how to output masked genome from MAKER

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how to output masked genome from MAKER

Valerie Soza
Hi MAKER community

I am wondering whether it is possible to get the entire masked genome generated by MAKER as an output. I think I have found it in pieces in the query.masked.fasta files generated for each scaffold by MAKER in theVoid directories. Is there a script that anyone has used to collate these files?

I am aware of the fast_merge script that comes bundled with MAKER, but it does not seem to collate the query.masked.fasta files. Could this perl script be modified to do this action?

Thanks for any help or insights.

-Valerie

Valerie Soza, Ph.D.
c/o Hall Lab
Department of Biology
University of Washington
Johnson Hall 202A
Box 351800
Seattle, WA 98195-1800
206-543-6740
http://staff.washington.edu/vsoza/


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Re: how to output masked genome from MAKER

Carson Holt-2
You will just have to find and concatenate the files yourself.

Something like —> find assembly.maker.output -name 'query.masked.fasta' | xargs cat > assembly_masked.fasta

—Carson


> On Mar 7, 2018, at 2:19 PM, Valerie Soza <[hidden email]> wrote:
>
> Hi MAKER community
>
> I am wondering whether it is possible to get the entire masked genome generated by MAKER as an output. I think I have found it in pieces in the query.masked.fasta files generated for each scaffold by MAKER in theVoid directories. Is there a script that anyone has used to collate these files?
>
> I am aware of the fast_merge script that comes bundled with MAKER, but it does not seem to collate the query.masked.fasta files. Could this perl script be modified to do this action?
>
> Thanks for any help or insights.
>
> -Valerie
>
> Valerie Soza, Ph.D.
> c/o Hall Lab
> Department of Biology
> University of Washington
> Johnson Hall 202A
> Box 351800
> Seattle, WA 98195-1800
> 206-543-6740
> http://staff.washington.edu/vsoza/
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: how to output masked genome from MAKER

Valerie Soza
Hi Carson

Thanks, that is simple and it worked.

I did the following to sort and concatenate the query.masked.fasta files into one fasta:

$ find Rwill7.maker.output -name 'query.masked.fasta' | sort -t "/" -k 5 | xargs cat > Rwill7.maker.assembly_masked.sorted.fasta

-Valerie

> On Mar 15, 2018, at 8:31 AM, Carson Holt <[hidden email]> wrote:
>
> You will just have to find and concatenate the files yourself.
>
> Something like —> find assembly.maker.output -name 'query.masked.fasta' | xargs cat > assembly_masked.fasta
>
> —Carson
>
>
>> On Mar 7, 2018, at 2:19 PM, Valerie Soza <[hidden email]> wrote:
>>
>> Hi MAKER community
>>
>> I am wondering whether it is possible to get the entire masked genome generated by MAKER as an output. I think I have found it in pieces in the query.masked.fasta files generated for each scaffold by MAKER in theVoid directories. Is there a script that anyone has used to collate these files?
>>
>> I am aware of the fast_merge script that comes bundled with MAKER, but it does not seem to collate the query.masked.fasta files. Could this perl script be modified to do this action?
>>
>> Thanks for any help or insights.
>>
>> -Valerie
>>
>> Valerie Soza, Ph.D.
>> c/o Hall Lab
>> Department of Biology
>> University of Washington
>> Johnson Hall 202A
>> Box 351800
>> Seattle, WA 98195-1800
>> 206-543-6740
>> http://staff.washington.edu/vsoza/
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> [hidden email]
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

Valerie Soza, Ph.D.
c/o Hall Lab
Department of Biology
University of Washington
Johnson Hall 202A
Box 351800
Seattle, WA 98195-1800
206-543-6740
http://staff.washington.edu/vsoza/


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August failing for one contig only during Maker run

Aditi Rambani
In reply to this post by Carson Holt-2

Hello, 


Maker successfully annotated the genome but keeps failing for one contig with error message attached below. Can you please help me troubleshoot this ? There is no issue with augustus for rest of the contigs. 


Thank you


Aditi 


#--------- command -------------#
Widget::augustus:
~/augustus-3.2/bin/augustus --species=Cxxx --strand=forward --UTR=off --hintsfile=/tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.xdef.augustus --extrinsicCfgFile=/data/home/srs57/programs/augustus-3.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus.fasta > /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus
#-------------------------------#
Sampling error in intron model. state=14 base=4422

~/augustus-3.2/bin/augustus: ERROR
Tried to sample from empty list.

Sampling error in intron model. state=14 base=4422
~/augustus-3.2/bin/augustus: ERROR
Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:Contigxxx

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:Contigxxx

examining contents of the fasta file and run log



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Re: August failing for one contig only during Maker run

Carson Holt-2
The failure is internal to Augustus. Try updating Augustus to 3.3. If it still fails after that let me know. We will have to isolate the command and files used, so you can send it as a test dataset to the Augustus devlopers.

—Carson

On Apr 20, 2018, at 8:47 AM, Aditi Rambani <[hidden email]> wrote:

Hello, 

Maker successfully annotated the genome but keeps failing for one contig with error message attached below. Can you please help me troubleshoot this ? There is no issue with augustus for rest of the contigs. 

Thank you

Aditi 

#--------- command -------------#
Widget::augustus:
~/augustus-3.2/bin/augustus --species=Cxxx --strand=forward --UTR=off --hintsfile=/tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.xdef.augustus --extrinsicCfgFile=/data/home/srs57/programs/augustus-3.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus.fasta > /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus
#-------------------------------#
Sampling error in intron model. state=14 base=4422

~/augustus-3.2/bin/augustus: ERROR
Tried to sample from empty list.

Sampling error in intron model. state=14 base=4422
~/augustus-3.2/bin/augustus: ERROR
Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:Contigxxx

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:Contigxxx

examining contents of the fasta file and run log


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