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This repository was archived by the owner on Jan 29, 2026. It is now read-only.
GRCh38 not installing #19
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Description
Hi,
I'm getting this error:
> install("GRCh38", rsync=FALSE, bash=TRUE)
Tool | Installed
-----------------------
curl | True
wget | True
rsync | True
INFO - Downloading GRCh38...
INFO - Attempt to download from alexandrovlab failed: [Errno 104] Connection reset by peer
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (56) Recv failure: Connection reset by peer
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator//GRCh38.tar.gz']' returned non-zero exit status 56..
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator//GRCh38.tar.gz']' returned non-zero exit status 56.
INFO - Attempt to download from sanger failed: [Errno 104] Connection reset by peer
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0
curl: (56) Recv failure: Connection reset by peer
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://ngs.sanger.ac.uk/scratch/project/mutographs/SigProf//GRCh38.tar.gz']' returned non-zero exit status 56..
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://ngs.sanger.ac.uk/scratch/project/mutographs/SigProf//GRCh38.tar.gz']' returned non-zero exit status 56.
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
FileNotFoundError: [Errno 2] No such file or directory: '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz'
Run `reticulate::py_last_error()` for details.
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