substr outside of string in PhatHits_utils.pm

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substr outside of string in PhatHits_utils.pm

Ole Kristian Tørresen-2
Dear all,
I'm having an issue with MAKER which I'm unable to wrap my head around. Hopefully the issue is easily identifiable and resolvable for someone with more insight than me. Please find the log output attached below. I cannot find any more information than this in any logs. Many scaffolds do complete fine, but some of the longest ones have issues.

Thank you.

Sincerely,
Ole K. Tørresen

Error message:

#--------- command -------------#
Widget::augustus:
/projects/cees/bin/augustus/augustus-3.2.3/bin/augustus  --strand=backward --species=gadMor2_code_braker2 --UTR=off --hintsfile=/tmp/18899594.d/maker_m8xwVp/0/34_2.22239-28465.gadMor2_code_brak
er2.auto_annotator.xdef.augustus --extrinsicCfgFile=/projects/cees/bin/augustus/augustus-3.2.3/config/extrinsic/extrinsic.MPE.cfg --AUGUSTUS_CONFIG_PATH=/projects/cees/bin/augustus/augustus-3.2
.3/config /tmp/18899594.d/maker_m8xwVp/0/34_2.22239-28465.gadMor2_code_braker2.auto_annotator.augustus.fasta > /tmp/18899594.d/maker_m8xwVp/0/34_2.22239-28465.gadMor2_code_braker2.auto_annotato
r.augustus
#-------------------------------#
deleted:0 genes
begin called get_best_alt_splices1
 ...processing 0 of 2
 ...processing 1 of 2
end called get_best_alt_splices1
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
 ...processing 19 of 20
substr outside of string at /projects/cees/bin/maker/maker-3.1.1/bin/../lib/PhatHit_utils.pm line 850.
--> rank=NA, hostname=compute-31-18.local
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:GmG20150304_scaffold_8692

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:GmG20150304_scaffold_8692

examining contents of the fasta file and run log
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Re: substr outside of string in PhatHits_utils.pm

Carson Holt-2
My first guess is that if you are using gff3 files as input to anything, then there may be an  issue with your GFF3 file. My second suggestion is to try MAKER 3.02.02 to see if it has the same issue.

—Carson


> On Nov 9, 2017, at 2:44 AM, Ole Kristian Tørresen <[hidden email]> wrote:
>
> Dear all,
> I'm having an issue with MAKER which I'm unable to wrap my head around. Hopefully the issue is easily identifiable and resolvable for someone with more insight than me. Please find the log output attached below. I cannot find any more information than this in any logs. Many scaffolds do complete fine, but some of the longest ones have issues.
>
> Thank you.
>
> Sincerely,
> Ole K. Tørresen
>
> Error message:
>
> #--------- command -------------#
> Widget::augustus:
> /projects/cees/bin/augustus/augustus-3.2.3/bin/augustus  --strand=backward --species=gadMor2_code_braker2 --UTR=off --hintsfile=/tmp/18899594.d/maker_m8xwVp/0/34_2.22239-28465.gadMor2_code_brak
> er2.auto_annotator.xdef.augustus --extrinsicCfgFile=/projects/cees/bin/augustus/augustus-3.2.3/config/extrinsic/extrinsic.MPE.cfg --AUGUSTUS_CONFIG_PATH=/projects/cees/bin/augustus/augustus-3.2
> .3/config /tmp/18899594.d/maker_m8xwVp/0/34_2.22239-28465.gadMor2_code_braker2.auto_annotator.augustus.fasta > /tmp/18899594.d/maker_m8xwVp/0/34_2.22239-28465.gadMor2_code_braker2.auto_annotato
> r.augustus
> #-------------------------------#
> deleted:0 genes
> begin called get_best_alt_splices1
> ...processing 0 of 2
> ...processing 1 of 2
> end called get_best_alt_splices1
> ...processing 0 of 20
> ...processing 1 of 20
> ...processing 2 of 20
> ...processing 3 of 20
> ...processing 4 of 20
> ...processing 5 of 20
> ...processing 6 of 20
> ...processing 7 of 20
> ...processing 8 of 20
> ...processing 9 of 20
> ...processing 10 of 20
> ...processing 11 of 20
> ...processing 12 of 20
> ...processing 13 of 20
> ...processing 14 of 20
> ...processing 15 of 20
> ...processing 16 of 20
> ...processing 17 of 20
> ...processing 18 of 20
> ...processing 19 of 20
> substr outside of string at /projects/cees/bin/maker/maker-3.1.1/bin/../lib/PhatHit_utils.pm line 850.
> --> rank=NA, hostname=compute-31-18.local
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:GmG20150304_scaffold_8692
>
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:GmG20150304_scaffold_8692
>
> examining contents of the fasta file and run log
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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