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

Tue Sep 5 14:56:01 MDT 2017

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 <willett4 at email.unc.edu> 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.
> 
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