tomazc/iCount

Problems connecting to ENSEMBL FTP server

Opened this issue · 4 comments

Faitero commented

Cannot download ENSEMBL annotation from the cluster. It work on my computer but never from the HPC. Do you have any idea why this is happening?

iCount annotation --release 75 --out_dir iCount_genomes --annotation hs75.gtf.gz homo_sapiens
Executing the following command: iCount annotation --release 75 --out_dir iCount_genomes --annotation hs75.gtf.gz homo_sapiens
Input parameters for function 'annotation' in iCount.genomes.ensembl
    species: homo_sapiens
    release: 75
    out_dir: iCount_genomes
    annotation: hs75.gtf.gz
Input parameters for function 'species' in iCount.genomes.ensembl
    release: 84
[ConnectionError] Problems connecting to ENSEMBL FTP server.
  File "/home/skgtiru/programs/ENV/lib/python3.5/site-packages/iCount-2.0.0.dev0-py3.5.egg/iCount/cli.py", line 438, in main
    result_object = func(**args)

  File "/home/skgtiru/programs/ENV/lib/python3.5/site-packages/iCount-2.0.0.dev0-py3.5.egg/iCount/genomes/ensembl.py", line 141, in annotation
    if species not in iCount.genomes.ensembl.species():

  File "/home/skgtiru/programs/ENV/lib/python3.5/site-packages/iCount-2.0.0.dev0-py3.5.egg/iCount/genomes/ensembl.py", line 105, in species
    ftp = get_ftp_instance()

  File "/home/skgtiru/programs/ENV/lib/python3.5/site-packages/iCount-2.0.0.dev0-py3.5.egg/iCount/genomes/ensembl.py", line 54, in get_ftp_instance
    raise ConnectionError('Problems connecting to ENSEMBL FTP server.')
JureZmrzlikar commented
  • Log to HPC machine
  • start interactive python session by typing python (or python3)
  • import ftplib
  • ftp = ftplib.FTP('ftp.ensembl.org')
  • ftp.login()

Last or second last command should fail. Please paste the error message here.

Faitero commented 
$ python3
Python 3.5.1 (default, Apr 18 2016, 19:33:49) 
[GCC 4.7.2 20121015 (Red Hat 4.7.2-5)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ftplib
>>> ftp = ftplib.FTP('ftp.ensembl.org')
>>> ftp.login()
'230 Anonymous access granted, restrictions apply'
JureZmrzlikar commented

Strange, this is a succes, not an error... Can you try again with the original command?

Faitero commented

It works on a interactive session... I'll try again with SGE scheduler job. Let you know