Re: [trinityrnaseq-users] Difficulty executing ./Build_Trinotate_Boilerplate_SQLite_db.pl

[Brian Haas]

Hi James,

Are you running this on linux?   'set -euo pipefail' should be compatible with most linux distros I'm familiar with.

~b

On Sun, Dec 25, 2016 at 7:54 PM, <jvi...@cub.uca.edu> wrote:

I'm running into an issue executing ./Build_Trinotate_Boilerplate_SQLite_db.pl
I am running the current Trinity and Trinotate versions.

I keep getting the following output:

loki@loki-Z97X-Gaming-7:/usr/local/bin/Trinotate-3.0.1/admin$ sudo ./Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate_V3.sqlite
-- Skipping CMD: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz", checkpoint exists.
-- Skipping CMD: /usr/local/bin/Trinotate-3.0.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate_V3.sqlite, checkpoint exists.
-- Skipping CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep, checkpoint exists.
-- Skipping CMD: /usr/local/bin/Trinotate-3.0.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate_V3.sqlite.sqlite --create, checkpoint exists.
-- Skipping CMD: /usr/local/bin/Trinotate-3.0.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate_V3.sqlite.sqlite --uniprot_index Trinotate_V3.sqlite.UniprotIndex, checkpoint exists.
-- Skipping CMD: /usr/local/bin/Trinotate-3.0.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate_V3.sqlite.sqlite --taxonomy_index Trinotate_V3.sqlite.TaxonomyIndex, checkpoint exists.
-- Skipping CMD: wget "http://eggnogdb.embl.de/download/latest/data/NOG/NOG.annotations.tsv.gz", checkpoint exists.
* Running CMD: set -euo pipefail; gunzip -c NOG.annotations.tsv.gz | /usr/local/bin/Trinotate-3.0.1/admin/util/print.pl 1 5 > NOG.annotations.tsv.gz.bulk_load
sh: 1: set: Illegal option -o pipefail
Error, cmd: set -euo pipefail; gunzip -c NOG.annotations.tsv.gz | /usr/local/bin/Trinotate-3.0.1/admin/util/print.pl 1 5 > NOG.annotations.tsv.gz.bulk_load died with ret 512 at /usr/local/bin/Trinotate-3.0.1/admin/../PerlLib/Pipeliner.pm line 102.
    Pipeliner::run(Pipeliner=HASH(0xa92b90)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 117

Any help would be much appreciated.

Thanks,
James

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[jvi...@cub.uca.edu]

I am running Ubuntu 16.04 LTS. Would using the standard Trinotate_V3.sqlite provided be sufficient for most projects?

Thank you,
James

[Brian Haas]

I wouldn't have expected this to error out on ubuntu.

If you just execute

     set -euo pipefail

from a terminal, does it give a similar error?

Wrt Trinotate_V3, that's the latest version.  I should put out a new version (V4) sometime in early 2017.

best,

~b

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[jvi...@cub.uca.edu]

When running  set -euo pipefail I do not get an error or any additional terminal output. I'm looking forward to your 2017 release.

Thank you,
James

[Brian Haas]

ok, I can't explain the set -euo pipefail issue, then...  it could be that there's something else going on and what we're seeing in the error message is just a side-effect of some sort.

you can always just hack it to remove that in the command and see if it helps.

~b

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[Eduardo Zattara]

Hi Brian,

I just ran into the same issue. I am currently running the Ubuntu bash installed from WLS in Windows 10. Same symptoms, hacked the "o" out of the options, worked as a charm.

Thanks for this wonderful tool!

Cheers!

 -Ed-

On Thursday, December 29, 2016 at 7:58:40 PM UTC-3, Brian Haas wrote:

ok, I can't explain the set -euo pipefail issue, then...  it could be that there's something else going on and what we're seeing in the error message is just a side-effect of some sort.

you can always just hack it to remove that in the command and see if it helps.

~b

On Thu, Dec 29, 2016 at 4:43 PM, <jvi...@cub.uca.edu> wrote:

When running  set -euo pipefail I do not get an error or any additional terminal output. I'm looking forward to your 2017 release.

Thank you,
James

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[Ngân Trần]

Hi,

I am using Ubuntu 16.04 LTS. I had the same problem. 

Thank Brian and Eduardo. Removing o works for me.

Cheers!

Ngan 

[Brian Haas]

Thanks, guys!  Great to know.   

Will the following work?

  set -eu -o pipefail

or do you need to remove the -o altogether?

I'm thinking (hoping) maybe it's the -euo that's the problem.

~b

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[Eduardo Zattara]

I don't know, but the error complains specifically about the -o option in -euo, so I believe it might now work even if specified separately. But will try and let you know.

"Only in silence the word,
only in dark the light,
only in dying life :
bright the hawk's flight on the empty sky"

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email: ezat...@gmail.com
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On Fri, Jan 6, 2017 at 12:06 PM, Brian Haas <bh...@broadinstitute.org> wrote:

Thanks, guys!  Great to know.   

Will the following work?

  set -eu -o pipefail

or do you need to remove the -o altogether?

I'm thinking (hoping) maybe it's the -euo that's the problem.

~b

On Fri, Jan 6, 2017 at 1:07 AM, Ngân Trần <tkng...@gmail.com> wrote:

Hi,

I am using Ubuntu 16.04 LTS. I had the same problem. 

Thank Brian and Eduardo. Removing o works for me.

Cheers!

Ngan 

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[Brian Haas]

Basically, this is what we're trying to do there:

set -o pipefail

set -o pipefail causes a pipeline (for example, curl -s http://sipb.mit.edu/ | grep foo) to produce a failure return code if any command errors. Normally, pipelines only return a failure if the last command errors. In combination with set -e, this will make your script exit if any command in a pipeline errors.

https://sipb.mit.edu/doc/safe-shell/

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[robert....@sagebase.org]

Just noting that I also encountered this issue on Ubuntu and tried the suggestions above, but I still got the error. I switched to an EC2 Amazon Linux instance and didn't have the problem there. 

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[Brian Haas]

Thx for the info.

I'm wondering if it has something to do with hte default shell being used.

If I wrap the entire piped command into 

     cmd = "bash -c \" set -eof pipefail &&  .... | ... \"  ";

and execute that, perhaps that'll work, forcing the bash interpreter to run. 

~b

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[duart...@gmail.com]

Hello all,

I also had the same problem and have no idea what is causing it. But I solved it by removing

"set -euo pipefail; "

from the Build_Trinotate_Boilerplate_SQLite_db.pl script (EGGNOG, extract fields).

Best wishes,

Gustavo

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[Brian Haas]

It sounds like older versions of linux might be having trouble with the 

   set -o pipefail

cmd.  I'll just remove this and put out a bugfix release.

best,

~b

[Brian Haas]

Patch release 3.0.2 is out

https://github.com/Trinotate/Trinotate/releases/tag/v3.0.2

best,

~b

[Giorgio Casaburi]

HI Brian,

Even using the newer version I am still getting this error. Any idea on what's going on?

Thanks,

Giorgio

* Running CMD: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz"

--2017-03-04 15:39:11--  ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz

           => 'uniprot_sprot.dat.gz'

Resolving ftp.uniprot.org... 141.161.180.197

Connecting to ftp.uniprot.org|141.161.180.197|:21... connected.

Logging in as anonymous ... Logged in!

==> SYST ... done.    ==> PWD ... done.

==> TYPE I ... done.  ==> CWD (1) /pub/databases/uniprot/current_release/knowledgebase/complete ... done.

==> SIZE uniprot_sprot.dat.gz ... 545651826

==> PASV ... 

Cannot initiate PASV transfer.

Error, cmd: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" died with ret 2048 at /Users/casaburi/Desktop/Trinotate-3.0.2/admin/../PerlLib/Pipeliner.pm line 102.

Pipeliner::run('Pipeliner=HASH(0x7fc3cd003528)') called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 117 

 

[Brian Haas]

I wonder if there's an issue w/ uniprot right now.  Can you just run:

  wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz

directly and see if that works?

All it's doing is trying to download a file from uniprot that they provide on their ftp site.

best,

~b

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[Giorgio Casaburi]

Hi Brian,

Thank for the quick reply. I thought that was the problem too but the link it's still there and wget starts downloading it no problem. I see a lot of folks is experiencing the same issue. Is it possible to just access to the old .sqlite database and populate it? Just in case this issue is not solved.

Giorgio

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[Brian Haas]

I haven't seen a lot of problems w/ the download step....    there were problems later on w/ some 'pipefail' issue that's resolved in the latest release.

Try running the script again. If it works when you run wget directly, I don't see why it shouldn't work when you run the script that executes it.   If I remember correctly, the script will resume from where it left off in case there are other earlier parts that did work ok.

best,

~b

[Giorgio Casaburi]

Thank you Brian, it does not seem to fix the problem. Same exact error.

[Brian Haas]

I'll see if I can find a quick alternative....

more soon

~b

[Giorgio Casaburi]

Thank you Brian!

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[Brian Haas]

I think it's a problem with the uniprot ftp server, as I'm unable to pull down the file using 'wget' or 'curl' due to the same errors:

curl "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" > uniprot_sprot.dat.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (13) Bad PASV/EPSV response: 500
wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" 
--2017-03-04 18:41:38--  ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz

           => 'uniprot_sprot.dat.gz'
Resolving ftp.uniprot.org... 141.161.180.197
Connecting to ftp.uniprot.org|141.161.180.197|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/databases/uniprot/current_release/knowledgebase/complete ... done.
==> SIZE uniprot_sprot.dat.gz ... 545651826
==> PASV ... 
Cannot initiate PASV transfer.

It might just be a temporary glitch.  Let's assume it'll all start working again by Monday at the latest.

best,

~brian

[Giorgio Casaburi]

That's bizzare, cuz it did download the file using wget (about 500mb file). Let's see if next week it will work again. 

--

[Brian Haas]

The uniprot ftp site appears to be behaving now.

Note, we still have the old pre-compiled sqlite database and related search databases here:

https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/

but they're over a year old now, and so I'd recommend going through the 'build-on-the-fly' process that we now support in order to ensure you're getting the latest data. It does however require that the resource sites are all up and behaving. :-)

best of luck

~b

[Giorgio Casaburi]

Hi Brian,

Thank you so much for the old links. The Build_Trinotate_Boilerplate_SQLite_db.p script now works and it finished all the pipeline. I guess it was a link problem together with some Perl Version issue (which was the second error I was getting and that you said was unusual). 

Anyway all fixed now! :)

[Brian Haas]

great!  thx for the update,

~b

[Jason Toy]

Hi Brian,

I'm trying to run the Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate command on v3.2.0 and it's failing because of a bad url for eggnog:

```

Resolving eggnog5.embl.de... 194.94.44.170

Reusing existing connection to eggnogdb.embl.de:80.

HTTP request sent, awaiting response... 404 Not Found

2020-04-24 16:12:49 ERROR 404: Not Found.

Error, cmd: wget "http://eggnogdb.embl.de/download/latest/data/NOG/NOG.annotations.tsv.gz" died with ret 2048 at /hb/groups/bernardi_lab/programs/miniconda3/envs/trinotate/lib/site_perl/5.26.2/Pipeliner.pm line 102.

Pipeliner::run(Pipeliner=HASH(0x555754a28e68)) called at /hb/groups/bernardi_lab/programs/miniconda3/envs/trinotate/bin/Build_Trinotate_Boilerplate_SQLite_db.pl line 120

```

I assume this is the bug that is fixed with the newest 3.2.1 release, however, I'm running this through a conda env, and there doesn't seem to be a package for the new release. Is there a quick fix for this like a simple line replacement in the source? Or is there a way to update the conda package that I'm not aware of?

Thanks for all your help!

Jason

[Brian Haas]

Hi Jason,

The release 3.2.1 resolves this:

https://github.com/Trinotate/Trinotate/releases

best,

~b

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[Jason Toy]

Hi Brian. I assumed so, but do you know how to install this version in a conda environment without a package?

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[Brian Haas]

Hi Jason,

This shouldn't need anything special in conda. You can just download and unpack the tar.gz file and you should be able to run it from there.

best,

~b

[Jason Toy]

Hm. Okay, so I should just upack the tarball in the conda env directory created for the trinity environment?

[Brian Haas]

I think you should be able to unpack it anywhere, but if you have a workplace set up for conda, putting it there should be fine too.

[Jason Toy]

Great, thanks for your help, Brian.

Jason

[Stephanie Trench Fiol]

Dear Brian,

I am experiencing the same issue. However, I work in a computing cluster where I don't have the right to install the new version as an administrator, or to change the eggnog url on the script. I already asked the support team if they could change the url, but still didn't receive a response. Any ideas on other way to solve it? I also tried to wget the file from the current location and place it in the boilerplate directory, but still caused errors after... 

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[Brian Haas]

Hi Stephanie,

You can install it anywhere that you have access privileges. It doesn't need to be centrally installed.  Just untar it and you're ready to go.

best,

~b

Dear Brian,

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[Stephanie Trench Fiol]

Thank you, Brian! I thought it would not be possible but I just tried and it worked =)

On Monday, 27 April 2020 18:24:15 UTC+2, Brian Haas wrote:

Hi Stephanie,

You can install it anywhere that you have access privileges. It doesn't need to be centrally installed.  Just untar it and you're ready to go.

best,

~b

Dear Brian,

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The Broad Institute
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[Brian Haas]

awesome!

Dear Brian,

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