[maker-devel] MAKER RepeatRunner error on long scaffolds only

[Carson Holt]

The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.

—Carson


> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi all,
> 
> I’ve been having an issue with MAKER (v. 2.31.8) that I haven’t been able to overcome, and no former questions have really addressed or helped fix the problem. I’ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
> 
> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can’t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I’m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
> 
> Any help would be greatly appreciated.
> Daren Card
> 
> University of Texas Arlington
> 
> ###################################################
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
> #-------------------------------#
> deleted:0 hits
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=3, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
> #-------------------------------#
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> deleted:0 hits
> deleted:0 hits
> ###################################################
> 
> 
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