Error in Trinotate

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Dan Jethro Masacupan

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Apr 13, 2017, 3:24:27 AM4/13/17
to trinityrnaseq-users
Hi,


I would like ask for help regarding trinotate error, I used this command: 

$TRINOTATE_HOME/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate


  (try:20) => ‘uniprot_sprot.dat.gz’
Connecting to 10.16.5.120:8080... connected.
Logging in as anonymous ...
Error in server response, closing control connection.
Giving up.

Error, cmd: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" died with ret 1024 at /apps/Trinotate-3.0.1/admin/../PerlLib/Pipeliner.pm line 102.
        Pipeliner::run(Pipeliner=HASH(0x1e722f0)) called at /apps/Trinotate-3.0.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 117


thank you

Brian Haas

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Apr 13, 2017, 7:02:24 AM4/13/17
to Dan Jethro Masacupan, trinityrnaseq-users
Hi Dan,


Try it again and let's see if it works.   The link seems to be working for me right now.

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

Dan Jethro Masacupan

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Apr 13, 2017, 11:47:14 PM4/13/17
to Brian Haas, trinityrnaseq-users
  (try:20) => ‘uniprot_sprot.dat.gz’
Connecting to 10.16.5.120:8080... connected.
Logging in as anonymous ...
Error in server response, closing control connection.
Giving up.

Error, cmd: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" died with ret 1024 at /apps/Trinotate-3.0.1/admin/../PerlLib/Pipeliner.pm line 102.
  Pipeliner::run(Pipeliner=HASH(0x1f4cd90)) called at /apps/Trinotate-3.0.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 117


thank you,
Dan


On Thu, Apr 13, 2017 at 7:02 PM, Brian Haas <bh...@broadinstitute.org> wrote:
Hi Dan,


Try it again and let's see if it works.   The link seems to be working for me right now.

~b
On Thu, Apr 13, 2017 at 3:24 AM, Dan Jethro Masacupan <djmas...@gmail.com> wrote:
Hi,


I would like ask for help regarding trinotate error, I used this command: 

$TRINOTATE_HOME/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate


  (try:20) => ‘uniprot_sprot.dat.gz’
Connecting to 10.16.5.120:8080... connected.
Logging in as anonymous ...
Error in server response, closing control connection.
Giving up.

Error, cmd: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" died with ret 1024 at /apps/Trinotate-3.0.1/admin/../PerlLib/Pipeliner.pm line 102.
        Pipeliner::run(Pipeliner=HASH(0x1e722f0)) called at /apps/Trinotate-3.0.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 117


thank you

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Brian Haas

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Apr 14, 2017, 6:57:05 AM4/14/17
to Dan Jethro Masacupan, trinityrnaseq-users
Anyone else having trouble downloading this?  Seems to be working for me.

~b

Irene Liu

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Oct 26, 2017, 4:19:21 PM10/26/17
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The link seems to have changed. When I downloaded Pfam for the homology retention step in TransDecoder, I had to use wget "ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.fasta.gz." The current_release link kept returning invalid port responses.

I hacked the Build_Trinotate_Boilerplate_SQLite_db.pl and changed the line.

Irene Liu

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Oct 26, 2017, 4:50:39 PM10/26/17
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Brian Haas

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Oct 26, 2017, 6:12:38 PM10/26/17
to Irene Liu, trinityrnaseq-users
Interesting.  It must have happened very recently.    

Thx for the info

-Brian
(by iPhone)

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