ERROR: Can't call method "start" on an undefined value at ../lib/maker/join.pm line 535

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ERROR: Can't call method "start" on an undefined value at ../lib/maker/join.pm line 535

Willett, Christopher S
Hi Everyone-

I was wondering if anyone had any ideas about this error that I am seeing for some of our contigs that is causing them to fail but not others. Here is the error message:

"Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.”

This is either coming up in the augustus or snap portions of the analysis. See below for errors from 4 different contigs compiled. They are from two different runs where I was trying to exclude a couple different parts in each to see if I could isolate the problem. It seems like slightly different errors but the same contigs are failing in both.

We recently improved our genome and are trying to do a reannotation on it. I am using a very similar MAKER setup that I used previously with an earlier version of the genome and did not have any contigs fail in that case but now 8 of the 12 large contigs are failing (sizes ~18Mb). The MAKER version is 2.31.8.

If anyone has any thoughts on what the issue might be and how I could resolve it I would appreciate it (or if I should provide more information).

Thanks,

Best,

Chris Willett



error 48600

#--------- command -------------#
Widget::augustus:
/nas02/apps/maker-2.31.8/src/augustus-3.2.2/bin/augustus --species=Tigriopus_californicus --strand=forward --UTR=off --hintsfile=/tmp/maker_H_uEHb/0/19_0.1142953-1147539.Tigriopus_californicus.auto_annotator.xdef.augustus --extrinsicCfgFile=/nas02/apps/maker-2.31.8/src/augustus-3.2.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_H_uEHb/0/19_0.1142953-1147539.Tigriopus_californicus.auto_annotator.augustus.fasta > /tmp/maker_H_uEHb/0/19_0.1142953-1147539.Tigriopus_californicus.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
--> rank=NA, hostname=c-195-51.kd.unc.edu
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:Chromosome_3

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:Chromosome_3

error 48599

Widget::augustus:
/nas02/apps/maker-2.31.8/src/augustus-3.2.2/bin/augustus --species=Tigriopus_californicus --strand=forward --UTR=off --hintsfile=/tmp/maker_TQWBu_/0/49_0.7061374-7062552.Tigriopus_californicus.auto_annotator.xdef.augustus --extrinsicCfgFile=/nas02/apps/maker-2.31.8/src/augustus-3.2.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_TQWBu_/0/49_0.7061374-7062552.Tigriopus_californicus.auto_annotator.augustus.fasta > /tmp/maker_TQWBu_/0/49_0.7061374-7062552.Tigriopus_californicus.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 10
 ...processing 1 of 10
 ...processing 2 of 10
 ...processing 3 of 10
 ...processing 4 of 10
 ...processing 5 of 10
 ...processing 6 of 10
 ...processing 7 of 10
 ...processing 8 of 10
 ...processing 9 of 10
Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
--> rank=NA, hostname=c-195-51.kd.unc.edu
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:Chromosome_11

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:Chromosome_11

error 48592

#--------- command -------------#
Widget::snap:
/nas02/apps/maker-2.31.8/src/maker/exe/snap/snap -plus /proj/willetlb/users/cwillett/MAKER_analyses/SD_full/PB11_12_eukscafs_sp3_sum_hm1.hmm -xdef /tmp/maker_WADb1j/0/38_0.1656654-1673307.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.x
def.snap  /tmp/maker_WADb1j/0/38_0.1656654-1673307.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap.fasta > /tmp/maker_WADb1j/0/38_0.1656654-1673307.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
--> rank=NA, hostname=c-193-25.kd.unc.edu
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:Chromosome_5

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:Chromosome_5

error 47069

#--------- command -------------#
Widget::snap:
/nas02/apps/maker-2.31.8/src/maker/exe/snap/snap -plus /proj/willetlb/users/cwillett/MAKER_analyses/SD_full/PB11_12_eukscafs_sp3_sum_hm1.hmm -xdef /tmp/maker__PSNX1/0/53_0.6154539-6169567.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.x
def.snap  /tmp/maker__PSNX1/0/53_0.6154539-6169567.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap.fasta > /tmp/maker__PSNX1/0/53_0.6154539-6169567.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 10
 ...processing 1 of 10
 ...processing 2 of 10
 ...processing 3 of 10
 ...processing 4 of 10
 ...processing 5 of 10
 ...processing 6 of 10
 ...processing 7 of 10
 ...processing 8 of 10
 ...processing 9 of 10
Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
--> rank=NA, hostname=c-183-35.kd.unc.edu
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:Chromosome_12

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:Chromosome_12


Can't call method "start" on an undefined value at ../lib/maker/join.pm line 535.
 
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Re: ERROR: Can't call method "start" on an undefined value at ../lib/maker/join.pm line 535

Carson Holt-2
Did you use gff3 input to MAKER for any steps (example pred_gff or est_gff)?

—Carson

> On Sep 1, 2017, at 9:22 AM, Willett, Christopher S <[hidden email]> wrote:
>
> Hi Everyone-
>
> I was wondering if anyone had any ideas about this error that I am seeing for some of our contigs that is causing them to fail but not others. Here is the error message:
>
> "Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.”
>
> This is either coming up in the augustus or snap portions of the analysis. See below for errors from 4 different contigs compiled. They are from two different runs where I was trying to exclude a couple different parts in each to see if I could isolate the problem. It seems like slightly different errors but the same contigs are failing in both.
>
> We recently improved our genome and are trying to do a reannotation on it. I am using a very similar MAKER setup that I used previously with an earlier version of the genome and did not have any contigs fail in that case but now 8 of the 12 large contigs are failing (sizes ~18Mb). The MAKER version is 2.31.8.
>
> If anyone has any thoughts on what the issue might be and how I could resolve it I would appreciate it (or if I should provide more information).
>
> Thanks,
>
> Best,
>
> Chris Willett
>
>
>
> error 48600
>
> #--------- command -------------#
> Widget::augustus:
> /nas02/apps/maker-2.31.8/src/augustus-3.2.2/bin/augustus --species=Tigriopus_californicus --strand=forward --UTR=off --hintsfile=/tmp/maker_H_uEHb/0/19_0.1142953-1147539.Tigriopus_californicus.auto_annotator.xdef.augustus --extrinsicCfgFile=/nas02/apps/maker-2.31.8/src/augustus-3.2.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_H_uEHb/0/19_0.1142953-1147539.Tigriopus_californicus.auto_annotator.augustus.fasta > /tmp/maker_H_uEHb/0/19_0.1142953-1147539.Tigriopus_californicus.auto_annotator.augustus
> #-------------------------------#
> deleted:0 genes
> ...processing 0 of 5
> ...processing 1 of 5
> ...processing 2 of 5
> ...processing 3 of 5
> ...processing 4 of 5
> Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
> --> rank=NA, hostname=c-195-51.kd.unc.edu
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:Chromosome_3
>
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:Chromosome_3
>
> error 48599
>
> Widget::augustus:
> /nas02/apps/maker-2.31.8/src/augustus-3.2.2/bin/augustus --species=Tigriopus_californicus --strand=forward --UTR=off --hintsfile=/tmp/maker_TQWBu_/0/49_0.7061374-7062552.Tigriopus_californicus.auto_annotator.xdef.augustus --extrinsicCfgFile=/nas02/apps/maker-2.31.8/src/augustus-3.2.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_TQWBu_/0/49_0.7061374-7062552.Tigriopus_californicus.auto_annotator.augustus.fasta > /tmp/maker_TQWBu_/0/49_0.7061374-7062552.Tigriopus_californicus.auto_annotator.augustus
> #-------------------------------#
> deleted:0 genes
> ...processing 0 of 10
> ...processing 1 of 10
> ...processing 2 of 10
> ...processing 3 of 10
> ...processing 4 of 10
> ...processing 5 of 10
> ...processing 6 of 10
> ...processing 7 of 10
> ...processing 8 of 10
> ...processing 9 of 10
> Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
> --> rank=NA, hostname=c-195-51.kd.unc.edu
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:Chromosome_11
>
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:Chromosome_11
>
> error 48592
>
> #--------- command -------------#
> Widget::snap:
> /nas02/apps/maker-2.31.8/src/maker/exe/snap/snap -plus /proj/willetlb/users/cwillett/MAKER_analyses/SD_full/PB11_12_eukscafs_sp3_sum_hm1.hmm -xdef /tmp/maker_WADb1j/0/38_0.1656654-1673307.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.x
> def.snap  /tmp/maker_WADb1j/0/38_0.1656654-1673307.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap.fasta > /tmp/maker_WADb1j/0/38_0.1656654-1673307.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap
> #-------------------------------#
> scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
> deleted:0 genes
> ...processing 0 of 5
> ...processing 1 of 5
> ...processing 2 of 5
> ...processing 3 of 5
> ...processing 4 of 5
> Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
> --> rank=NA, hostname=c-193-25.kd.unc.edu
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:Chromosome_5
>
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:Chromosome_5
>
> error 47069
>
> #--------- command -------------#
> Widget::snap:
> /nas02/apps/maker-2.31.8/src/maker/exe/snap/snap -plus /proj/willetlb/users/cwillett/MAKER_analyses/SD_full/PB11_12_eukscafs_sp3_sum_hm1.hmm -xdef /tmp/maker__PSNX1/0/53_0.6154539-6169567.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.x
> def.snap  /tmp/maker__PSNX1/0/53_0.6154539-6169567.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap.fasta > /tmp/maker__PSNX1/0/53_0.6154539-6169567.PB11_12_eukscafs_sp3_sum_hm1.hmm.auto_annotator.snap
> #-------------------------------#
> scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
> deleted:0 genes
> ...processing 0 of 10
> ...processing 1 of 10
> ...processing 2 of 10
> ...processing 3 of 10
> ...processing 4 of 10
> ...processing 5 of 10
> ...processing 6 of 10
> ...processing 7 of 10
> ...processing 8 of 10
> ...processing 9 of 10
> Can't call method "start" on an undefined value at /nas02/apps/maker-2.31.8/src/maker/bin/../lib/maker/join.pm line 535.
> --> rank=NA, hostname=c-183-35.kd.unc.edu
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:Chromosome_12
>
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:Chromosome_12
>
>
> Can't call method "start" on an undefined value at ../lib/maker/join.pm line 535.
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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