Using AnnotationHub with job schedular causes an error

Bắt đầu với ah.R và quá trình khởi tạo AnnotationHub(), sau đó tái hiện lỗi bằng Snakefile được cung cấp trên OpenGridEngine hoặc Slurm. Theo dõi phần thiết lập cơ sở dữ liệu bộ nhớ đệm liên quan đến các cảnh báo đã báo cáo về cache_size, synchronous và việc tải xuống; được xem là hoàn tất khi các job song song có thể truy xuất và lưu tài nguyên mà không gặp lỗi cơ sở dữ liệu chỉ-đọc.

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