Maker problem

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Maker problem

Jan FABI
Dear Maker team

I am experiencing a problem while running maker and cannot find a solution to it online.

I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered.

This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns.

I include the relevant portion of the log below. Could you help me determine the cause of this error.



setting up GFF3 output and fasta chunks
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx-VirtualBox
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

--
Regards
Jan Nagel
----------------------------------------------------------------------
PhD Genetics student
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
FABI 1, Room 1-55
University of Pretoria
74 Lunnon Rd. Hillcrest
0002
Gauteng Province
South Africa

Email : [hidden email]

Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961

This message and attachments are subject to a disclaimer.
Please refer to http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf 
for full details.

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Maker problem

Carson Holt-2
If you look in the folder of the failed contig under the .../theVoid directory there will be a file called query.masked.fasta.

Copy that file somewhere. Then because maker gave you the command that failed, you can run it all by itself outside of MAKER

Example —> 
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off query.masked.fasta

If it still fails, you now have a test file and command you can send to Mario Stanke ([hidden email]). He made Augustus. It may be a bug he has already fixed (current Augustus version is 3.3) or there may be something in the species file causing the error that he can point out.

—Carson


On Oct 12, 2017, at 1:37 AM, Jan FABI <[hidden email]> wrote:

Dear Maker team

I am experiencing a problem while running maker and cannot find a solution to it online.

I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered.

This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns.

I include the relevant portion of the log below. Could you help me determine the cause of this error.



setting up GFF3 output and fasta chunks
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx-VirtualBox
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

--
Regards
Jan Nagel
----------------------------------------------------------------------
PhD Genetics student
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
FABI 1, Room 1-55
University of Pretoria
74 Lunnon Rd. Hillcrest
0002
Gauteng Province
South Africa

Email : [hidden email]

Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961

This message and attachments are subject to a disclaimer.
Please refer to http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf 
for full details.
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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