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markziemann / dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
http://dee2.io
GNU General Public License v3.0
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Some errors generated #25

Closed markziemann closed 6 years ago

markziemann commented 6 years ago

some errors getting generated. some code needs to be tidied up.

ecoli Starting pipeline ./volunteer_pipeline.sh: line 20: [: ==: unary operator expected SRR5985593 --2018-02-19 10:59:02-- https://www.ncbi.nlm.nih.gov/sra/SRR5985593 Resolving www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)... 130.14.29.110, 2607:f220:41e:4290::110 Connecting to www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)|130.14.29.110|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: 'SRR5985593.html'

SRR5985593.html [ <=> ] 60.97K 140KB/s in 0.4s

2018-02-19 10:59:05 (140 KB/s) - 'SRR5985593.html' saved [62435]

User input species and SRA metadata match. OK. md5sum: ./volunteer_pipeline.sh: No such file or directory cp: cannot stat './volunteer_pipeline.sh': No such file or directory Starting ./volunteer_pipeline.sh SRR5985593 current disk space = 385617816 free memory = 128381928 SRR5985593 check if SRA file exists and download if neccessary SRR5985593.sra

markziemann commented 6 years ago

END_MODULE Kmer Content pass END_MODULE perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C").

markziemann commented 6 years ago

These minor errors have been fixed in the dev branch