<div dir="ltr"><div><div><div>Hi Matthieu,<br><br></div>your suggestion solves this particular problem, but it looks that it messes up the next step:<br><br>Database changed<br>mysql> SELECT * FROM msg;<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>| 9 | copy_ncbi_table | 1 | 5 | 3 | 3 | 2018-01-15 18:38:31 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows | 0 |<br>| 9 | copy_ncbi_table | 2 | 6 | 4 | 4 | 2018-01-15 18:41:47 | 0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows | 0 |<br>| 10 | populate_method_links_from_db | 3 | 7 | 6 | 6 | 2018-01-15 18:43:04 | 0 | WRITE_OUTPUT | Successfully copied 19 'method_link' rows | 0 |<br>| 16 | create_mlss_ss | 4 | 10 | 9 | 9 | 2018-01-15 18:46:08 | 0 | WRITE_OUTPUT | The Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' / SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased] MethodLinkSpeciesSet could not be found in the master database | 1 |<br>| 16 | create_mlss_ss | 5 | 10 | 10 | 10 | 2018-01-15 18:47:10 | 1 | WRITE_OUTPUT | The Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' / SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased] MethodLinkSpeciesSet could not be found in the master database | 1 |<br>| 16 | create_mlss_ss | 6 | 10 | 11 | 11 | 2018-01-15 18:48:10 | 2 | WRITE_OUTPUT | The Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' / SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased] MethodLinkSpeciesSet could not be found in the master database | 1 |<br>| 16 | create_mlss_ss | 7 | 10 | 12 | 12 | 2018-01-15 18:49:12 | 3 | WRITE_OUTPUT | The Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' / SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased] MethodLinkSpeciesSet could not be found in the master database | 1 |<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>7 rows in set (0.01 sec)<br><br></div>Cheers,<br></div>Francesco.<br></div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-15 17:52 GMT+01:00 muffato <span dir="ltr"><<a href="mailto:muffato@ebi.ac.uk" target="_blank">muffato@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi there,<br>
<br>
I think I know what's going on. See there are two spaces between between "The" and "species-set" in "The species-set could not be found in the master database" ? There is supposed to be the content of the set there, but it's an empty string. Probably because the species-set it needs to use is actually empty. In other words, the pipeline may be requiring an empty species-set to be in the master database too. Give it a try by creating a new row in species_set_header with (17, 'empty', 0, NULL, NULL) and rerunning the job<br>
<br>
Matthieu<span class=""><br>
<br>
On 2018-01-15 16:28, Wasiu Akanni wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
I would suggest setting the first release to the ensembl code version<br>
that you are using.<br>
<br>
On 15/01/2018 16:22, Francesco Lamanna wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Wasiu,<br>
<br>
this is the output of the species_set_header table:<br>
<br>
mysql> SELECT * FROM species_set_header;<br>
<br>
</blockquote>
+----------------+------------<wbr>-------------------+------+---<wbr>------------+--------------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| species_set_id | name | size |<br>
first_release | last_release |<br>
<br>
</blockquote>
+----------------+------------<wbr>-------------------+------+---<wbr>------------+--------------+<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
| 1 | H.sap-G.gal | 2 |<br>
NULL | NULL |<br>
| 2 | H.sap-B.flo | 2 |<br>
NULL | NULL |<br>
| 3 | H.sap-P.mar | 2 |<br>
NULL | NULL |<br></span>
| 4 | <a href="http://H.sap-C.mil" rel="noreferrer" target="_blank">H.sap-C.mil</a> [1] | 2 |<span class=""><br>
NULL | NULL |<br>
| 5 | G.gal-B.flo | 2 |<br>
NULL | NULL |<br>
| 6 | G.gal-P.mar | 2 |<br>
NULL | NULL |<br></span>
| 7 | <a href="http://G.gal-C.mil" rel="noreferrer" target="_blank">G.gal-C.mil</a> [2] | 2 |<span class=""><br>
NULL | NULL |<br>
| 8 | B.flo-P.mar | 2 |<br>
NULL | NULL |<br></span>
| 9 | <a href="http://B.flo-C.mil" rel="noreferrer" target="_blank">B.flo-C.mil</a> [3] | 2 |<br>
NULL | NULL |<br>
| 10 | <a href="http://P.mar-C.mil" rel="noreferrer" target="_blank">P.mar-C.mil</a> [4] | 2 |<span class=""><br>
NULL | NULL |<br>
| 11 | H.sap | 1 |<br>
NULL | NULL |<br>
| 12 | G.gal | 1 |<br>
NULL | NULL |<br>
| 13 | B.flo | 1 |<br>
NULL | NULL |<br>
| 14 | P.mar | 1 |<br>
NULL | NULL |<br>
| 15 | C.mil | 1 |<br>
NULL | NULL |<br></span>
| 16 | <a href="http://H.sap-G.gal-B.flo-P.mar-C.mil" rel="noreferrer" target="_blank">H.sap-G.gal-B.flo-P.mar-C.mil</a> [5] | 5 |<br>
NULL | NULL |<br>
<br>
</blockquote><div><div class="h5">
+----------------+------------<wbr>-------------------+------+---<wbr>------------+--------------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
16 rows in set (0.05 sec)<br>
<br>
It looks ok<br>
<br>
2018-01-15 17:19 GMT+01:00 Wasiu Akanni <<a href="mailto:waakanni@ebi.ac.uk" target="_blank">waakanni@ebi.ac.uk</a>>:<br>
<br>
Hi Francesco,<br>
<br>
Have you checked the species_set_header table?<br>
<br>
On 15/01/2018 14:39, Francesco Lamanna wrote:<br>
<br>
Hi Matthieu,<br>
<br>
thank you for your suggestion, it fixed the problem.<br>
<br>
However, I still get the following error:<br>
<br>
mysql> SELECT * FROM msg;<br>
<br>
</blockquote>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>--------------------+---------<wbr>-+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| analysis_id | logic_name | log_message_id |<br>
job_id | role_id | worker_id | when_logged | retry | status<br>
| msg |<br>
is_error |<br>
<br>
</blockquote>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>--------------------+---------<wbr>-+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| 9 | copy_ncbi_table | 1 |<br>
5 | 3 | 3 | 2018-01-15 14:49:29 | 0 |<br>
WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows<br>
| 0 |<br>
| 9 | copy_ncbi_table | 2 |<br>
6 | 4 | 4 | 2018-01-15 14:50:36 | 0 |<br>
WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows<br>
| 0 |<br>
| 10 | populate_method_links_from_db | 3 |<br>
7 | 6 | 6 | 2018-01-15 14:52:06 | 0 |<br>
WRITE_OUTPUT | Successfully copied 19 'method_link' rows<br>
| 0 |<br>
| 16 | create_mlss_ss | 4 |<br>
10 | 9 | 9 | 2018-01-15 14:55:10 | 0 |<br>
WRITE_OUTPUT | The species-set could not be found in the master<br>
database | 1 |<br>
| 16 | create_mlss_ss | 5 |<br>
10 | 10 | 10 | 2018-01-15 14:56:11 | 1 |<br>
WRITE_OUTPUT | The species-set could not be found in the master<br>
database | 1 |<br>
| 16 | create_mlss_ss | 6 |<br>
10 | 11 | 11 | 2018-01-15 14:57:12 | 2 |<br>
WRITE_OUTPUT | The species-set could not be found in the master<br>
database | 1 |<br>
| 16 | create_mlss_ss | 7 |<br>
10 | 12 | 12 | 2018-01-15 14:58:21 | 3 |<br>
WRITE_OUTPUT | The species-set could not be found in the master<br>
database | 1 |<br>
<br>
</blockquote>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>--------------------+---------<wbr>-+<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
7 rows in set (0.01 sec)<br>
<br>
But my species_set in the master_db is not empty:<br>
<br>
mysql> SELECT * FROM species_set;<br>
+----------------+------------<wbr>--+<br>
| species_set_id | genome_db_id |<br>
+----------------+------------<wbr>--+<br>
| 1 | 1 |<br>
| 1 | 2 |<br>
| 2 | 1 |<br>
| 2 | 3 |<br>
| 3 | 1 |<br>
| 3 | 4 |<br>
| 4 | 1 |<br>
| 4 | 5 |<br>
| 5 | 2 |<br>
| 5 | 3 |<br>
| 6 | 2 |<br>
| 6 | 4 |<br>
| 7 | 2 |<br>
| 7 | 5 |<br>
| 8 | 3 |<br>
| 8 | 4 |<br>
| 9 | 3 |<br>
| 9 | 5 |<br>
| 10 | 4 |<br>
| 10 | 5 |<br>
| 11 | 1 |<br>
| 12 | 2 |<br>
| 13 | 3 |<br>
| 14 | 4 |<br>
| 15 | 5 |<br>
| 16 | 1 |<br>
| 16 | 2 |<br>
| 16 | 3 |<br>
| 16 | 4 |<br>
| 16 | 5 |<br>
+----------------+------------<wbr>--+<br>
30 rows in set (0.00 sec)<br>
<br>
I am quite puzzled by this error.<br>
<br>
Cheers,<br>
Francesco.<br>
<br>
2018-01-12 17:48 GMT+01:00 Matthieu Muffato <<a href="mailto:muffato@ebi.ac.uk" target="_blank">muffato@ebi.ac.uk</a>>:<br>
Hi Francesco<br>
<br>
Homoeologues are only used when running on plant genomes (which have<br>
polyploid genomes), but the pipeline configuration is shared and<br>
expects this method_link to be present<br>
<br>
This how it looks in the Ensembl Plants database. You can insert<br>
this row in your database and it should work<br>
<br>
<a href="http://ensro@mysql-eg-publicsql.ebi.ac.uk:4157/ensembl_compara_plants_38_91" rel="noreferrer" target="_blank">ensro@mysql-eg-publicsql.ebi.a<wbr>c.uk:4157/ensembl_compara_plan<wbr>ts_38_91</a><br></div></div>
[6] [Fri Jan 12 16:46:32 2018] > SELECT * FROM method_link WHERE<div><div class="h5"><br>
method_link_id = 206;<br>
+----------------+------------<wbr>----------+-------------------<wbr>+<br>
| method_link_id | type | class |<br>
+----------------+------------<wbr>----------+-------------------<wbr>+<br>
| 206 | ENSEMBL_HOMOEOLOGUES | Homology.homology |<br>
+----------------+------------<wbr>----------+-------------------<wbr>+<br>
<br>
Regards,<br>
Matthieu<br>
<br>
On 12/01/18 14:01, Francesco Lamanna wrote:<br>
Hi Mateus,<br>
<br>
I could solve this problem by commenting out the line: "die "The<br>
master dabase must be defined with a collection" if<br>
$self->o('master_db') and not $self->o('collection');"<br>
<br>
in LoadMembers_conf.pm. The member_db is now correctly set up.<br>
<br>
However, when I run the Protein trees pipeline I get the following<br>
error message<br>
<br>
mysql> SELECT * FROM msg;<br>
<br>
</div></div></blockquote><div><div class="h5">
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| analysis_id | logic_name | log_message_id |<br>
job_id | role_id | worker_id | when_logged | retry | status<br>
| msg<br>
<br>
| is_error |<br>
<br>
</blockquote>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| 9 | copy_ncbi_table | 1 |<br>
5 | 3 | 3 | 2018-01-12 14:21:39 | 0 |<br>
WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows<br>
<br>
| 0 |<br>
| 9 | copy_ncbi_table | 2 |<br>
6 | 4 | 4 | 2018-01-12 14:25:27 | 0 |<br>
WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows<br>
<br>
| 0 |<br>
| 10 | populate_method_links_from_db | 3 |<br>
7 | 6 | 6 | 2018-01-12 14:26:54 | 0 |<br>
WRITE_OUTPUT | Successfully copied 18 'method_link' rows<br>
<br>
| 0 |<br>
| 16 | create_mlss_ss | 4 |<br>
10 | 9 | 9 | 2018-01-12 14:29:56 | 0 | FETCH_INPUT<br>
| Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 70. | 1 |<br>
| 16 | create_mlss_ss | 5 |<br>
10 | 10 | 10 | 2018-01-12 14:30:57 | 1 | FETCH_INPUT<br>
| Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 70. | 1 |<br>
| 16 | create_mlss_ss | 6 |<br>
10 | 11 | 11 | 2018-01-12 14:31:58 | 2 | FETCH_INPUT<br>
| Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 70. | 1 |<br>
| 16 | create_mlss_ss | 7 |<br>
10 | 12 | 12 | 2018-01-12 14:33:00 | 3 | FETCH_INPUT<br>
| Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 70. | 1 |<br>
| 16 | create_mlss_ss | 8 |<br>
10 | 13 | 13 | 2018-01-12 14:38:36 | 1 | FETCH_INPUT<br>
| Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 70. | 1 |<br>
<br>
</blockquote>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
8 rows in set (0.01 sec)<br>
<br>
I wasn't aware about this method_link.<br>
<br>
Do you know how can I fix this?<br>
<br>
Thanks,<br>
Francesco.<br>
<br>
2018-01-11 13:28 GMT+01:00 Francesco Lamanna<br>
<<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a> <mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>>:<br>
<br>
Hi Mateus,<br>
<br>
if I try to initialize the LoadMemebers pipeline without<br>
“--collection ensembl”, I get the following error:<br>
<br>
The following options are missing:<br>
{'collection'}<br>
<br>
I also tried to set 'collection' => undef, in the conf file, but<br>
I<br>
get another error:<br>
<br>
The master dabase must be defined with a collection at<br>
<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/PipeConfig/<wbr>LoadMembers_conf.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 190.<br>
<br>
Cheers,<br>
Francesco<br>
<br>
2018-01-11 12:01 GMT+01:00 Mateus Patricio <<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a><br>
<mailto:<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>>>:<br>
<br>
Hi Francesco,<br>
<br>
In your case the solution should be starting the LoadMembers<br>
without the option “--collection ensembl”.<br>
<br>
If you start the pipeline without it, it should use all the<br>
current species in your master database.<br>
<br>
In Ensembl we have different collections that are used for<br>
different purposes, and the default one is “ensembl”.<br>
<br>
Please let me know if this works.<br>
<br>
Cheers,<br>
<br>
Mateus.<br>
<br>
On 11 Jan 2018, at 10:13, Francesco Lamanna<br>
<<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a><br>
<br>
<mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>> wrote:<br>
<br>
Hi Mateus,<br>
<br>
many thanks for your answer.<br>
<br>
I am trying to launch the LoadMembers pipeline in order to<br>
make a member_db, but I get the following error:<br>
<br>
mysql> SELECT * from msg;<br>
<br>
<br>
</blockquote>
+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| analysis_id | logic_name | log_message_id |<br>
job_id | role_id | worker_id | when_logged | retry |<br>
status | msg | is_error |<br>
<br>
<br>
</blockquote>
+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| 3 | copy_table_from_master | 1 |<br>
4 | 3 | 3 | 2018-01-11 11:04:02 | 0 |<br>
WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node'<br>
rows | 0 |<br>
| 3 | copy_table_from_master | 2 |<br>
5 | 4 | 4 | 2018-01-11 11:05:46 | 0 |<br>
WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name'<br>
rows | 0 |<br>
| 4 | load_genomedb_factory | 3 |<br>
3 | 5 | 5 | 2018-01-11 11:07:06 | 0 |<br>
FETCH_INPUT | Could not fetch collection ss with<br>
name=ensembl<br>
at<br>
<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 106. | 1 |<br>
| 4 | load_genomedb_factory | 4 |<br>
3 | 6 | 6 | 2018-01-11 11:08:00 | 1 |<br>
FETCH_INPUT | Could not fetch collection ss with<br>
name=ensembl<br>
at<br>
<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 106. | 1 |<br>
| 4 | load_genomedb_factory | 5 |<br>
3 | 7 | 7 | 2018-01-11 11:08:25 | 2 |<br>
FETCH_INPUT | Could not fetch collection ss with<br>
name=ensembl<br>
at<br>
<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 106. | 1 |<br>
| 4 | load_genomedb_factory | 6 |<br>
3 | 8 | 8 | 2018-01-11 11:09:25 | 3 |<br>
FETCH_INPUT | Could not fetch collection ss with<br>
name=ensembl<br>
at<br>
<br>
<br>
</blockquote>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
line 106. | 1 |<br>
<br>
<br>
</blockquote>
+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
6<br>
<br>
Cheers,<br>
Francesco.<br>
<br>
2018-01-10 17:31 GMT+01:00 Mateus Patricio <<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a><br>
<mailto:<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>>>:<br>
<br>
Hi Francesco<br>
<br>
The protein tree pipeline reuses the genes and sequence<br>
members from the 'reuse_db' parameter, which in this<br>
case<br>
should point to a members database.<br>
<br>
This members database can be created by running the<br>
LoadMembers pipeline.<br>
<br>
You can initiate the pipeline with the following command<br>
line:<br>
<br>
</div></div><a href="http://init_pipeline.pl" rel="noreferrer" target="_blank">init_pipeline.pl</a> [7] <<a href="http://init_pipeline.pl/" rel="noreferrer" target="_blank">http://init_pipeline.pl/</a>><div><div class="h5"><br>
<br>
Bio::EnsEMBL::Compara::PipeCon<wbr>fig::EBI::Ensembl::LoadMembers<wbr>_conf<br>
--collection ensembl<br>
<br>
Then you should point the parameter reuse_db to this<br>
database on your Protein Tree config file.<br>
<br>
'reuse_db' => 'mysql://ensro@host:port/datab<wbr>ase',<br>
<br>
Please do let me know if you have further questions.<br>
<br>
Cheers,<br>
<br>
Mateus.<br>
<br>
On 10 Jan 2018, at 16:06, Francesco Lamanna<br>
<<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a><br>
<br>
<mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>> wrote:<br>
<br>
Hi all,<br>
<br>
when I try to run the protein tree pipeline (v91) using<br>
the core Human and Chicken genomes I get the following<br>
error message:<br>
<br>
mysql> SELECT * from msg;<br>
<br>
<br>
</div></div></blockquote><div><div class="h5">
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| analysis_id | logic_name |<br>
log_message_id | job_id | role_id | worker_id |<br>
when_logged | retry | status | msg<br>
| is_error |<br>
<br>
<br>
</blockquote>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
| 9 | copy_ncbi_table<br>
| 1 | 5 | 3 | 4 |<br>
2018-01-10 16:40:13 | 0 | WRITE_OUTPUT |<br>
Successfully<br>
copied 1646504 'ncbi_taxa_node' rows | 0<br>
|<br>
| 9 | copy_ncbi_table<br>
| 2 | 6 | 4 | 3 |<br>
2018-01-10 16:42:04 | 0 | WRITE_OUTPUT |<br>
Successfully<br>
copied 2504391 'ncbi_taxa_name' rows | 0<br>
|<br>
| 10 | populate_method_links_from_db<br>
| 3 | 7 | 6 | 6 |<br>
2018-01-10 16:43:44 | 0 | WRITE_OUTPUT |<br>
Successfully<br>
copied 18 'method_link' rows | 0<br>
|<br>
| 25 | genome_member_copy<br>
| 4 | 13 | 11 | 11 |<br>
2018-01-10 16:47:49 | 0 | FETCH_INPUT | ParamError:<br>
value for param_required('reuse_db') is required and has<br>
to be defined | 1 |<br>
| 25 | genome_member_copy<br>
| 5 | 14 | 12 | 12 |<br>
2018-01-10 16:47:49 | 0 | FETCH_INPUT | ParamError:<br>
value for param_required('reuse_db') is required and has<br>
to be defined | 1 |<br>
<br>
<br>
</blockquote>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<br>
I have no clue about what to put in the 'reuse_db'<br>
parameter (nor could I find any information in the<br>
compara docs).<br>
<br>
Can anyone please help me to solve this issue?<br>
<br>
Thanks,<br>
Francesco.<br>
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<br>
--<br>
Matthieu Muffato, Ph.D.<br>
Ensembl Compara and TreeFam Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus, Hinxton<br>
Cambridge, CB10 1SD, United Kingdom<br>
Room A3-145<br></span>
Phone + 44 (0) 1223 49 4631 [9]<br>
Fax + 44 (0) 1223 49 4468 [10]<span class=""><br>
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<br>
--<br></span>
WASIU AJENIFUJA AKANNI<br>
Developer<br>
<br>
Compara group<br>
EMBL-EBI<br>
Phone: + 44 (0) 1223 494 237 [11]<span class=""><br>
Room A3145, West building | Wellcome Trust Genome Campus | Hinxton |<br>
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<br>
--<br></span>
WASIU AJENIFUJA AKANNI<span class=""><br>
Developer<br>
<br>
Compara group<br>
EMBL-EBI<br>
Phone: <a href="tel:%2B%2044%20%280%29%201223%20494%20237" value="+441223494237" target="_blank">+ 44 (0) 1223 494 237</a><br>
Room A3145, West building | Wellcome Trust Genome Campus | Hinxton |<br>
Cambridge | CB10 1SD | UK<br>
<br></span>
Links:<br>
------<br>
[1] <a href="http://H.sap-C.mil" rel="noreferrer" target="_blank">http://H.sap-C.mil</a><br>
[2] <a href="http://G.gal-C.mil" rel="noreferrer" target="_blank">http://G.gal-C.mil</a><br>
[3] <a href="http://B.flo-C.mil" rel="noreferrer" target="_blank">http://B.flo-C.mil</a><br>
[4] <a href="http://P.mar-C.mil" rel="noreferrer" target="_blank">http://P.mar-C.mil</a><br>
[5] <a href="http://H.sap-G.gal-B.flo-P.mar-C.mil" rel="noreferrer" target="_blank">http://H.sap-G.gal-B.flo-P.mar<wbr>-C.mil</a><br>
[6] <a href="http://ensro@mysql-eg-publicsql.ebi.ac.uk:4157/ensembl_compara_plants_38_91" rel="noreferrer" target="_blank">http://ensro@mysql-eg-publicsq<wbr>l.ebi.ac.uk:4157/ensembl_<wbr>compara_plants_38_91</a><br>
[7] <a href="http://init_pipeline.pl" rel="noreferrer" target="_blank">http://init_pipeline.pl</a><br>
[8] <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailm<wbr>an/listinfo/dev</a><br>
[9] tel:%2B%2044%20%280%29%201223%<wbr>2049%204631<br>
[10] tel:%2B%2044%20%280%29%201223%<wbr>2049%204468<br>
[11] tel:+44%201223%20494237<span class=""><br>
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</span></blockquote><div class="HOEnZb"><div class="h5">
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</div></div></blockquote></div><br></div>