Export to cDNA/CDS/peptide

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Export to cDNA/CDS/peptide

ronnie.dejonge
Dear WebApollo developers, 

I'm currently running into some sort of weird error whenever I'm trying to export data from the WebApollo admin/scaffold selection page. When I select one particular (scaffold_21 in this case) scaffold and use File>Export>Fasta>cDNA (or CDS or peptide, but not in the case of GFF3) it gives the error "Error writing cDNA" and nothing happens. This doesn't happen with other scaffolds. Furthermore, I can open the scaffold (by clicking it) and it does display (correctly) the annotations and manual adjustments. 

When I look at the catalina.out log in /var/logs/tomcat7/ there's a number of error messages, basically evolving around this particular line:

"java.io.FileNotFoundException:/var/lib/tomcat7/webapps/cercospora_1/jbrowse/data/seq/scaffold_21/107374.txt (No such file or directory)"

This sequence .../data/seq/scaffold21/107374.txt indeed doesn't exist (there are only 67 *.txt files in that directory). How should I go about fixing this problem? 

I'm running WebApollo release 2013-05-16 by the way (on an Ubuntu 64-bit server).
Thanks for your help.

Kind regards,
Ronnie
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Re: Export to cDNA/CDS/peptide

Chris Childers
Hi Ronnie,

Did you see any errors when you were running prepare-refseqs?  Also, when you go to this problematic region, do you see the reference sequence when you zoom in to the base level? 

Best regards,
Chris


On Tue, Jan 28, 2014 at 10:33 AM, Ronnie de Jonge <[hidden email]> wrote:
Dear WebApollo developers, 

I'm currently running into some sort of weird error whenever I'm trying to export data from the WebApollo admin/scaffold selection page. When I select one particular (scaffold_21 in this case) scaffold and use File>Export>Fasta>cDNA (or CDS or peptide, but not in the case of GFF3) it gives the error "Error writing cDNA" and nothing happens. This doesn't happen with other scaffolds. Furthermore, I can open the scaffold (by clicking it) and it does display (correctly) the annotations and manual adjustments. 

When I look at the catalina.out log in /var/logs/tomcat7/ there's a number of error messages, basically evolving around this particular line:

"java.io.FileNotFoundException:/var/lib/tomcat7/webapps/cercospora_1/jbrowse/data/seq/scaffold_21/107374.txt (No such file or directory)"

This sequence .../data/seq/scaffold21/107374.txt indeed doesn't exist (there are only 67 *.txt files in that directory). How should I go about fixing this problem? 

I'm running WebApollo release 2013-05-16 by the way (on an Ubuntu 64-bit server).
Thanks for your help.

Kind regards,
Ronnie



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211

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Re: Export to cDNA/CDS/peptide

ronnie.dejonge
Hi Chris,

To answer your first question; although I couldn't be 100% sure, it's been a while since I'm using this instance, I don't recall any errors when preparing. For the second question, yes I can zoom in to the base level. No problems there. 

I digged a bit deeper and I noticed this particular line in the exported GFF3:
scaffold_21     .       mRNA    -2147483648     -2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
Obviously, this doesn't make sense...

I then decided to remove the two gene annotations at this position and re-export the GFF3 (fasta still doesn't work). Now the GFF3 contains at that position two lines with negative start/stop positions:
scaffold_21     .       gene    -2147483648     -2147483648     .       -       .       Name=35692FCFD194A22CE39C5F0BF752EA7E;ID=35692FCFD194A22CE39C5F0BF752EA7E
scaffold_21     .       mRNA    -2147483648     -2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
I'm not sure what's going on here... Any ideas?

Cheers,
Ronnie


2014-01-28 Chris Childers <[hidden email]>
Hi Ronnie,

Did you see any errors when you were running prepare-refseqs?  Also, when you go to this problematic region, do you see the reference sequence when you zoom in to the base level? 

Best regards,
Chris


On Tue, Jan 28, 2014 at 10:33 AM, Ronnie de Jonge <[hidden email]> wrote:
Dear WebApollo developers, 

I'm currently running into some sort of weird error whenever I'm trying to export data from the WebApollo admin/scaffold selection page. When I select one particular (scaffold_21 in this case) scaffold and use File>Export>Fasta>cDNA (or CDS or peptide, but not in the case of GFF3) it gives the error "Error writing cDNA" and nothing happens. This doesn't happen with other scaffolds. Furthermore, I can open the scaffold (by clicking it) and it does display (correctly) the annotations and manual adjustments. 

When I look at the catalina.out log in /var/logs/tomcat7/ there's a number of error messages, basically evolving around this particular line:

"java.io.FileNotFoundException:/var/lib/tomcat7/webapps/cercospora_1/jbrowse/data/seq/scaffold_21/107374.txt (No such file or directory)"

This sequence .../data/seq/scaffold21/107374.txt indeed doesn't exist (there are only 67 *.txt files in that directory). How should I go about fixing this problem? 

I'm running WebApollo release 2013-05-16 by the way (on an Ubuntu 64-bit server).
Thanks for your help.

Kind regards,
Ronnie



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211


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Re: Export to cDNA/CDS/peptide

Ed Lee
Hi Ronnie,

Not sure how you've gotten some negative coordinates.  Unfortunately it doesn't seem to be a reproducible bug.  Anyway, I've written a tool that will allow you to directly access the annotation database and then delete the offending genes.

You can download the tool at:


Uncompress the tarball and run:

remove_top_level_feature_by_id.sh -w $TOMCAT_WEBAPPS_DIR/WebApollo -i $ANNOTATION_DIR -I $ID_TO_REMOVE

In your case, you'll want to run something like this:

remove_top_level_feature_by_id.sh -w $TOMCAT_WEBAPPS_DIR/WebApollo -i $DATASTORE_DIRECTORY/Annotations-scaffold_21 -I 35692FCFD194A22CE39C5F0BF752EA7E

Note that this tool is based on the current release of WebApollo, so $TOMCAT_WEBAPPS_DIR/WebApollo should point to the current release.  However, if you don't want to update your installation quite yet, you can just uncompress the war from the current release somewhere and point -w to that location.

You might want to backup your annotations directory before updating just to be safe.

Hopefully this will fix the export problem.

Cheers,
Ed


On Wed, Jan 29, 2014 at 1:19 AM, Ronnie de Jonge <[hidden email]> wrote:
Hi Chris,

To answer your first question; although I couldn't be 100% sure, it's been a while since I'm using this instance, I don't recall any errors when preparing. For the second question, yes I can zoom in to the base level. No problems there. 

I digged a bit deeper and I noticed this particular line in the exported GFF3:
scaffold_21     .       mRNA    -<a href="tel:2147483648" value="+12147483648" target="_blank">2147483648     -<a href="tel:2147483648" value="+12147483648" target="_blank">2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
Obviously, this doesn't make sense...

I then decided to remove the two gene annotations at this position and re-export the GFF3 (fasta still doesn't work). Now the GFF3 contains at that position two lines with negative start/stop positions:
scaffold_21     .       gene    -<a href="tel:2147483648" value="+12147483648" target="_blank">2147483648     -<a href="tel:2147483648" value="+12147483648" target="_blank">2147483648     .       -       .       Name=35692FCFD194A22CE39C5F0BF752EA7E;ID=35692FCFD194A22CE39C5F0BF752EA7E
scaffold_21     .       mRNA    -<a href="tel:2147483648" value="+12147483648" target="_blank">2147483648     -<a href="tel:2147483648" value="+12147483648" target="_blank">2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
I'm not sure what's going on here... Any ideas?

Cheers,
Ronnie


2014-01-28 Chris Childers <[hidden email]>

Hi Ronnie,

Did you see any errors when you were running prepare-refseqs?  Also, when you go to this problematic region, do you see the reference sequence when you zoom in to the base level? 

Best regards,
Chris


On Tue, Jan 28, 2014 at 10:33 AM, Ronnie de Jonge <[hidden email]> wrote:
Dear WebApollo developers, 

I'm currently running into some sort of weird error whenever I'm trying to export data from the WebApollo admin/scaffold selection page. When I select one particular (scaffold_21 in this case) scaffold and use File>Export>Fasta>cDNA (or CDS or peptide, but not in the case of GFF3) it gives the error "Error writing cDNA" and nothing happens. This doesn't happen with other scaffolds. Furthermore, I can open the scaffold (by clicking it) and it does display (correctly) the annotations and manual adjustments. 

When I look at the catalina.out log in /var/logs/tomcat7/ there's a number of error messages, basically evolving around this particular line:

"java.io.FileNotFoundException:/var/lib/tomcat7/webapps/cercospora_1/jbrowse/data/seq/scaffold_21/107374.txt (No such file or directory)"

This sequence .../data/seq/scaffold21/107374.txt indeed doesn't exist (there are only 67 *.txt files in that directory). How should I go about fixing this problem? 

I'm running WebApollo release 2013-05-16 by the way (on an Ubuntu 64-bit server).
Thanks for your help.

Kind regards,
Ronnie



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211



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Re: Export to cDNA/CDS/peptide

Scott Cain
Those negative coordinates looks suspiciously like an underflow, not that I have any idea how that might have happened.

Scott


Sent from Mailbox for iPad


On Tue, Feb 4, 2014 at 4:33 PM, Ed Lee <[hidden email]> wrote:

Hi Ronnie,

Not sure how you've gotten some negative coordinates.  Unfortunately it doesn't seem to be a reproducible bug.  Anyway, I've written a tool that will allow you to directly access the annotation database and then delete the offending genes.

You can download the tool at:


Uncompress the tarball and run:

remove_top_level_feature_by_id.sh -w $TOMCAT_WEBAPPS_DIR/WebApollo -i $ANNOTATION_DIR -I $ID_TO_REMOVE

In your case, you'll want to run something like this:

remove_top_level_feature_by_id.sh -w $TOMCAT_WEBAPPS_DIR/WebApollo -i $DATASTORE_DIRECTORY/Annotations-scaffold_21 -I 35692FCFD194A22CE39C5F0BF752EA7E

Note that this tool is based on the current release of WebApollo, so $TOMCAT_WEBAPPS_DIR/WebApollo should point to the current release.  However, if you don't want to update your installation quite yet, you can just uncompress the war from the current release somewhere and point -w to that location.

You might want to backup your annotations directory before updating just to be safe.

Hopefully this will fix the export problem.

Cheers,
Ed


On Wed, Jan 29, 2014 at 1:19 AM, Ronnie de Jonge <[hidden email]> wrote:
Hi Chris,

To answer your first question; although I couldn't be 100% sure, it's been a while since I'm using this instance, I don't recall any errors when preparing. For the second question, yes I can zoom in to the base level. No problems there. 

I digged a bit deeper and I noticed this particular line in the exported GFF3:
scaffold_21     .       mRNA    -<a href="tel:2147483648">2147483648     -<a href="tel:2147483648">2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
Obviously, this doesn't make sense...

I then decided to remove the two gene annotations at this position and re-export the GFF3 (fasta still doesn't work). Now the GFF3 contains at that position two lines with negative start/stop positions:
scaffold_21     .       gene    -<a href="tel:2147483648">2147483648     -<a href="tel:2147483648">2147483648     .       -       .       Name=35692FCFD194A22CE39C5F0BF752EA7E;ID=35692FCFD194A22CE39C5F0BF752EA7E
scaffold_21     .       mRNA    -<a href="tel:2147483648">2147483648     -<a href="tel:2147483648">2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
I'm not sure what's going on here... Any ideas?

Cheers,
Ronnie


2014-01-28 Chris Childers <[hidden email]>

Hi Ronnie,

Did you see any errors when you were running prepare-refseqs?  Also, when you go to this problematic region, do you see the reference sequence when you zoom in to the base level? 

Best regards,
Chris


On Tue, Jan 28, 2014 at 10:33 AM, Ronnie de Jonge <[hidden email]> wrote:
Dear WebApollo developers, 

I'm currently running into some sort of weird error whenever I'm trying to export data from the WebApollo admin/scaffold selection page. When I select one particular (scaffold_21 in this case) scaffold and use File>Export>Fasta>cDNA (or CDS or peptide, but not in the case of GFF3) it gives the error "Error writing cDNA" and nothing happens. This doesn't happen with other scaffolds. Furthermore, I can open the scaffold (by clicking it) and it does display (correctly) the annotations and manual adjustments. 

When I look at the catalina.out log in /var/logs/tomcat7/ there's a number of error messages, basically evolving around this particular line:

"java.io.FileNotFoundException:/var/lib/tomcat7/webapps/cercospora_1/jbrowse/data/seq/scaffold_21/107374.txt (No such file or directory)"

This sequence .../data/seq/scaffold21/107374.txt indeed doesn't exist (there are only 67 *.txt files in that directory). How should I go about fixing this problem? 

I'm running WebApollo release 2013-05-16 by the way (on an Ubuntu 64-bit server).
Thanks for your help.

Kind regards,
Ronnie



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




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Re: Export to cDNA/CDS/peptide

Monica Poelchau
Hi everyone,

Just fyi, we're seeing the same problem with the negative coordinates: 

Scaffold461     WebApollo       gene    -2147483648     -2147483648     .       +       .       Name=4CF614975F80E552F030EE54462FC244;date_creation=2014-06-31;ID=4CF614975F80E552F030EE54462FC244;d

ate_last_modified=2014-06-31

Scaffold461     WebApollo       mRNA    -2147483648     -2147483648     .       +       .       Name=OfasTmpA009957-RA;date_creation=2014-06-31;Parent=4CF614975F80E552F030EE54462FC244;ID=38F654C91

We can easily flag and remove these, but it would be interesting to know what is causing this problem...

Monica





On Wed, Feb 5, 2014 at 9:42 AM, Scott Cain <[hidden email]> wrote:
Those negative coordinates looks suspiciously like an underflow, not that I have any idea how that might have happened.

Scott


Sent from Mailbox for iPad


On Tue, Feb 4, 2014 at 4:33 PM, Ed Lee <[hidden email]> wrote:

Hi Ronnie,

Not sure how you've gotten some negative coordinates.  Unfortunately it doesn't seem to be a reproducible bug.  Anyway, I've written a tool that will allow you to directly access the annotation database and then delete the offending genes.

You can download the tool at:


Uncompress the tarball and run:

remove_top_level_feature_by_id.sh -w $TOMCAT_WEBAPPS_DIR/WebApollo -i $ANNOTATION_DIR -I $ID_TO_REMOVE

In your case, you'll want to run something like this:

remove_top_level_feature_by_id.sh -w $TOMCAT_WEBAPPS_DIR/WebApollo -i $DATASTORE_DIRECTORY/Annotations-scaffold_21 -I 35692FCFD194A22CE39C5F0BF752EA7E

Note that this tool is based on the current release of WebApollo, so $TOMCAT_WEBAPPS_DIR/WebApollo should point to the current release.  However, if you don't want to update your installation quite yet, you can just uncompress the war from the current release somewhere and point -w to that location.

You might want to backup your annotations directory before updating just to be safe.

Hopefully this will fix the export problem.

Cheers,
Ed


On Wed, Jan 29, 2014 at 1:19 AM, Ronnie de Jonge <[hidden email]> wrote:
Hi Chris,

To answer your first question; although I couldn't be 100% sure, it's been a while since I'm using this instance, I don't recall any errors when preparing. For the second question, yes I can zoom in to the base level. No problems there. 

I digged a bit deeper and I noticed this particular line in the exported GFF3:
scaffold_21     .       mRNA    -<a href="tel:2147483648" target="_blank">2147483648     -<a href="tel:2147483648" target="_blank">2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
Obviously, this doesn't make sense...

I then decided to remove the two gene annotations at this position and re-export the GFF3 (fasta still doesn't work). Now the GFF3 contains at that position two lines with negative start/stop positions:
scaffold_21     .       gene    -<a href="tel:2147483648" target="_blank">2147483648     -<a href="tel:2147483648" target="_blank">2147483648     .       -       .       Name=35692FCFD194A22CE39C5F0BF752EA7E;ID=35692FCFD194A22CE39C5F0BF752EA7E
scaffold_21     .       mRNA    -<a href="tel:2147483648" target="_blank">2147483648     -<a href="tel:2147483648" target="_blank">2147483648     .       -       .       Name=scaffold_21:115501-117203;Parent=35692FCFD194A22CE39C5F0BF752EA7E;ID=487D98788757112FCCE9A06B1B389F61
I'm not sure what's going on here... Any ideas?

Cheers,
Ronnie


2014-01-28 Chris Childers <[hidden email]>

Hi Ronnie,

Did you see any errors when you were running prepare-refseqs?  Also, when you go to this problematic region, do you see the reference sequence when you zoom in to the base level? 

Best regards,
Chris


On Tue, Jan 28, 2014 at 10:33 AM, Ronnie de Jonge <[hidden email]> wrote:
Dear WebApollo developers, 

I'm currently running into some sort of weird error whenever I'm trying to export data from the WebApollo admin/scaffold selection page. When I select one particular (scaffold_21 in this case) scaffold and use File>Export>Fasta>cDNA (or CDS or peptide, but not in the case of GFF3) it gives the error "Error writing cDNA" and nothing happens. This doesn't happen with other scaffolds. Furthermore, I can open the scaffold (by clicking it) and it does display (correctly) the annotations and manual adjustments. 

When I look at the catalina.out log in /var/logs/tomcat7/ there's a number of error messages, basically evolving around this particular line:

"java.io.FileNotFoundException:/var/lib/tomcat7/webapps/cercospora_1/jbrowse/data/seq/scaffold_21/107374.txt (No such file or directory)"

This sequence .../data/seq/scaffold21/107374.txt indeed doesn't exist (there are only 67 *.txt files in that directory). How should I go about fixing this problem? 

I'm running WebApollo release 2013-05-16 by the way (on an Ubuntu 64-bit server).
Thanks for your help.

Kind regards,
Ronnie



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211