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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, #36

Open tseemann opened 5 years ago

tseemann commented 5 years ago 
seroba  getPneumocat seroba
--2019-04-03 09:34:36--  https://github.com/phe-bioinformatics/PneumoCaT/archive/v1.1.tar.gz
Resolving github.com (github.com)... 192.30.255.113, 192.30.255.112
Connecting to github.com (github.com)|192.30.255.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/phe-bioinformatics/PneumoCaT/tar.gz/v1.1 [following]
--2019-04-03 09:34:37--  https://codeload.github.com/phe-bioinformatics/PneumoCaT/tar.gz/v1.1
Resolving codeload.github.com (codeload.github.com)... 192.30.255.120, 192.30.255.121
Connecting to codeload.github.com (codeload.github.com)|192.30.255.120|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: 'v1.1.tar.gz'

v1.1.tar.gz                  [              <=>               ] 320.07M  3.77MB/s    in 78s     

2019-04-03 09:35:56 (4.09 MB/s) - 'v1.1.tar.gz' saved [335618305]

/home/linuxbrew/.linuxbrew/opt/python/lib/python3.7/site-packages/seroba/get_pneumocat_data.py:47: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  allele_snp=yaml.load( open( os.path.join(serogroup_dir,subdir,'mutationdb.yml'), "rb" ) )