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tobiasrausch / ATACseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
https://tobiasrausch.com/courses/atac/
BSD 3-Clause "New" or "Revised" License
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Error with cd bed/ && Rscript promoter.R && cd .. #6

Open salizadeh-bit opened 5 months ago

salizadeh-bit commented 5 months ago

I am getting the following error when running this code: "Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Download the ccdsGene table ... Error: Failed to connect: Lost connection to MySQL server at 'handshake: reading initial communication packet', system error: 1 04 Execution halted". I am not sure how to fix this. Perhaps to troubleshoot, knowing what end point is the package trying to pull the data from and what port is it using would be helpful

tobiasrausch commented 5 months ago

Possibly some firewall issue. Maybe this helps: https://stackoverflow.com/questions/5755819/lost-connection-to-mysql-server-at-reading-initial-communication-packet-syste