<div dir="ltr"><div dir="ltr">Hi Ben,<div><br></div><div>It came back this morning:</div><div><br></div><div><div>2019-01-31 15:08:44,914 local [volume: 0] data_refinery_workers.downloaders.transcriptome_index DEBUG [downloader_job: 1]: Downloading file from <a href="ftp://ftp.ensembl.org/pub/release-95/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz">ftp://ftp.ensembl.org/pub/release-95/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz</a> to /home/user/data_store/Caenorhabditis_elegans/Caenorhabditis_elegans.fa.gz.</div><div>2019-01-31 15:10:55,982 local [volume: 0] data_refinery_workers.downloaders.transcriptome_index ERROR [downloader_job: 1]: Exception caught while downloading file from: <a href="ftp://ftp.ensembl.org/pub/release-95/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz">ftp://ftp.ensembl.org/pub/release-95/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz</a></div><div>Traceback (most recent call last):</div><div> File "/usr/lib/python3.5/urllib/request.py", line 1478, in ftp_open</div><div> fp, retrlen = fw.retrfile(file, type)</div><div> File "/usr/lib/python3.5/urllib/request.py", line 2347, in retrfile</div><div> conn, retrlen = self.ftp.ntransfercmd(cmd)</div><div> File "/usr/lib/python3.5/ftplib.py", line 360, in ntransfercmd</div><div> source_address=self.source_address)</div><div> File "/usr/lib/python3.5/socket.py", line 711, in create_connection</div><div> raise err</div><div> File "/usr/lib/python3.5/socket.py", line 702, in create_connection</div><div> sock.connect(sa)</div><div>TimeoutError: [Errno 110] Connection timed out</div><div><br></div><div>During handling of the above exception, another exception occurred:</div><div><br></div><div>Traceback (most recent call last):</div><div> File "/home/user/data_refinery_workers/downloaders/transcriptome_index.py", line 42, in _download_file</div><div> with closing(urllib.request.urlopen(download_url)) as request:</div><div> File "/usr/lib/python3.5/urllib/request.py", line 163, in urlopen</div><div> return opener.open(url, data, timeout)</div><div> File "/usr/lib/python3.5/urllib/request.py", line 466, in open</div><div> response = self._open(req, data)</div><div> File "/usr/lib/python3.5/urllib/request.py", line 484, in _open</div><div> '_open', req)</div><div> File "/usr/lib/python3.5/urllib/request.py", line 444, in _call_chain</div><div> result = func(*args)</div><div> File "/usr/lib/python3.5/urllib/request.py", line 1489, in ftp_open</div><div> raise exc.with_traceback(sys.exc_info()[2])</div><div> File "/usr/lib/python3.5/urllib/request.py", line 1478, in ftp_open</div><div> fp, retrlen = fw.retrfile(file, type)</div><div> File "/usr/lib/python3.5/urllib/request.py", line 2347, in retrfile</div><div> conn, retrlen = self.ftp.ntransfercmd(cmd)</div><div> File "/usr/lib/python3.5/ftplib.py", line 360, in ntransfercmd</div><div> source_address=self.source_address)</div><div> File "/usr/lib/python3.5/socket.py", line 711, in create_connection</div><div> raise err</div><div> File "/usr/lib/python3.5/socket.py", line 702, in create_connection</div><div> sock.connect(sa)</div><div>urllib.error.URLError: <urlopen error ftp error: TimeoutError(110, 'Connection timed out')></div><div>2019-01-31 15:10:56,025 local [volume: 0] data_refinery_workers.downloaders.utils INFO [downloader_job: 1] [failure_reason: Exception caught while downloading file from: <a href="ftp://ftp.ensembl.org/pub/release-95/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz">ftp://ftp.ensembl.org/pub/release-95/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz</a>] [downloader_task: TRANSCRIPTOME_INDEX]: Downloader job failed!<br><br><br></div></div><div>It's somewhat unfortunate that it was working when you tried it. We've been seeing it work occasionally, but recently we have been finding it be down more than it has been up. Do the servers have any monitoring set up?</div><div><br></div><div>Thanks,</div><div><br></div><div>- Kurt</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jan 31, 2019 at 6:20 AM Ben Moore <<a href="mailto:bmoore@ebi.ac.uk">bmoore@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Hi Kurt,<div><br></div><div>I’ve tried to replicate the error, but have been able to download the <i>C. elegans</i> GTF file from the FTP server. It is possible that you have encountered intermittent errors, but we believe that there are no issues currently affecting the FTP server. Please try again, and get back in touch if you continue to experience the same issues.</div><div><br></div><div>We apologise for any inconvenience you’ve experienced.</div><div><div><br></div><div>Best wishes</div><div><br></div><div>Ben<br><div><br><blockquote type="cite"><div>On 30 Jan 2019, at 19:06, Kurt Wheeler <<a href="mailto:kurt.wheeler91@gmail.com" target="_blank">kurt.wheeler91@gmail.com</a>> wrote:</div><br class="gmail-m_-1498981642396525237Apple-interchange-newline"><div><div dir="ltr"><div dir="ltr"><div dir="ltr">Hello,<div><br></div><div>My application has been having trouble downloading files from the Ensembl FTP server. One specific file I have had trouble downloading is:</div><div><br></div><div> <a href="ftp://ftp.ensembl.org/pub/release-95/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.95.gtf.gz" target="_blank">ftp://ftp.ensembl.org/pub/release-95/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.95.gtf.gz</a></div><div><br></div><div>However, I also am usually unable to even view a directory such as:</div><div><br></div><div> <a href="ftp://ftp.ensembl.org/pub/release-95/gtf/" target="_blank">ftp://ftp.ensembl.org/pub/release-95/gtf/</a></div><div><br></div><div>This makes me think the FTP server has not been running for large amounts of time. While I was writing this email it seems to have come back up, but a colleague of mine and I have observed it coming up for small periods of time over the last week or so while remaining generally unreachable.</div><div><br></div><div>Is anyone able to look into this?</div><div><br></div><div>Thanks,</div><div><br></div><div>- Kurt</div></div></div></div>
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<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>Ben Moore</div><div>Ensembl Outreach Officer</div><div><br></div><div>European Bioinformatics Institute (EMBL-EBI)</div><div>European Molecular Biology Laboratory</div><div>Wellcome Trust Genome Campus</div><div>Hinxton</div><div>Cambridge</div><div>CB10 1SD</div><div>UK</div><div><br></div><div><a href="mailto:bmoore@ebi.ac.uk" target="_blank">bmoore@ebi.ac.uk</a></div><div>+44 (0)1223 494265</div></div></div>
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