MAKER v3 ERROR: Failed while processing all repeats

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MAKER v3 ERROR: Failed while processing all repeats

kapeel
Hi,

I am using MAKER v3 to update community annotation with new RNA-seq evidence data. Part of my problem is that MAKER shows below error when repeat masking. I have attached the community annotation gff, maker log and maker_opts.ctl for your reference.  I searched for this error  in the maker-dev google group and found some hints to update BLAST to 2.7, rmblast to 2.6 and reconfigure RepeatMasker which I did but it still fails with the error. Any help appreciated.

deleted:0 hits

collecting blastx repeatmasking

processing all repeats

in cluster::shadow_cluster...

Died at /mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.

--> rank=1, hostname=bnbcompute15.blacknblue.cshl.edu

ERROR: Failed while processing all repeats

ERROR: Chunk failed at level:3, tier_type:1

FAILED CONTIG:Chr06

 

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:Chr06

 
Thanks

Kapeel
--

Kapeel Chougule
Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/


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Chr06.gff (10M) Download Attachment
maker_opts.ctl (6K) Download Attachment
maker.run.log (7M) Download Attachment
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Re: MAKER v3 ERROR: Failed while processing all repeats

Carson Holt-2
Hi Kapeel,

The failure is caused by the absence of a start or end coordinate (usually caused by a BLAST report truncation - there is a BLAST bug supposably fixed now where reports were being truncated by BLAST). If you’ve done all the updates to installed tools, make sure you aslo set the location of the updated tools in maker_exe.ctl and reran the ./configure script for RepeatMasker (internal to it’s install directory) or the old tool is likely still being used.

Also if that doesn’t fix it, try the following. Use the attached file to replace …/maker/lib/Widget/RepeatMasker.pm

There is also an as of yet unfixed RepeatMasker bug where it reports a 0 value for the start/end coordinate when configured with RMBLAST (RepeatMasker uses a 1 based coordinate system, so 0 is not supposed to be possible and it only happens with RMBLAST). The change I made to the parser is a hack where I have MAKER change the RepeatMasker coordinate to 1 whenever it sees the invalid 0.

—Carson





On May 1, 2018, at 10:16 AM, Kapeel Chougule <[hidden email]> wrote:

Hi,

I am using MAKER v3 to update community annotation with new RNA-seq evidence data. Part of my problem is that MAKER shows below error when repeat masking. I have attached the community annotation gff, maker log and maker_opts.ctl for your reference.  I searched for this error  in the maker-dev google group and found some hints to update BLAST to 2.7, rmblast to 2.6 and reconfigure RepeatMasker which I did but it still fails with the error. Any help appreciated.

deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:Chr06

 

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:Chr06

 
Thanks

Kapeel
--

Kapeel Chougule
Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/

<Chr06.gff><maker_opts.ctl><maker.run.log>_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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[hidden email]
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RepeatMasker.pm (9K) Download Attachment
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Re: MAKER v3 ERROR: Failed while processing all repeats

kapeel
Thanks Carson,

It works now. I only had to replace the Repeat Masker perl module and it ran without any errors.

Best

Kapeel

On Fri, May 4, 2018 at 2:46 PM, Carson Holt <[hidden email]> wrote:
Hi Kapeel,

The failure is caused by the absence of a start or end coordinate (usually caused by a BLAST report truncation - there is a BLAST bug supposably fixed now where reports were being truncated by BLAST). If you’ve done all the updates to installed tools, make sure you aslo set the location of the updated tools in maker_exe.ctl and reran the ./configure script for RepeatMasker (internal to it’s install directory) or the old tool is likely still being used.

Also if that doesn’t fix it, try the following. Use the attached file to replace …/maker/lib/Widget/RepeatMasker.pm

There is also an as of yet unfixed RepeatMasker bug where it reports a 0 value for the start/end coordinate when configured with RMBLAST (RepeatMasker uses a 1 based coordinate system, so 0 is not supposed to be possible and it only happens with RMBLAST). The change I made to the parser is a hack where I have MAKER change the RepeatMasker coordinate to 1 whenever it sees the invalid 0.

—Carson





On May 1, 2018, at 10:16 AM, Kapeel Chougule <[hidden email]> wrote:

Hi,

I am using MAKER v3 to update community annotation with new RNA-seq evidence data. Part of my problem is that MAKER shows below error when repeat masking. I have attached the community annotation gff, maker log and maker_opts.ctl for your reference.  I searched for this error  in the maker-dev google group and found some hints to update BLAST to 2.7, rmblast to 2.6 and reconfigure RepeatMasker which I did but it still fails with the error. Any help appreciated.

deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:Chr06

 

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:Chr06

 
Thanks

Kapeel
--

Kapeel Chougule
Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/

<Chr06.gff><maker_opts.ctl><maker.run.log>_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org






--

Kapeel Chougule
Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org