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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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utrrnaseq segmentation fault #11

Closed rorycraig337 closed 5 years ago

rorycraig337 commented 5 years ago

Hi,

I am running BRAKER with UTR prediction, and I have spit my RNA-seq into plus and minus strands as recommended here: https://www.biostars.org/p/92935/

My command is:

braker.pl --species=c_incerta_v1.3 --genome=../../repeat_masking/Chlamydomonas_incerta.V3.softmask_v1.fa --softmasking --bam=../plus.bam,../minus.bam --stranded=+,- --UTR=on –-cores=16 --PYTHON3_PATH=/usr/local/bin/

I am getting the following segmentation fault error to standard out:

sh: line 1: 132194 Segmentation fault /home/craigror/programs/augustus-3.3.1/config//../bin/utrrnaseq --in-scaffold-file /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/genome.fa -C /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/stops.and.starts.gff -I /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/rnaseq.utr.hints -W /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/rnaseq_plus.wig -o /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/utrs_plus.gff -r 76 -v 100 -n 15 -i 0.7 -m 0.3 -w 70 -c 100 -p 0.5 > /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/rnaseq2utr_plus.stdout 2> /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/errors/rnaseq2utr_plus.err ERROR in file /home/craigror/programs/BRAKER/scripts/braker.pl at line 8496 Failed to execute: /home/craigror/programs/augustus-3.3.1/config//../bin/utrrnaseq --in-scaffold-file /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/genome.fa -C /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/stops.and.starts.gff -I /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/rnaseq.utr.hints -W /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/rnaseq_plus.wig -o /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/utrs_plus.gff -r 76 -v 100 -n 15 -i 0.7 -m 0.3 -w 70 -c 100 -p 0.5 1> /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/rnaseq2utr_plus.stdout 2> /scratch/research/projects/chlamydomonas/Cincerta_deNovo/analysis/assembly_V3/BRAKER2/run_v1.3/braker/c_incerta_v1.3/errors/rnaseq2utr_plus.err!

The file rnaseq2utr_plus.stdout contains:

Read in of scaffold file finished successfully! Read in of coding region file finished successfully! Read in of intron file finished successfully! Input Data procession finished successfully!

and rnaseq2utr_plus.err is empty. I can reproduce the fault if I run the final utrrnaseq command by itself. Any help would be much appreciated.

Cheers, Rory

KatharinaHoff commented 5 years ago

Hi Rory, thank you very much for reporting this. Can you build a small toy dataset from your data to reproduce the error and share it with us (katharina.hoff[at]uni-greifswald[dot].de). I mean, only a toy data set for utrrnaseq (the command that you ran outside of braker.pl). Best, Katharina

rorycraig337 commented 5 years ago

Hi Katharina, Thanks for following this up. I've not been able to replicate this on a toy data set, and after a bit of trial and error subsampling the genome the segmentation fault only appears to happen somewhere between running the command with 100 and 150 contigs (out of a total of 451 contigs). For context, 100 contigs contains ~90% of the 130 Mb genome. rnaseq2utr_plus.err is empty, and rnaseq2utr_plus.stdout contains:

Read in of scaffold file finished successfully! Read in of coding region file finished successfully! Read in of intron file finished successfully! Input Data procession finished successfully!

I'm also getting an error reported to when running without UTR prediction ("failed to execute optimize_augustus.pl"), although BRAKER finishes successfully, and I don't see this when running with UTR prediction. I'm going to try a new install on a different server and see if I can replicate the error there - will report back.

Thanks, Rory

rorycraig337 commented 5 years ago

All running smoothly with a new install of BRAKER, Augustus etc. on a different server. So possibly the fault was down to a system specific issue, or a problem with my initial installation? Either way, problem is fixed, thanks!

KatharinaHoff commented 5 years ago

Glad to hear that. Issue closes :-)