Curious error Need help to understand and troubleshoot

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Curious error Need help to understand and troubleshoot

abhijit.synl@gmail.com
Hello All,

I am loading into Apollo fasta files (Refseq) and gff3 annotation files. The prepare-refseqs.pl and the flatfile-to-json.pl commands run OK for the refseq and most of the annotation tracks. except for spaln. When I run the following command

"/app/Apollo/bin/flatfile-to-json.pl --gff /annotation/Apollo-TEMP/spaln.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel SPALN --out /annotation/genome/2496/data/

I get the following error

Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Load2Apollo_2496_genome.sh: line 34: 25499 Killed                  /app/Apollo/bin/flatfile-to-json.pl --gff /annotation/Apollo-TEMP/spaln.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel SPALN --out /annotation/genome/2496/data/

The command after that which is generate-names.pl runs ok. In Apollo I am able to see all the tracks except that for SPALN... because the execution was killed. How do I rectify this error. I am on Apollo 2.0.4

Thank u,





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Re: Curious error Need help to understand and troubleshoot

Deepak Unni
Hi Abhijit,

Those "Deep recursion" messages are warnings and not errors thrown by the referenced perl module. But even I am curious as to why your shell script failed.

Would it be possible for you to share the GFF3 (spaln.gff3)? If you feel uncomfortable sharing it on the mailing list then you can send it to my email address: [hidden email]

Cheers,

Deepak



On Sun, Sep 10, 2017 at 9:20 AM, Abhijit Sanyal <[hidden email]> wrote:
Hello All,

I am loading into Apollo fasta files (Refseq) and gff3 annotation files. The prepare-refseqs.pl and the flatfile-to-json.pl commands run OK for the refseq and most of the annotation tracks. except for spaln. When I run the following command

"/app/Apollo/bin/flatfile-to-json.pl --gff /annotation/Apollo-TEMP/spaln.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel SPALN --out /annotation/genome/2496/data/

I get the following error

Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Load2Apollo_2496_genome.sh: line 34: 25499 Killed                  /app/Apollo/bin/flatfile-to-json.pl --gff /annotation/Apollo-TEMP/spaln.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel SPALN --out /annotation/genome/2496/data/

The command after that which is generate-names.pl runs ok. In Apollo I am able to see all the tracks except that for SPALN... because the execution was killed. How do I rectify this error. I am on Apollo 2.0.4

Thank u,





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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Re: Curious error Need help to understand and troubleshoot

Deepak Unni
For future reference:

The input GFF3 was 1.1 GB in size, which means flatfile-to-json.pl had to parse through millions of records.
The quick solution to this problem is to split your GFF3 into smaller chunks - preferably based on chromosomes and then run flatfile-to-json.pl on each one of them as follows:

bin/flatfile-to-json.pl --gff features_chr1.gff3 --out data --trackLabel "My Features" 

bin/flatfile-to-json.pl --gff features_chr2.gff3 --out data --trackLabel "My Features"


Keeping the trackLabel same will ensure that all the data end up on the same track.

Cheers,

Deepak

On Sun, Sep 10, 2017 at 9:31 PM, Deepak Unni <[hidden email]> wrote:
Hi Abhijit,

Those "Deep recursion" messages are warnings and not errors thrown by the referenced perl module. But even I am curious as to why your shell script failed.

Would it be possible for you to share the GFF3 (spaln.gff3)? If you feel uncomfortable sharing it on the mailing list then you can send it to my email address: [hidden email]

Cheers,

Deepak



On Sun, Sep 10, 2017 at 9:20 AM, Abhijit Sanyal <[hidden email]> wrote:
Hello All,

I am loading into Apollo fasta files (Refseq) and gff3 annotation files. The prepare-refseqs.pl and the flatfile-to-json.pl commands run OK for the refseq and most of the annotation tracks. except for spaln. When I run the following command

"/app/Apollo/bin/flatfile-to-json.pl --gff /annotation/Apollo-TEMP/spaln.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel SPALN --out /annotation/genome/2496/data/

I get the following error

Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Deep recursion on subroutine "LazyNCList::iterHelper" at /app/Apollo-2.0.4/bin/../src/perl5/LazyNCList.pm line 260.
Load2Apollo_2496_genome.sh: line 34: 25499 Killed                  /app/Apollo/bin/flatfile-to-json.pl --gff /annotation/Apollo-TEMP/spaln.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel SPALN --out /annotation/genome/2496/data/

The command after that which is generate-names.pl runs ok. In Apollo I am able to see all the tracks except that for SPALN... because the execution was killed. How do I rectify this error. I am on Apollo 2.0.4

Thank u,





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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.