Tripal BLAST UI undefined variable db_file_id about tripal_blast

[ekcannon]

@oklonova are you trying to upload a target database or selecting the "Blast database" node you created from the target dropdown? Could you provide a screenshot of the error and form state?

[bradfordcondon]

I also wonder how I can blast against my local Tripal/Chado database (provide this option in the list of databases that appear under "Select a Dataset" button).

You need to create a blast db node for each database. You can do this at content -> add Content -> blast database.

Notice: Undefined variable: db_file_id in blast_ui_per_blast_program_form

I'd bet this error will go away when you add a blast database/if you disable allowing custom database upload? I don't actually see this variable get set so maybe it requires a minor fix?

tripal_blast/includes/blast_ui.form_per_program.inc

Line 254 in e30bbb2

'#default_value' => variable_get($db_file_id, ''),

@laceysanderson @ekcannon what do you think? $db_file_id doesnt appear to get set ever? Do we need those or can we just remove the default value key?

[oklonova]

Thank you for the answers!

Here is what I have after I disabled allowing custom file upload:

You need to create a blast db node for each database. You can do this at content -> add Content -> blast database.

What should the path to this database be, if it is a local one?

One more thing which confuses me. Maybe it is related to the problem. I downloaded a database from NCBI using update_blastdb.pl script, but running makeblastdb produces an error:

$ perl update_blastdb.pl swissprot
Connected to NCBI
Downloading swissprot.tar.gz... [OK]
$ tar -xf swissprot.tar.gz -C /var/www/html/sites/default/files/blastdb/swissprot
$ makeblastdb -in /var/www/html/sites/default/files/blastdb/swissprot -dbtype prot -parse_seqids

Building a new DB, current time: 06/07/2018 12:27:13
New DB name: /var/www/html/sites/default/files/blastdb/swissprot
New DB title: /var/www/html/sites/default/files/blastdb/swissprot
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
BLAST options error: File /var/www/html/sites/default/files/blastdb/swissprot does not exist

[ekcannon]

Hi @oklonova. Here are some answers:

The path to the database should be the full local path.

It looks to me like the swissprot download is already formatted, so you shouldn't need to run makeblastdb. Look in the directory you downloaded from swissprot and see if you have these files:
swissprot.00.phr
swissprot.00.pin
swissprot.00.pnd
swissprot.00.pni
swissprot.00.pog
swissprot.00.ppd
swissprot.00.ppi
swissprot.00.psd
swissprot.00.psi
swissprot.00.psq
swissprot.pal
taxdb.btd
taxdb.bti

If you do, then the path to the BLAST database will look like:
/var/www/html/sites/default/files/blastdb/swissprot/swissprot.00

I'm guessing both of the errors at the top of your BLAST input form are related to not finding the swissprot BLAST database.

I hope this helps!

[oklonova]

Hi!

Yes, looks like swissprot.00 was the one that was missing in the path. It was not that obvious before, as it is now :) Thanks a lot!

Those errors are gone now, but an error and a couple of warnings remain:

1. The BLAST command (with the default parameters in the advanced settings) produces the following:
   Executing blastp

Query: /tmp/2018Jun08_094943_query.fasta
Database: sites/default/files/blastdb/swissprot/swissprot.00
Results File: sites/default/files/tripal/tripal_blast/2018Jun08_094943.blast.asn
Options:
max_target_seqs: 500
evalue: 0.001
word_size: 3
gapopen: 11
gapextend: 1
matrix: BLOSUM62

Executing the following BLAST command:
'/home/user/ncbi-blast-2.7.1+/bin/blastp' -query '/tmp/2018Jun08_094943_query.fasta' -db '/sites/default/files/blastdb/swissprot/swissprot.00' -out 'sites/default/files/tripal/tripal_blast/2018Jun08_094943.blast.asn' -outfmt=11 -'max_target_seqs' '500' -'evalue' '0.001' -'word_size' '3' -'gapopen' '11' -'gapextend' '1' -'matrix' 'BLOSUM62' -num_threads '1'
Command line argument error: Argument "out". File is not accessible: `sites/default/files/tripal/tripal_blast/2018Jun08_094943.blast.asn'
WD blast_ui: BLAST did not complete successfully as is implied by the [error]
lack of output file
(sites/default/files/tripal/tripal_blast/2018Jun08_094943.blast.asn).
The command run was '/home/docker/ncbi-blast-2.7.1+/bin/blastp'
-query '/tmp/2018Jun08_094943_query.fasta' -db
'/sites/default/files/blastdb/swissprot/swissprot.00'
-out
'sites/default/files/tripal/tripal_blast/2018Jun08_094943.blast.asn'
-outfmt=11 -'max_target_seqs' '500' -'evalue' '0.001' -'word_size'
'3' -'gapopen' '11' -'gapextend' '1' -'matrix' 'BLOSUM62'
-num_threads '1'

The server has full read/write access to all the directories under files, including tripal and tripal_blast. What am I missing here?

2. A warning appears after I press the BLAST button:

   Warning: date_timezone_set() expects parameter 1 to be DateTime, boolean given in format_date() (line 2063 of /var/www/html/includes/common.inc).
   Warning: date_format() expects parameter 1 to be DateTimeInterface, boolean given in format_date() (line 2073 of /var/www/html/includes/common.inc).

3. A warning on top of Tripal BLAST UI settings page:

Warning: file_get_contents(/cvit.conf): failed to open stream: No such file or directory in blast_ui_get_cvit_conf_text() (line 891 of /var/www/html/sites/all/modules/tripal_blast/api/blast_ui.api.inc).

I do not need genome views, as it is so far a protein-only database. CViTjs is not enabled. I wonder why it is there.

Thank you for your time.

[laceysanderson]

Hi @oklonova

1. File is not accessible.

This is almost always a permission issue on the sites/default/files/tripal/tripal_blast directory. Just a bit of clarification: when you say the "server has full read/write access to all the directories under files, including tripal and tripal_blast", do you mean all users have full read/write access? Since the blast job is run via Tripal Jobs, the linux user who needs permission is the one you execute drush trp-run-jobs as. Can you show us what ls -lh sites/default/files/tripal/tripal_blast gives you to make sure we're not making incorrect assumptions? :-)

2. Date warning.

This warning is due to not having the Drupal date module configured. You can configure it at [your drupal site]/admin/config/regional/date-time.

3. CViTjs warning on settings page.

This is a bug, I've created an issue for it here #40.

Note: It's easier to answer questions if you submit one issue to the repo per problem. That way the conversations don't get all entangled, we can confirm that none get missed and we already have a separate issue for any bugs you find :-)

[oklonova]

Hi,

thank you and sorry it took some time to reply.
I changed the owner of tripal_blast back from www-data to the user who creates the files.

Here is the output of ls -lh:

/var/www/html/sites/default/files/tripal$ ls -lh
total 8,0K
drwxrwxr-x 2 docker www-data 4,0K juni 12 14:42 tripal_blast
drwxrwxr-x 2 docker www-data 4,0K mai 8 12:39 tripal_organism

Now blast is working, but I would like to make sure I am doing things the right way.

[laceysanderson]

Yes, that looks right to me :-) I'm glad it's working for you now. If you run into any more issues or even just need clarification/guidance feel free to open another issue :-)

[kyrenya]

I'm having an issue also with the blast execution and what I guess is a matter of permissions also.. but I dont manage to fix it..

here's my ls -lh

not sure I understood the comment above about changing the owner of tripal_blast..

thanks in advance!

[kyrenya]

solved! it was an issue about apache2 config of tmp files, they were kind of private. If someone needs detail of how to solve it, let me know!

[theBowja]

hi @kyrenya, how did you solve the issue with tmp files?

[theBowja]

I got it. In Drupal I did: Administration -> Configuration -> Media -> Temporary Directory = sites/default/files/tmp

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