我正在尝试运行此pipeline，它是通过Nextflow实现的，并且使用Docker容器。不幸的是，我不能使用Docker，因为它与HPC不兼容（没有sudo），所以我使用的是Singularity而不是Docker。但是，由于我收到此错误，似乎路径未正确安装：
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:
.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'
}
我试图为此找到一种解决方案，我唯一能找到的是autoMounts = true选项（上面已注释），该选项在启用时导致管道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：
我遵循了tsnowlan的建议，并将--debug添加到singularity.engineOptions中。但是，有问题的路径似乎已挂载：
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
Edit2： 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)
我想容器内部的权限设置不正确。
答案 0 :(得分：1)
奇异性可能无法正确转换用户环境定义的Docker容器。确保奇异性映像定义了PATH以及项目Dockerfile https://github.com/sanger-pathogens/companion/blob/master/Dockerfile#L107
答案 1 :(得分：1)
如pditommaso所述，您需要确保奇异图像内部的环境设置正确。您可以通过奇点定义文件中的%environment块或在主机环境中导出SINGULARITY_$VARNAME来执行此操作。例如，nextflow配置的SINGULARITY_PERL5LIB=/opt/ORTHOMCLV1.4/:/opt/RATT/:/opt/ABACAS2/:$PERL5LIB块中的env，可以在容器内设置PERL5LIB变量。
您可能还需要指定数据的位置，以将其装入singularity.runOptions中的容器中。具体信息取决于您所使用的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/安装
基本格式为-B /host/path:/image/path。如果奇点映像中不存在/image/path，并且OS内核中未启用OverlayFS，则会收到错误消息：WARNING: Skipping user bind, non existent bind point (directory/file) in container: '/image/path'。 directory/file所在的位置。
您可以使用版本3+的--debug标志或版本2的-vv查看正在装入的内容。在nextflow中，这将添加到singularity.engineOptions中。
请注意，如果引用的路径在奇异映像中不可用，则挂载目录中的任何符号链接都会被破坏。
如果装入的数据包含符号链接，则很有可能它们引用未装入容器的文件，并且在运行奇异性映像时它们似乎是断开的链接。
编辑2：文件权限
构建奇异性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，则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，则将它们放在%post块中。与Docker不同，奇异性不使用每个命令的层来创建映像，因此您不必担心链接some_command && some_other_command && so_on && etc。
答案 2 :(得分：0)
此修复程序将有助于解决truncate_headers.lua脚本不存在的问题。