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我又一次在我的 snakemake 工作流程中遇到了一个对我来说没有任何意义的错误。

这是我得到的错误：

[Thu Jan 25 10:47:00 2018] Building DAG of jobs...
[Thu Jan 25 10:47:01 2018] Provided cores: 24
[Thu Jan 25 10:47:01 2018] Rules claiming more threads will be scaled down.
[Thu Jan 25 10:47:01 2018] Job counts:
[Thu Jan 25 10:47:01 2018]  count   jobs
[Thu Jan 25 10:47:01 2018]  1   merging_seurat
[Thu Jan 25 10:47:01 2018]  1

[Thu Jan 25 10:47:01 2018] Job 0: --- Merging samples using seurat.

Error in setClass("Snakemake", slots = c(input = "list", output = "list",  : 
  unused argument(s) (slots = c(input = "list", output = "list", params = "list", wildcards = "list", threads = "numeric", log = "list", resources = "list", config = "list", rule = "character"))
Execution halted
[Thu Jan 25 10:47:02 2018] Error in rule merging_seurat:
[Thu Jan 25 10:47:02 2018]     jobid: 0
[Thu Jan 25 10:47:02 2018]     output: merging_seurat/12_top10_heatmap_all_wilcox.pdf, merging_seurat/13_top10_heatmap_all_roc.pdf, merging_seurat/merging_seurat.RData

[Thu Jan 25 10:47:02 2018] RuleException:
[Thu Jan 25 10:47:02 2018] CalledProcessError in line 372 of .../snakemake_pipeline/Snakefile:
[Thu Jan 25 10:47:02 2018] Command ' set -euo pipefail;  Rscript .../snakemake_pipeline/scripts/.snakemake.jv8ijpiw.merging_seurat.R ' returned non-zero exit status 1
[Thu Jan 25 10:47:02 2018]   File ".../snakemake_pipeline/Snakefile", line 372, in __rule_merging_seurat
[Thu Jan 25 10:47:02 2018]   File ".../tools/anaconda3/envs/Seurat/lib/python3.5/concurrent/futures/thread.py", line 55, in run
[Thu Jan 25 10:47:02 2018] Will exit after finishing currently running jobs.
[Thu Jan 25 10:47:02 2018] Exiting because a job execution failed. Look above for error message
[Thu Jan 25 10:47:02 2018] Complete log: .../snakemake_6/.snakemake/log/2018-01-25T104700.498155.snakemake.log

这是有问题的规则：

rule merging_seurat:
  input:   expand("{sample}/molecule_count/counts_wide.tsv", sample=config["samples"]),
  output:  "merging_seurat/12_top10_heatmap_all_wilcox.pdf",
           "merging_seurat/13_top10_heatmap_all_roc.pdf",
           "merging_seurat/merging_seurat.RData"
  message: "--- Merging samples using seurat."
  script:   "scripts/merging_seurat.R"

在这里，我们有仍在执行的 R 脚本的顶部：

sink('merging_seurat/output.txt')
print(installed.packages())
print(sessionInfo())
sink()

这些是 R 脚本中不再执行的以下行：

library('Seurat')
library('dplyr')
library('org.Hs.eg.db')

因为我记录了可用的包，所以我知道应该加载的三个包也已安装，因此它不应该因此而失败。事实上，注释掉这些行并没有改变任何东西，脚本仍然会中断，并且应该在加载包后立即出现的日志消息不会写入日志文件。

最后，这是我用来运行snakemake的命令：

snakemake --use-conda \
--latency-wait 90 \
--rerun-incomplete \
--keep-going \
--timestamp \
--cluster-config SGE.json \
--cluster "qsub -cwd -N {cluster.name} -l h_vmem={cluster.h_vmem},h_stack=256M -o {cluster.stdout}{cluster.name}.o -e {cluster.stderr}{cluster.name}.e -m {cluster.mailtype} -M {cluster.mailuser}" \
-j 8 \
--directory .../snakemake_6

有人知道错误消息可能意味着什么吗？unused argumentsnakemake R 对象的属性很奇怪，因为我稍后在脚本中调用了多个参数。

更奇怪的是，我有另一个 R 脚本，它适用于不同的包，但第一行非常相似，运行良好。我记得一开始我对该脚本有同样的问题（同样的错误消息），但不记得我是如何解决的。

任何帮助都将不胜感激。

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