Connection Error When Running plot2DO.R

[ZHONGHONGXIN]

Hi,

I encountered an error while running plot2DO.R with the following command:

Rscript plot2DO.R \
--file=mapping_mm10.bam \
-g mm10 \
-m 0.015 \
--simplifyPlot=on \
--minLength=50 \
--maxLength=250  

The script failed with the following error:
Ensembl site unresponsive, trying www mirror
Error in curl::curl_fetch_memory(url, handle = handle) :
  Could not resolve host: oct2018.archive.ensembl.org
Calls: Main ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted 

It seems the script is unable to connect to the Ensembl archive server to fetch required data. Could you please:
Update the Ensembl archive URL in the code to a working mirror Or add an option to use local genome files instead of fetching from Ensembl
System details:
R version: 4.1.3
Operating system: Linux

[paulati]

Hi,
you can modify line 253 in the file config/annotation_config.yaml.
Use nov2020.archive.ensembl.org instead of oct2018.archive.ensembl.org
Best,
Paula

[ZHONGHONGXIN]

Hi, you can modify line 253 in the file config/annotation_config.yaml. Use nov2020.archive.ensembl.org instead of oct2018.archive.ensembl.org Best, Paula

Hi Paula,

Thank you for your suggestion. I tried modifying line 253 in config/annotation_config.yaml from oct2018.archive.ensembl.org to nov2020.archive.ensembl.org as suggested, but I'm still encountering connection errors.

The error message remains:
Error in curl::curl_fetch_memory(url, handle = handle) :
Could not resolve host: nov2020.archive.ensembl.org
Calls: Main ... request_fetch -> request_fetch.write_memory ->
Execution halted

Could you please suggest:

1. Alternative Ensembl archive mirrors that are currently accessible
2. Or a way to use local genome files instead of fetching from Ensembl
3. Or provide the necessary genome data files that I could download separately

My system details:

• R version: 4.1.3
• OS: Linux
• plot2DO version: latest from GitHub

Thank you for your help!

Best regards,
ZHONGHONGXIN

[paulati]

Hi ZHONGHONGXIN,
I've tried with https://nov2020.archive.ensembl.org and it works (just adding "https://")
Line 253 in the file config/annotation_config.yaml should be
host: https://nov2020.archive.ensembl.org
I hope this helps.
Best,
Paula