Re: [Gmod-ajax] bulk adding annotations 401 error

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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


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Re: [Gmod-ajax] bulk adding annotations 401 error

Sofia Robb
Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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Re: [Gmod-ajax] bulk adding annotations 401 error

Sofia Robb
Should I stop tomcat before loading? 

On Wed, Jun 7, 2017 at 3:46 PM, Nathan Dunn <[hidden email]> wrote:

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn
No.  Tomcat will have to be active. 

Nathan

On Jun 7, 2017, at 2:57 PM, Sofia Robb <[hidden email]> wrote:

Should I stop tomcat before loading? 

On Wed, Jun 7, 2017 at 3:46 PM, Nathan Dunn <[hidden email]> wrote:

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax








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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn
Yes, I would definitely break it up into smaller chunks.  

Nathan

On Jun 8, 2017, at 7:49 AM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

If a large number of mRNAs are being added, is it best to break them up into smaller chunks and run the load script multiple times. My load was running very fast at first but it slowed down and now (next morning) it is still trying to load, but i am getting
 
Processing individual features for failed chunks
error: 500 read timeout

Thanks,
Sofia

On Wed, Jun 7, 2017 at 4:09 PM, Lbl <[hidden email]> wrote:
No.  Tomcat will have to be active. 

Nathan

On Jun 7, 2017, at 2:57 PM, Sofia Robb <[hidden email]> wrote:

Should I stop tomcat before loading? 

On Wed, Jun 7, 2017 at 3:46 PM, Nathan Dunn <[hidden email]> wrote:

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax









This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn
In reply to this post by nathandunn
26 lines on the GFF should be almost instant. 

1 - Have you added the organism after cleaning out the database? 
2 - Are you able to login to the system (and what do you see)?
3 - What version of Apollo are you running?
4 - Are you getting any catalina.out errors from the server? 
5 - If no obvious solution presents itself from the above question, feel free to send me the GFF3. 

Nathan

On Jun 8, 2017, at 10:07 AM, Sofia Robb <[hidden email]> wrote:

I think I broke something. 

I split up my gff. I reset my db back to the way it was before i started loaded. This gff has only 26 lines.
It has been trying to load one of my small gff for 30min now:

MT.ref_Nfu_20140520_top_level.modified.gff3
Processing MT



On Thu, Jun 8, 2017 at 9:00 AM, Lbl <[hidden email]> wrote:
Yes, I would definitely break it up into smaller chunks.  

Nathan

On Jun 8, 2017, at 7:49 AM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

If a large number of mRNAs are being added, is it best to break them up into smaller chunks and run the load script multiple times. My load was running very fast at first but it slowed down and now (next morning) it is still trying to load, but i am getting
 
Processing individual features for failed chunks
error: 500 read timeout

Thanks,
Sofia

On Wed, Jun 7, 2017 at 4:09 PM, Lbl <[hidden email]> wrote:
No.  Tomcat will have to be active. 

Nathan

On Jun 7, 2017, at 2:57 PM, Sofia Robb <[hidden email]> wrote:

Should I stop tomcat before loading? 

On Wed, Jun 7, 2017 at 3:46 PM, Nathan Dunn <[hidden email]> wrote:

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn

Possibly the transaction from the server was still stuck on the database.  

Glad you got it fixed. 

Nathan

On Jun 8, 2017, at 10:35 AM, Sofia Robb <[hidden email]> wrote:

Thanks! your list of steps helped. Organism was still valid,  the webserver was really sluggish. no errors in catalina.out.  i stopped and restarted tomcat, and it is working again. wheww.

Thanks for your help.
Sofia

 

On Thu, Jun 8, 2017 at 11:12 AM, Nathan Dunn <[hidden email]> wrote:
26 lines on the GFF should be almost instant. 

1 - Have you added the organism after cleaning out the database? 
2 - Are you able to login to the system (and what do you see)?
3 - What version of Apollo are you running?
4 - Are you getting any catalina.out errors from the server? 
5 - If no obvious solution presents itself from the above question, feel free to send me the GFF3. 

Nathan

On Jun 8, 2017, at 10:07 AM, Sofia Robb <[hidden email]> wrote:

I think I broke something. 

I split up my gff. I reset my db back to the way it was before i started loaded. This gff has only 26 lines.
It has been trying to load one of my small gff for 30min now:

MT.ref_Nfu_20140520_top_level.modified.gff3
Processing MT



On Thu, Jun 8, 2017 at 9:00 AM, Lbl <[hidden email]> wrote:
Yes, I would definitely break it up into smaller chunks.  

Nathan

On Jun 8, 2017, at 7:49 AM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

If a large number of mRNAs are being added, is it best to break them up into smaller chunks and run the load script multiple times. My load was running very fast at first but it slowed down and now (next morning) it is still trying to load, but i am getting
 
Processing individual features for failed chunks
error: 500 read timeout

Thanks,
Sofia

On Wed, Jun 7, 2017 at 4:09 PM, Lbl <[hidden email]> wrote:
No.  Tomcat will have to be active. 

Nathan

On Jun 7, 2017, at 2:57 PM, Sofia Robb <[hidden email]> wrote:

Should I stop tomcat before loading? 

On Wed, Jun 7, 2017 at 3:46 PM, Nathan Dunn <[hidden email]> wrote:

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn

Do you have the catalina.out (tomcat logs) that corresponds to you running the script? 

Nathan

On Jun 9, 2017, at 1:50 PM, Sofia Robb <[hidden email]> wrote:

Mostly things are looking great, but I have another question. I have some error that pops up a few times during my load. Is there something weird in my gff?

error: String index out of range: -2
Processing individual features for failed chunks
error: String index out of range: -2


Here are my gff lines for this gene:
##sequence-region   scaffold00727 7 64235
scaffold00727   Gnomon  gene    7       1272    .       +       .       ID=107395900:gene21848;Dbxref=GeneID:107395900;Name=znf235(10of148);end_range=1272,.;gbkey=Gene;gene=znf235(10of148);gene_biotype=protein_coding;partial=true;start_range=.,7
scaffold00727   Gnomon  mRNA    7       1272    .       +       .       ID=107395900:rna36037;Parent=107395900:gene21848;Dbxref=GeneID:107395900,Genbank:XM_015975375.1;Name=XM_015975375.1;end_range=1272,.;gbkey=mRNA;gene=LOC107395900;model_evidence=Supporting evidence includes similarity to: 6 Proteins%2C and 70%25 coverage of the annotated genomic feature by RNAseq alignments;partial=true;product=zinc finger protein 235-like;start_range=.,7;transcript_id=XM_015975375.1
scaffold00727   Gnomon  exon    7       156     .       +       .       ID=107395900:id472062;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XM_015975375.1;gbkey=mRNA;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;start_range=.,7;transcript_id=XM_015975375.1
scaffold00727   Gnomon  CDS     7       156     .       +       0       ID=107395900:cds33094:7.156;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XP_015830861.1;Name=XP_015830861.1;gbkey=CDS;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;protein_id=XP_015830861.1;start_range=.,7
scaffold00727   Gnomon  exon    493     1272    .       +       .       ID=107395900:id472063;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XM_015975375.1;end_range=1272,.;gbkey=mRNA;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;transcript_id=XM_015975375.1
scaffold00727   Gnomon  CDS     493     1272    .       +       0       ID=107395900:cds33094:493.1272;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XP_015830861.1;Name=XP_015830861.1;end_range=1272,.;gbkey=CDS;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;protein_id=XP_015830861.1



On Thu, Jun 8, 2017 at 11:42 AM, Nathan Dunn <[hidden email]> wrote:

Possibly the transaction from the server was still stuck on the database.  

Glad you got it fixed. 

Nathan

On Jun 8, 2017, at 10:35 AM, Sofia Robb <[hidden email]> wrote:

Thanks! your list of steps helped. Organism was still valid,  the webserver was really sluggish. no errors in catalina.out.  i stopped and restarted tomcat, and it is working again. wheww.

Thanks for your help.
Sofia

 

On Thu, Jun 8, 2017 at 11:12 AM, Nathan Dunn <[hidden email]> wrote:
26 lines on the GFF should be almost instant. 

1 - Have you added the organism after cleaning out the database? 
2 - Are you able to login to the system (and what do you see)?
3 - What version of Apollo are you running?
4 - Are you getting any catalina.out errors from the server? 
5 - If no obvious solution presents itself from the above question, feel free to send me the GFF3. 

Nathan

On Jun 8, 2017, at 10:07 AM, Sofia Robb <[hidden email]> wrote:

I think I broke something. 

I split up my gff. I reset my db back to the way it was before i started loaded. This gff has only 26 lines.
It has been trying to load one of my small gff for 30min now:

MT.ref_Nfu_20140520_top_level.modified.gff3
Processing MT



On Thu, Jun 8, 2017 at 9:00 AM, Lbl <[hidden email]> wrote:
Yes, I would definitely break it up into smaller chunks.  

Nathan

On Jun 8, 2017, at 7:49 AM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

If a large number of mRNAs are being added, is it best to break them up into smaller chunks and run the load script multiple times. My load was running very fast at first but it slowed down and now (next morning) it is still trying to load, but i am getting
 
Processing individual features for failed chunks
error: 500 read timeout

Thanks,
Sofia

On Wed, Jun 7, 2017 at 4:09 PM, Lbl <[hidden email]> wrote:
No.  Tomcat will have to be active. 

Nathan

On Jun 7, 2017, at 2:57 PM, Sofia Robb <[hidden email]> wrote:

Should I stop tomcat before loading? 

On Wed, Jun 7, 2017 at 3:46 PM, Nathan Dunn <[hidden email]> wrote:

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


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Re: [Gmod-ajax] bulk adding annotations 401 error

nathandunn

Just to follow-up, it was a minor bug to do with sequence alterations that is now fixed in master.  


Thanks again for reporting this Sofia,

Nathan

On Jun 9, 2017, at 3:02 PM, Sofia Robb <[hidden email]> wrote:

Nothing in my tomcat catalina.out file. 

On Fri, Jun 9, 2017 at 3:42 PM, Nathan Dunn <[hidden email]> wrote:

Do you have the catalina.out (tomcat logs) that corresponds to you running the script? 

Nathan

On Jun 9, 2017, at 1:50 PM, Sofia Robb <[hidden email]> wrote:

Mostly things are looking great, but I have another question. I have some error that pops up a few times during my load. Is there something weird in my gff?

error: String index out of range: -2
Processing individual features for failed chunks
error: String index out of range: -2


Here are my gff lines for this gene:
##sequence-region   scaffold00727 7 64235
scaffold00727   Gnomon  gene    7       1272    .       +       .       ID=107395900:gene21848;Dbxref=GeneID:107395900;Name=znf235(10of148);end_range=1272,.;gbkey=Gene;gene=znf235(10of148);gene_biotype=protein_coding;partial=true;start_range=.,7
scaffold00727   Gnomon  mRNA    7       1272    .       +       .       ID=107395900:rna36037;Parent=107395900:gene21848;Dbxref=GeneID:107395900,Genbank:XM_015975375.1;Name=XM_015975375.1;end_range=1272,.;gbkey=mRNA;gene=LOC107395900;model_evidence=Supporting evidence includes similarity to: 6 Proteins%2C and 70%25 coverage of the annotated genomic feature by RNAseq alignments;partial=true;product=zinc finger protein 235-like;start_range=.,7;transcript_id=XM_015975375.1
scaffold00727   Gnomon  exon    7       156     .       +       .       ID=107395900:id472062;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XM_015975375.1;gbkey=mRNA;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;start_range=.,7;transcript_id=XM_015975375.1
scaffold00727   Gnomon  CDS     7       156     .       +       0       ID=107395900:cds33094:7.156;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XP_015830861.1;Name=XP_015830861.1;gbkey=CDS;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;protein_id=XP_015830861.1;start_range=.,7
scaffold00727   Gnomon  exon    493     1272    .       +       .       ID=107395900:id472063;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XM_015975375.1;end_range=1272,.;gbkey=mRNA;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;transcript_id=XM_015975375.1
scaffold00727   Gnomon  CDS     493     1272    .       +       0       ID=107395900:cds33094:493.1272;Parent=107395900:rna36037;Dbxref=GeneID:107395900,Genbank:XP_015830861.1;Name=XP_015830861.1;end_range=1272,.;gbkey=CDS;gene=LOC107395900;partial=true;product=zinc finger protein 235-like;protein_id=XP_015830861.1



On Thu, Jun 8, 2017 at 11:42 AM, Nathan Dunn <[hidden email]> wrote:

Possibly the transaction from the server was still stuck on the database.  

Glad you got it fixed. 

Nathan

On Jun 8, 2017, at 10:35 AM, Sofia Robb <[hidden email]> wrote:

Thanks! your list of steps helped. Organism was still valid,  the webserver was really sluggish. no errors in catalina.out.  i stopped and restarted tomcat, and it is working again. wheww.

Thanks for your help.
Sofia

 

On Thu, Jun 8, 2017 at 11:12 AM, Nathan Dunn <[hidden email]> wrote:
26 lines on the GFF should be almost instant. 

1 - Have you added the organism after cleaning out the database? 
2 - Are you able to login to the system (and what do you see)?
3 - What version of Apollo are you running?
4 - Are you getting any catalina.out errors from the server? 
5 - If no obvious solution presents itself from the above question, feel free to send me the GFF3. 

Nathan

On Jun 8, 2017, at 10:07 AM, Sofia Robb <[hidden email]> wrote:

I think I broke something. 

I split up my gff. I reset my db back to the way it was before i started loaded. This gff has only 26 lines.
It has been trying to load one of my small gff for 30min now:

MT.ref_Nfu_20140520_top_level.modified.gff3
Processing MT



On Thu, Jun 8, 2017 at 9:00 AM, Lbl <[hidden email]> wrote:
Yes, I would definitely break it up into smaller chunks.  

Nathan

On Jun 8, 2017, at 7:49 AM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

If a large number of mRNAs are being added, is it best to break them up into smaller chunks and run the load script multiple times. My load was running very fast at first but it slowed down and now (next morning) it is still trying to load, but i am getting
 
Processing individual features for failed chunks
error: 500 read timeout

Thanks,
Sofia

On Wed, Jun 7, 2017 at 4:09 PM, Lbl <[hidden email]> wrote:
No.  Tomcat will have to be active. 

Nathan

On Jun 7, 2017, at 2:57 PM, Sofia Robb <[hidden email]> wrote:

Should I stop tomcat before loading? 

On Wed, Jun 7, 2017 at 3:46 PM, Nathan Dunn <[hidden email]> wrote:

Excellent.  Glad I could help.  

Nathan

On Jun 7, 2017, at 2:44 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Yes! Thank you! I was using the postgres user/pass. My user/pass for the Web interface works! Yeah!!

Thank you,
Sofia



On Wed, Jun 7, 2017 at 2:00 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

Are you using the username / password for your database or an admin username / password for one of the admin users on the system (they should not be the same)?  It should be the latter.

The common name of the organism is correct.  

Nathan



On Jun 7, 2017, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

Hi!

I am having a problem bulk loading annotations:


here is my command:
tools/data/add_transcripts_from_gff3_to_annotations.pl  -U genomesdev.stowers.org:8080/apollo -u web_apollo_admin -p password -i /var/other_data/organisms/killifish/Nfur/transcriptomes/refseq_r100/ref_Nfu_20140520_top_level.fixedrenamed.newGeneNames.gff3 -o "Killifish" -t mRNA


Is organism the the common name or the genus and species?

I doubled checked my user and password in my apollo-config.groovy file. 

I tried localhost:8080/apollo as well.

None of what I have tried works. What simple thing am I missing?

Thank you!
Sofia


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