Failed to create a new organism

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Failed to create a new organism

Michael Campbell
Hi all,

This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.

Run the prepare-refseqs.pl script to load the genome
#-----------------------------------------------
./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

Run flatfile-to-jason to load the gene models as a track
#-----------------------------------------------
./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.

Thanks,
Mike 














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Re: Failed to create a new organism

nathandunn

It looks like you followed the appropriate steps.  

Could you do two things?

1 - list the contents of that data directory
2 - you tomcat directory (if you are using tomcat) should have a catalina.out or other file.  If you could provide the contents of that . . . at least from where you tried to add the organism.  

Thanks,

Nathan

> On Dec 16, 2015, at 12:37 PM, Michael Campbell <[hidden email]> wrote:
>
> Hi all,
>
> This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.
>
> Run the prepare-refseqs.pl script to load the genome
> #-----------------------------------------------
> ./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
>
> Run flatfile-to-jason to load the gene models as a track
> #-----------------------------------------------
> ./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
>
> I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.
>
> Thanks,
> Mike
> <Screen Shot 2015-12-16 at 3.28.42 PM.png>
>
>
>
>
>
>
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Failed to create a new organism

Michael Campbell
Here are the contents of the directory

[mcampbel@brie data]$ pwd
/home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
[mcampbel@brie data]$ ll
total 8
-rw-rw-r--. 1 mcampbel mcampbel  399 Dec 16 10:52 trackList.json
drwxrwxr-x. 3 mcampbel mcampbel 4096 Dec 16 10:52 tracks
-rw-rw-r--. 1 mcampbel mcampbel    0 Dec 16 10:52 tracks.conf

And here is a tail of the catalina.out file

[mcampbel@brie tomcat]$ tail catalina.out
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

> On Dec 16, 2015, at 3:46 PM, Nathan Dunn <[hidden email]> wrote:
>
>
> It looks like you followed the appropriate steps.  
>
> Could you do two things?
>
> 1 - list the contents of that data directory
> 2 - you tomcat directory (if you are using tomcat) should have a catalina.out or other file.  If you could provide the contents of that . . . at least from where you tried to add the organism.  
>
> Thanks,
>
> Nathan
>
>> On Dec 16, 2015, at 12:37 PM, Michael Campbell <[hidden email]> wrote:
>>
>> Hi all,
>>
>> This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.
>>
>> Run the prepare-refseqs.pl script to load the genome
>> #-----------------------------------------------
>> ./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
>>
>> Run flatfile-to-jason to load the gene models as a track
>> #-----------------------------------------------
>> ./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
>>
>> I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.
>>
>> Thanks,
>> Mike
>> <Screen Shot 2015-12-16 at 3.28.42 PM.png>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
>> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Failed to create a new organism

nathandunn

It looks as though there was an error when preparing the reference sequence.  You should have a directory “seq” in that same directory.  This is one of mine:

ls /opt/apollo/cow/ 
seq trackList.json tracks tracks.conf

If you rerun the prepare-refseq command does it create the directory for you and/or are there any errors? 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 12:59 PM, Michael Campbell <[hidden email]> wrote:

Here are the contents of the directory

[mcampbel@brie data]$ pwd
/home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
[mcampbel@brie data]$ ll
total 8
-rw-rw-r--. 1 mcampbel mcampbel  399 Dec 16 10:52 trackList.json
drwxrwxr-x. 3 mcampbel mcampbel 4096 Dec 16 10:52 tracks
-rw-rw-r--. 1 mcampbel mcampbel    0 Dec 16 10:52 tracks.conf

And here is a tail of the catalina.out file

[mcampbel@brie tomcat]$ tail catalina.out
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 3:46 PM, Nathan Dunn <[hidden email]> wrote:


It looks like you followed the appropriate steps.  

Could you do two things?

1 - list the contents of that data directory
2 - you tomcat directory (if you are using tomcat) should have a catalina.out or other file.  If you could provide the contents of that . . . at least from where you tried to add the organism.  

Thanks,

Nathan

On Dec 16, 2015, at 12:37 PM, Michael Campbell <[hidden email]> wrote:

Hi all,

This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.

Run the prepare-refseqs.pl script to load the genome
#-----------------------------------------------
./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

Run flatfile-to-jason to load the gene models as a track
#-----------------------------------------------
./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.

Thanks,
Mike
<Screen Shot 2015-12-16 at 3.28.42 PM.png>













This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Failed to create a new organism

Michael Campbell
I reran the prepare-refseqs command and it completed without errors

Now the directory looks like this

[mcampbel@brie data]$ ls
seq  trackList.json  tracks  tracks.conf

But I get the same error when I try to create a new organism.

Here is the tail of the catalina.out file now

tail catalina.out
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 16:08:14,932 [http-bio-8080-exec-8] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 4:03 PM, Nathan Dunn <[hidden email]> wrote:


It looks as though there was an error when preparing the reference sequence.  You should have a directory “seq” in that same directory.  This is one of mine:

ls /opt/apollo/cow/ 
seq trackList.json tracks tracks.conf

If you rerun the prepare-refseq command does it create the directory for you and/or are there any errors? 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 12:59 PM, Michael Campbell <[hidden email]> wrote:

Here are the contents of the directory

[mcampbel@brie data]$ pwd
/home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
[mcampbel@brie data]$ ll
total 8
-rw-rw-r--. 1 mcampbel mcampbel  399 Dec 16 10:52 trackList.json
drwxrwxr-x. 3 mcampbel mcampbel 4096 Dec 16 10:52 tracks
-rw-rw-r--. 1 mcampbel mcampbel    0 Dec 16 10:52 tracks.conf

And here is a tail of the catalina.out file

[mcampbel@brie tomcat]$ tail catalina.out
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 3:46 PM, Nathan Dunn <[hidden email]> wrote:


It looks like you followed the appropriate steps.  

Could you do two things?

1 - list the contents of that data directory
2 - you tomcat directory (if you are using tomcat) should have a catalina.out or other file.  If you could provide the contents of that . . . at least from where you tried to add the organism.  

Thanks,

Nathan

On Dec 16, 2015, at 12:37 PM, Michael Campbell <[hidden email]> wrote:

Hi all,

This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.

Run the prepare-refseqs.pl script to load the genome
#-----------------------------------------------
./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

Run flatfile-to-jason to load the gene models as a track
#-----------------------------------------------
./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.

Thanks,
Mike
<Screen Shot 2015-12-16 at 3.28.42 PM.png>













This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: Failed to create a new organism

nathandunn

Alright, I’ve go ta few things to try.

The only reason that error should be thrown is if the directory you specified isn’t a directory (which it clearly is) or if that directory is unreadable.   That is all it is checking for to produce that error. 

1 - I would do . . and make sure that “.” is readable by all:

ls -al /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data


2 -  I’m curious if you can add the mod_encode sample_data that comes with JBrowse (jbrowse_download/sample_data/mod_encode I think) or any other sample data. 

3 - Can you load that same directory using straight JBrowse? 

4 - Lastly, if you want to redeploy with debug level, it might tell you something (in case the JSON passed back to the server is somehow incorrect):


Basically you would add this in your apollo-config.groovy file. 

log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
           ...
    debug 'grails.app'
}

Let me know what you find!

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 1:12 PM, Michael Campbell <[hidden email]> wrote:

I reran the prepare-refseqs command and it completed without errors

Now the directory looks like this

[mcampbel@brie data]$ ls
seq  trackList.json  tracks  tracks.conf

But I get the same error when I try to create a new organism.

Here is the tail of the catalina.out file now

tail catalina.out
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 16:08:14,932 [http-bio-8080-exec-8] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 4:03 PM, Nathan Dunn <[hidden email]> wrote:


It looks as though there was an error when preparing the reference sequence.  You should have a directory “seq” in that same directory.  This is one of mine:

ls /opt/apollo/cow/ 
seq trackList.json tracks tracks.conf

If you rerun the prepare-refseq command does it create the directory for you and/or are there any errors? 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 12:59 PM, Michael Campbell <[hidden email]> wrote:

Here are the contents of the directory

[mcampbel@brie data]$ pwd
/home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
[mcampbel@brie data]$ ll
total 8
-rw-rw-r--. 1 mcampbel mcampbel  399 Dec 16 10:52 trackList.json
drwxrwxr-x. 3 mcampbel mcampbel 4096 Dec 16 10:52 tracks
-rw-rw-r--. 1 mcampbel mcampbel    0 Dec 16 10:52 tracks.conf

And here is a tail of the catalina.out file

[mcampbel@brie tomcat]$ tail catalina.out
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 3:46 PM, Nathan Dunn <[hidden email]> wrote:


It looks like you followed the appropriate steps.  

Could you do two things?

1 - list the contents of that data directory
2 - you tomcat directory (if you are using tomcat) should have a catalina.out or other file.  If you could provide the contents of that . . . at least from where you tried to add the organism.  

Thanks,

Nathan

On Dec 16, 2015, at 12:37 PM, Michael Campbell <[hidden email]> wrote:

Hi all,

This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.

Run the prepare-refseqs.pl script to load the genome
#-----------------------------------------------
./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

Run flatfile-to-jason to load the gene models as a track
#-----------------------------------------------
./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.

Thanks,
Mike
<Screen Shot 2015-12-16 at 3.28.42 PM.png>













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Re: Failed to create a new organism

Michael Campbell
It was permissions two directories up that was causing the problem. I got past the error and it says it is processing. It has been processing for some time now. How long should it take to process? Also if I run flatfile-to-json.pl to add more tracks will the new tracks automatically appear in the browser?

Thanks,
Mike 
On Dec 16, 2015, at 4:41 PM, Nathan Dunn <[hidden email]> wrote:


Alright, I’ve go ta few things to try.

The only reason that error should be thrown is if the directory you specified isn’t a directory (which it clearly is) or if that directory is unreadable.   That is all it is checking for to produce that error. 

1 - I would do . . and make sure that “.” is readable by all:

ls -al /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data


2 -  I’m curious if you can add the mod_encode sample_data that comes with JBrowse (jbrowse_download/sample_data/mod_encode I think) or any other sample data. 

3 - Can you load that same directory using straight JBrowse? 

4 - Lastly, if you want to redeploy with debug level, it might tell you something (in case the JSON passed back to the server is somehow incorrect):


Basically you would add this in your apollo-config.groovy file. 

log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
           ...
    debug 'grails.app'
}

Let me know what you find!

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 1:12 PM, Michael Campbell <[hidden email]> wrote:

I reran the prepare-refseqs command and it completed without errors

Now the directory looks like this

[mcampbel@brie data]$ ls
seq  trackList.json  tracks  tracks.conf

But I get the same error when I try to create a new organism.

Here is the tail of the catalina.out file now

tail catalina.out
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 16:08:14,932 [http-bio-8080-exec-8] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 4:03 PM, Nathan Dunn <[hidden email]> wrote:


It looks as though there was an error when preparing the reference sequence.  You should have a directory “seq” in that same directory.  This is one of mine:

ls /opt/apollo/cow/ 
seq trackList.json tracks tracks.conf

If you rerun the prepare-refseq command does it create the directory for you and/or are there any errors? 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 12:59 PM, Michael Campbell <[hidden email]> wrote:

Here are the contents of the directory

[mcampbel@brie data]$ pwd
/home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
[mcampbel@brie data]$ ll
total 8
-rw-rw-r--. 1 mcampbel mcampbel  399 Dec 16 10:52 trackList.json
drwxrwxr-x. 3 mcampbel mcampbel 4096 Dec 16 10:52 tracks
-rw-rw-r--. 1 mcampbel mcampbel    0 Dec 16 10:52 tracks.conf

And here is a tail of the catalina.out file

[mcampbel@brie tomcat]$ tail catalina.out
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 3:46 PM, Nathan Dunn <[hidden email]> wrote:


It looks like you followed the appropriate steps.  

Could you do two things?

1 - list the contents of that data directory
2 - you tomcat directory (if you are using tomcat) should have a catalina.out or other file.  If you could provide the contents of that . . . at least from where you tried to add the organism.  

Thanks,

Nathan

On Dec 16, 2015, at 12:37 PM, Michael Campbell <[hidden email]> wrote:

Hi all,

This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.

Run the prepare-refseqs.pl script to load the genome
#-----------------------------------------------
./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

Run flatfile-to-jason to load the gene models as a track
#-----------------------------------------------
./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.

Thanks,
Mike
<Screen Shot 2015-12-16 at 3.28.42 PM.png>













This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: Failed to create a new organism

nathandunn

On Dec 16, 2015, at 2:02 PM, Michael Campbell <[hidden email]> wrote:

It was permissions two directories up that was causing the problem. I got past the error and it says it is processing. It has been processing for some time now. How long should it take to process?

Its almost solely dependent on the number of sequences / scaffolds.   We did 100K in about 20 minutes on the upper-limit.  5K is usually about 30 seconds.  

I would copy your URL into another browser and see if the organism is there.   

I’d be willing to bet that not enough memory has been allocated if you are using the default tomcat settings.   

Look here:


if you continue to have trouble with performance.

Also if I run flatfile-to-json.pl to add more tracks will the new tracks automatically appear in the browser?

Absolutely.   If you regenerate your refseq in the same directory you will have trouble (I would create a new organism), but you can add as many tracks as you want to the existing sequence.  

Nathan



Thanks,
Mike 
On Dec 16, 2015, at 4:41 PM, Nathan Dunn <[hidden email]> wrote:


Alright, I’ve go ta few things to try.

The only reason that error should be thrown is if the directory you specified isn’t a directory (which it clearly is) or if that directory is unreadable.   That is all it is checking for to produce that error. 

1 - I would do . . and make sure that “.” is readable by all:

ls -al /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data


2 -  I’m curious if you can add the mod_encode sample_data that comes with JBrowse (jbrowse_download/sample_data/mod_encode I think) or any other sample data. 

3 - Can you load that same directory using straight JBrowse? 

4 - Lastly, if you want to redeploy with debug level, it might tell you something (in case the JSON passed back to the server is somehow incorrect):


Basically you would add this in your apollo-config.groovy file. 

log4j.main = {
    error 'org.codehaus.groovy.grails.web.servlet',  // controllers
          'org.codehaus.groovy.grails.web.pages',    // GSP
          'org.codehaus.groovy.grails.web.sitemesh', // layouts
           ...
    debug 'grails.app'
}

Let me know what you find!

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 1:12 PM, Michael Campbell <[hidden email]> wrote:

I reran the prepare-refseqs command and it completed without errors

Now the directory looks like this

[mcampbel@brie data]$ ls
seq  trackList.json  tracks  tracks.conf

But I get the same error when I try to create a new organism.

Here is the tail of the catalina.out file now

tail catalina.out
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 16:08:14,932 [http-bio-8080-exec-8] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 4:03 PM, Nathan Dunn <[hidden email]> wrote:


It looks as though there was an error when preparing the reference sequence.  You should have a directory “seq” in that same directory.  This is one of mine:

ls /opt/apollo/cow/ 
seq trackList.json tracks tracks.conf

If you rerun the prepare-refseq command does it create the directory for you and/or are there any errors? 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Dec 16, 2015, at 12:59 PM, Michael Campbell <[hidden email]> wrote:

Here are the contents of the directory

[mcampbel@brie data]$ pwd
/home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
[mcampbel@brie data]$ ll
total 8
-rw-rw-r--. 1 mcampbel mcampbel  399 Dec 16 10:52 trackList.json
drwxrwxr-x. 3 mcampbel mcampbel 4096 Dec 16 10:52 tracks
-rw-rw-r--. 1 mcampbel mcampbel    0 Dec 16 10:52 tracks.conf

And here is a tail of the catalina.out file

[mcampbel@brie tomcat]$ tail catalina.out
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 16, 2015 1:43:53 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 16, 2015 1:43:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 66283 ms
2015-12-16 10:22:27,631 [http-bio-8080-exec-3] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
2015-12-16 10:23:28,701 [http-bio-8080-exec-6] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data
sending logout for org.bbop.apollo.User : 1 via [hidden email]
sending to: '/topic/AnnotationNotification/user/' + [hidden email]
2015-12-16 15:28:12,990 [http-bio-8080-exec-10] ERROR apollo.OrganismController  - problem saving organism: java.lang.Exception: Invalid directory specified: /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

On Dec 16, 2015, at 3:46 PM, Nathan Dunn <[hidden email]> wrote:


It looks like you followed the appropriate steps.  

Could you do two things?

1 - list the contents of that data directory
2 - you tomcat directory (if you are using tomcat) should have a catalina.out or other file.  If you could provide the contents of that . . . at least from where you tried to add the organism.  

Thanks,

Nathan

On Dec 16, 2015, at 12:37 PM, Michael Campbell <[hidden email]> wrote:

Hi all,

This is my first experience with apollo 2.0.0. Things have changed a lot from the 1.x versions. I’m trying to create a new organism. I’ve done the following to load the data.

Run the prepare-refseqs.pl script to load the genome
#-----------------------------------------------
./bin/prepare-refseqs.pl --fasta /home/mcampbel/B73_AGPv4_contigs_2015_12_14/V4_ctg_all.fa —out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

Run flatfile-to-jason to load the gene models as a track
#-----------------------------------------------
./bin/flatfile-to-json.pl --gff /home/mcampbel/B73_AGPv4_contigs_2015_12_14/genes_49081_genes.gff --type mRNA --trackLabel MAKER --out /home/mcampbel/B73_AGPv4_contigs_2015_12_14/data

I then created the administrator account through the web interface and tried to create a new organism and got the error in the screen shot. I googled around to see if this is a common problem and didn’t find anything. Any help would be appreciated.

Thanks,
Mike
<Screen Shot 2015-12-16 at 3.28.42 PM.png>













This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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