8bbd8bd11ad1524800fb7e71556

编辑2:
我修复了错误的挂载点，这导致了另一个错误:

gt: error: could not execute script ...rk/project/ladsie_002/companion/bin/gff3_to_embl.lua:74: bad argument #1 to 'lines' (/opt/go.obo: Permission denied)

我猜容器内的权限设置不正确。

Answer 1

正如 pditommaso 所提到的，您需要确保奇点图像内的环境设置正确。您可以通过 %environment 进行此操作。奇点定义文件中的 block 或导出SINGULARITY_$VARNAME在宿主环境中。例如，SINGULARITY_PERL5LIB=/opt/ORTHOMCLV1.4/:/opt/RATT/:/opt/ABACAS2/:$PERL5LIB在 env用于设置 PERL5LIB 的 nextflow 配置 block 容器内的变量。

您还可能需要在 singularity.runOptions 中指定要挂载到容器中的数据位置。 .那里的细节取决于您使用的 Singularity 版本以及主机操作系统是否在其内核中启用了 OverlayFS。

编辑1:绑定(bind)/安装

基本形式是-B /host/path:/image/path .如果 /image/path奇点镜像中不存在，并且操作系统内核中未启用OverlayFS，您将收到错误消息:WARNING: Skipping user bind, non existent bind point (directory/file) in container: '/image/path' .在哪里 directory/file是正在安装的东西。

您可以使用 --debug 查看正在安装的内容带有版本 3+ 的标志，或 -vv在版本 2 中。在 nextflow 中，这被添加到 singularity.engineOptions .

请注意，如果挂载目录中的任何符号链接(symbolic link)引用了奇点镜像中不可用的路径，它们将被破坏。

如果挂载的数据包含符号链接(symbolic link)，则它们通常很有可能引用未挂载到容器中的文件，并且在运行奇点镜像时似乎是断开的链接。

编辑2:文件权限

构建奇点图像的最简单方法是sudo singularity build companion.sif docker://sangerpathogens/companion:latest .如果您需要修改任何内容，例如 /opt/go.obo文件，您需要创建一个定义文件。

Bootstrap: docker
From: sangerpathogens/companion:latest
# note: for reproducibility, it is best to use a tag whose target won't change over time

%post
    chmod 644 /opt/go.obo

如果需要任何其他更改，请进入 %post堵塞。与 Docker 不同，singularity 不会为每个命令使用层来创建镜像，因此您不必担心链接 some_command && some_other_command && so_on && etc .