Using AnnotationHub with job schedular causes an error
还没有人认领这个 Issue。
评估
调研方向
从 ah.R 和 AnnotationHub() 的初始化开始，然后使用提供的 Snakefile 在 OpenGridEngine 或 Slurm 下重现故障。跟踪与已报告的 cache_size、synchronous 和下载警告相关的缓存数据库设置；当并行作业能够获取并保存资源而不会出现只读数据库错误时，即表示完成。
由索引模型根据 Issue 内容生成。
描述
When using AnnotationHub in parallel with job schedular (OpenGridEngine and Slurm), whether a job can be calculated was stochastical and some jobs were failed with the error attempt to write a readonly database.
I don't know why but since some jobs can be calculated,
by performing the job queue, again and again, I could finally get the output.
As an alternative approach, by not using the job schedular,
I could perform the calculation without any error,
but it takes an enormous amount of time, so I want to know the reason for the error.
I wrote an Snakefile as follows:
rule all:
input:
expand('{id}.RData', id=list(range(24)))
rule ah:
output:
'{id}.RData'
log:
'logs/{id}.log'
shell:
'Rscript ah.R {id} >& {log}'
wrote the R-script (ah.R) as follows:
outfile = commandArgs(trailingOnly=TRUE)[1]
library("AnnotationHub")
ah = AnnotationHub()
id = names(ah)[sample(length(ah), 1)]
out = ah[[id]]
save(out, file=outfile)
and finally performed the snakemake workflow as follows:
# OpenGridEngine
snakemake -j 24 --cluster "qsub -S /bin/bash"
or
# Slurm
snakemake -j 24 --cluster sbatch
The error message was as follows:
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2019-10-29
downloading 1 resources
retrieving 1 resource
Error: failed to load resource
name: AH39322
title: E031-H3K23me2.imputed.pval.signal.bigwig
reason: 1 resources failed to download
In addition: Warning messages:
1: Couldn't set cache size: attempt to write a readonly database
Use `cache_size` = NULL to turn off this warning.
2: Couldn't set synchronous mode: attempt to write a readonly database
Use `synchronous` = NULL to turn off this warning.
3: download failed
hub path: ‘https://annotationhub.bioconductor.org/fetch/44762’
cache resource: ‘AH39322 : 44762’
reason: attempt to write a readonly database
Execution halted
- 主要语言
- R
- 星标
- 20
- 派生
- 16
- PR 合并指标
- 30 天内没有已合并 PR
环境准备
这个项目没有提供开发容器、Dockerfile 或贡献指南，环境需要你自己搭建：先看它的 README，通用步骤见我们的新手贡献指南。
从这里开始
- 先读完整个 Issue，再读项目的贡献指南。
- 在 Issue 下留言说明你要接手 —— 这能避免两个人做同样的事。
- Fork 仓库，在一个分支上完成修改。
- 提交 Pull Request，并在描述里引用这个 Issue 编号。
Bioconductor/AnnotationHub 的其他 Issue
-
难度 3/5 1-2 天 新手友好度 55/100
-
难度 4/5 3-5 天 新手友好度 45/100
Bioconductor/AnnotationHub#68 · 1 条评论 ·
-
难度 4/5 3-5 天 新手友好度 25/100
Bioconductor/AnnotationHub#67 · 1 条评论 ·
-
难度 5/5 一周以上 新手友好度 15/100
-
难度 3/5 1-2 天 新手友好度 35/100
Bioconductor/AnnotationHub#65 · 1 条评论 ·
查看 Bioconductor/AnnotationHub 的全部 Issue
相似的 Issue
-
难度 2/5 1-3 小时 新手友好度 72/100
rstudio/reticulate#1933 ·
-
难度 1/5 1 小时以内 新手友好度 62/100
-
难度 2/5 1-3 小时 新手友好度 66/100
维护者通常 1 天内回复
-
难度 2/5 1-3 小时 新手友好度 68/100
维护者通常 1 天内回复
-
难度 1/5 1 小时以内 新手友好度 82/100