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workflow4metabolomics / mtbls-dwnld

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Unable to unzip a MTBLS archive #24

Closed gabrielctn closed 6 years ago

gabrielctn commented 6 years ago

Hi, I used the mtbls-dwnld script to download the MTBLS74 study (randomly chosen) and I have this error occuring:

./mtbls-dwnld` MTBLS74
--2018-04-23 11:11:37--  http://www.ebi.ac.uk/metabolights/MTBLS74/files/MTBLS74
Resolving www.ebi.ac.uk (www.ebi.ac.uk)... 193.62.193.80
Connecting to www.ebi.ac.uk (www.ebi.ac.uk)|193.62.193.80|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.ebi.ac.uk/metabolights/MTBLS74/files/MTBLS74 [following]
--2018-04-23 11:11:38--  https://www.ebi.ac.uk/metabolights/MTBLS74/files/MTBLS74
Connecting to www.ebi.ac.uk (www.ebi.ac.uk)|193.62.193.80|:443... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2018-04-23 11:16:41--  (try: 2)  https://www.ebi.ac.uk/metabolights/MTBLS74/files/MTBLS74
Connecting to www.ebi.ac.uk (www.ebi.ac.uk)|193.62.193.80|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/zip]
Saving to: ‘MTBLS74.zip’

MTBLS74.zip                                                   [                 <=>                                                                                                                 ]   5,22G  11,5MB/s    in 12m 18s 

2018-04-23 11:28:59 (7,24 MB/s) - ‘MTBLS74.zip’ saved [5605229119]

Archive:  /home/docker/Development/Run_IPO_Workflow/studies/MTBLS74.zip
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of /home/docker/Development/Run_IPO_Workflow/studies/MTBLS74.zip or
        /home/docker/Development/Run_IPO_Workflow/studies/MTBLS74.zip.zip, and cannot find /home/docker/Development/Run_IPO_Workflow/studies/MTBLS74.zip.ZIP, period.
ERROR: Unable to unzip archive /home/docker/Development/Run_IPO_Workflow/studies/MTBLS74.zip.

There is no problem when using the aspera client though.

pkrog commented 6 years ago

Hi,

Where did you use it? I've just tested it on the Galaxy development instance of PhenoMeNal/EBI and it worked perfectly. Viewing your log, I see that the size saved ~5GB is smaller than the real file size (9.82GB). I guess your file was cut in the middle for some reason.

gabrielctn commented 6 years ago

I used it locally with the mtbls-dwnld script alone for several studies (there was this issue but not for all of them). But I now retried with the phnmnl/container-mtbls-dwnld and it worked, so I guess I didn't have the latest stable script version. Thank you for your fast answer !