Entering edit mode
4.7 years ago
O.rka
▴
710
I'm using the funannotate pipeline and it fails during the augustus step. I found which command it was running and tried running it outside of funannotate and got the following error. How do I fix this? I installed on linux server via conda.
augustus --stopCodonExcludedFromCDS=False --codingseq=1 --proteinprofile=/usr/local/scratch/METAGENOMICS/jespinoz/db/funannotate_db/dikarya/prfl/EOG092644X6.prfl --predictionStart=109668 --predictionEnd=120165 --species=anidulans test-predict_202108/annotate/predict_misc/busco/tmp/CP022970.1saccharomyces_4117535203_.temp
Segmentation fault (core dumped)
Is there a way to test my augustus installation?
Here's the head of my augustus log from funannotate:
(funannotate_env) -bash-4.1$ head -n 30 test-predict_239889/annotate/logfiles/busco.log
INFO ****************** Start a BUSCO 2.0 analysis, current time: 08/22/2019 16:58:15 ******************
INFO The lineage dataset is: dikarya_odb9 (eukaryota)
INFO Mode is: genome
INFO Maximum number of regions limited to: 3
INFO To reproduce this run: python /usr/local/devel/ANNOTATION/jespinoz/Packages/Funannotate-1.6.0/util/funannotate-BUSCO2.py -i /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/genome.softmasked.fa -o saccharomyces -l /usr/local/scratch/METAGENOMICS/jespinoz/db/funannotate_db/dikarya/ -m genome -c 4 -sp anidulans
INFO Check dependencies...
INFO Check input file...
INFO Temp directory is ./tmp/
INFO ****** Phase 1 of 2, initial predictions ******
INFO ****** Step 1/3, current time: 08/22/2019 16:58:17 ******
INFO Create blast database...
INFO [makeblastdb] Building a new DB, current time: 08/22/2019 16:58:18
INFO [makeblastdb] New DB name: /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/tmp/saccharomyces_664759016
INFO [makeblastdb] New DB title: /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/genome.softmasked.fa
INFO [makeblastdb] Sequence type: Nucleotide
INFO [makeblastdb] Keep MBits: T
INFO [makeblastdb] Maximum file size: 1000000000B
INFO [makeblastdb] Adding sequences from FASTA; added 6 sequences in 0.0955939 seconds.
INFO Running tblastn, writing output to /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/blast_output/tblastn_saccharomyces.tsv...
INFO ****** Step 2/3, current time: 08/22/2019 16:58:55 ******
INFO Getting coordinates for candidate regions...
INFO Pre-Augustus scaffold extraction...
INFO Running Augustus prediction using anidulans as species:
INFO [augustus] Please find all logs related to Augustus here: /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/augustus_output/augustus.log
INFO 08/22/2019 16:58:55 => 0% of predictions performed (743 to be done)
INFO [augustus] /bin/sh: line 1: 5413 Segmentation fault (core dumped) augustus --stopCodonExcludedFromCDS=False --codingseq=1 --proteinprofile=/usr/local/scratch/METAGENOMICS/jespinoz/db/funannotate_db/dikarya/prfl/EOG09261JCQ.prfl --predictionStart=306979 --predictionEnd=317740 --species=anidulans './tmp/CP022972.1saccharomyces_664759016_.temp' > /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/augustus_output/predicted_genes/EOG09261JCQ.out.1 2>> /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/augustus_output/augustus.log
INFO [augustus] /bin/sh: line 1: 5410 Segmentation fault (core dumped) augustus --stopCodonExcludedFromCDS=False --codingseq=1 --proteinprofile=/usr/local/scratch/METAGENOMICS/jespinoz/db/funannotate_db/dikarya/prfl/EOG092644X6.prfl --predictionStart=209773 --predictionEnd=220234 --species=anidulans './tmp/CP022970.1saccharomyces_664759016_.temp' > /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/augustus_output/predicted_genes/EOG092644X6.out.2 2>> /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/augustus_output/augustus.log
INFO [augustus] /bin/sh: line 1: 5411 Segmentation fault (core dumped) augustus --stopCodonExcludedFromCDS=False --codingseq=1 --proteinprofile=/usr/local/scratch/METAGENOMICS/jespinoz/db/funannotate_db/dikarya/prfl/EOG092644X6.prfl --predictionStart=126869 --predictionEnd=137222 --species=anidulans './tmp/CP022971.1saccharomyces_664759016_.temp' > /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/augustus_output/predicted_genes/EOG092644X6.out.3 2>> /local/ifs2_projdata/0568/projects/PLANKTON/illumina_aallen/jespinoz/testing/test-predict_239889/annotate/predict_misc/busco/run_saccharomyces/augustus_output/augustus.log
