Question: (Closed) Segmentation fault (core dumped) when running augustus
0
gravatar for O.rka
29 days ago by
O.rka120
O.rka120 wrote:

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
annotation genome augustus • 158 views
ADD COMMENTlink written 29 days ago by O.rka120
2

Segmentation faults are almost always related to available RAM (or, rather, the lack of available RAM). Please verify how much you have available to you.

ADD REPLYlink modified 29 days ago • written 29 days ago by Kevin Blighe48k
1

If the issue isn't RAM then please post an issue on github: https://github.com/Gaius-Augustus/Augustus

ADD REPLYlink written 29 days ago by Devon Ryan92k

I'm not sure if it's a memory issue: I ran this same command on a previous installation of funannotate and it worked. Here's my memory: (base) -bash-4.1$ free total used free shared buffers cached Mem: 8030344 7767784 262560 0 215704 7074324 -/+ buffers/cache: 477756 7552588 Swap: 8388604 135068 8253536

I tried running it on our server then using qsub on our high memory cluster. I got the same error both times. I've posted the error on GitHub but I haven't gotten any helpful responses for debugging this: https://github.com/Gaius-Augustus/Augustus/issues/75

The command I ran was: funannotate test -t all --cpus 4

Is there a way to test my augustus installation?

ADD REPLYlink written 26 days ago by O.rka120

Please see Devon's comment and post it on the GitHub issues page. In fact, you already did, 5 days ago: https://github.com/Gaius-Augustus/Augustus/issues/75

ADD REPLYlink written 26 days ago by Kevin Blighe48k

I posted it here b/c I wasn't getting any responses on GitHub. Do you recommend any other resources?

ADD REPLYlink written 26 days ago by O.rka120

No, well, the GitHub page is where the authors of the package are responding to you. KatharinaHoff just responded a few minutes ago.

ADD REPLYlink written 26 days ago by Kevin Blighe48k
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