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Cannot download snp/organisms/human_9606_b147_GRCh37p13/VCF #15

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lnicola opened this issue Jun 10, 2021 · 0 comments · May be fixed by #16
Open

Cannot download snp/organisms/human_9606_b147_GRCh37p13/VCF #15

lnicola opened this issue Jun 10, 2021 · 0 comments · May be fixed by #16

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@lnicola
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lnicola commented Jun 10, 2021

Command-line used to cause the issue

swiss-create-data

Program output

It sounds like a file is no longer available:

Genome build: GRCh37p13
dbSNP build: b147
Downloading rsID merge history...
RsMergeArch.bcp.gz: 153MB [00:42, 3.62MB/s]                                                                                                                                                                        
Downloading rsID deletion history...
SNPHistory.bcp.gz: 106MB [00:35, 2.98MB/s]                                                                                                                                                                         
Downloading NCBI dbSNP VCF for b147 / GRCh37p13 @ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/00-All.vcf.gz
00-All.vcf.gz: 0.00B [00:00, ?B/s]
Traceback (most recent call last):
  File "/usr/local/bin/swiss-create-data", line 22, in <module>
    main()
  File "/usr/local/lib/python2.7/dist-packages/swiss/create_data.py", line 671, in main
    vcf_path = download_dbsnp_vcf(opts.dbsnp_build,opts.genome_build)
  File "/usr/local/lib/python2.7/dist-packages/swiss/create_data.py", line 129, in download_dbsnp_vcf
    urlretrieve(url,filename=outpath,reporthook=tqdm_hook(t),data=None)
  File "/usr/lib/python2.7/urllib.py", line 98, in urlretrieve
    return opener.retrieve(url, filename, reporthook, data)
  File "/usr/lib/python2.7/urllib.py", line 247, in retrieve
    fp = self.open(url, data)
  File "/usr/lib/python2.7/urllib.py", line 215, in open
    return getattr(self, name)(url)
  File "/usr/lib/python2.7/urllib.py", line 552, in open_ftp
    ftpwrapper(user, passwd, host, port, dirs)
  File "/usr/lib/python2.7/urllib.py", line 879, in __init__
    self.init()
  File "/usr/lib/python2.7/urllib.py", line 891, in init
    self.ftp.cwd(_target)
  File "/usr/lib/python2.7/ftplib.py", line 574, in cwd
    return self.voidcmd(cmd)
  File "/usr/lib/python2.7/ftplib.py", line 256, in voidcmd
    return self.voidresp()
  File "/usr/lib/python2.7/ftplib.py", line 231, in voidresp
    resp = self.getresp()
  File "/usr/lib/python2.7/ftplib.py", line 226, in getresp
    raise error_perm, resp
IOError: [Errno ftp error] 550 snp/organisms/human_9606_b147_GRCh37p13/VCF: No such file or directory

Swiss version

1.1.1

@lnicola lnicola linked a pull request Jun 10, 2021 that will close this issue
@welchr welchr mentioned this issue Aug 9, 2021
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