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ncbi / egapx

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
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Offline mode: could not Download EGAPx related files from NCBI #36

Closed bismarck1008 closed 1 month ago

bismarck1008 commented 1 month ago

python3 ui/egapx.py -dl -lc ../EGAPx_local

!!WARNING!! This is an alpha release with limited features and organism scope to collect initial feedback on execution. Outputs are not yet complete and not intended for production use.

Downloading gnomon/2 Traceback (most recent call last): File "/data/bio-software/egapx/ui/egapx.py", line 810, in sys.exit(main(sys.argv)) ^^^^^^^^^^^^^^ File "/data/bio-software/egapx/ui/egapx.py", line 683, in main download_egapx_ftp_data(args.local_cache) File "/data/bio-software/egapx/ui/egapx.py", line 178, in download_egapx_ftp_data ftpd.connect(FTP_EGAP_SERVER) File "/data/bio-software/egapx/ui/egapx.py", line 67, in connect self.reconnect() ^^^^^^^^^^^^^^^^ File "/data/bio-software/egapx/ui/egapx.py", line 71, in reconnect self.ftp.login() File "/data/bio-software/mambaforge/envs/egapx/lib/python3.12/ftplib.py", line 414, in login resp = self.sendcmd('PASS ' + passwd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/bio-software/mambaforge/envs/egapx/lib/python3.12/ftplib.py", line 281, in sendcmd return self.getresp() ^^^^^^^^^^^^^^ File "/data/bio-software/mambaforge/envs/egapx/lib/python3.12/ftplib.py", line 244, in getresp resp = self.getmultiline() ^^^^^^^^^^^^^^^^^^^ File "/data/bio-software/mambaforge/envs/egapx/lib/python3.12/ftplib.py", line 230, in getmultiline line = self.getline() ^^^^^^^^^^^^^^ File "/data/bio-software/mambaforge/envs/egapx/lib/python3.12/ftplib.py", line 212, in getline line = self.file.readline(self.maxline + 1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/bio-software/mambaforge/envs/egapx/lib/python3.12/socket.py", line 720, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ TimeoutError: [Errno 110] Connection timed out

boukn commented 1 month ago

it looks like it might be network access? Does this command work?

$ curl https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/support_data/target_proteins/2/taxid.list

boukn commented 1 month ago

It is possible to run the -dl on a machine with access, copy the files yourself to internal resources, and then run it with -lc from, from machines that dont have access.