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Aborted (core dumped) with LTR digest #995
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Are you sure there are no more lines before the "This is a bug" line? I would need those to locate the issue, as they describe the error context. |
Thanks for the reply. To date I have solved the problem by giving ltr digest the output obtained from the EDTA 1.6 version. The above error appeared only when using the EDTA version 1.9 outputs. `tRNAs="/home/omar-almulla/Desktop/Prunus_TE_project/INPUT/Hmm_trna" gt -j 4 ltrdigest -outfileprefix Prunus_avium_NCBI_ltr -trnas $tRNAs/plants-tRNA_cat.fa -hmms $proteins/hmm_* -seqfile $genome/Prunus_avium_NCBI_genomic.fna -matchdescstart $EDTA_output_1_6_path/Prunus_avium_NCBI_genomic.fna.LTR.intact.fa_SORTED_.1.6.gff3 > $output/Prunus_avium_NCBI_digest.gff |
I see. I'll keep this one open but can not do much without the test data. I am unfortunately not familiar with EDTA or LTRpred but perhaps that tool creates weird GFF3 structure? Anyway, could you please still share the line you got before the "this is a bug, please report" line, if that's OK for you? It should contain something like "Assertion failed: ..." and would at least help us place the error somewhere, and also make this issue searchable for others with a similar problem. |
My script:
I could not replicate the same error. Now appear: Segmentation fault (core dumped) |
##gff-version 3 CM024352.1 EDTA repeat_region 1617430 1629426 . ? . ID=repeat_region2;name=CM024352.1:1617435..1629421;classification=LTR/Gypsy;sequence_ontology=SO:0000657;ltr_identity=1.0000;mathod=structural;motif=TGCA;tsd=CCAAT CM024352.1 EDTA repeat_region 1946186 1956558 . ? . ID=repeat_region3;name=CM024352.1:1946191..1956553;classification=LTR/unknown;sequence_ontology=SO:0000657;ltr_identity=0.9991;mathod=structural;motif=TGCA;tsd=GTAAT |
I am afraid the GFF3 file is not enough for me to replicate the issue, I would also need the other files (sequence FASTA and tRNA files). Basically I need a way to trigger the error on my side with your command line call. Thanks! |
Problem description
While using LTRdigest this error always pops up (which also appears in R studio using ltr digest via the LTRpred package)
This is a bug, please report it at
https://github.com/genometools/genometools/issues
Please make sure you are running the latest release which can be found at
http://genometools.org/pub/
You can check your version number with
gt -version
.Aborted (core dumped)
Exact command line call triggering the problem
What GenomeTools version are you reporting an issue for (as output by
gt -version
)?gt (GenomeTools) 1.6.2
Copyright (c) 2003-2016 G. Gremme, S. Steinbiss, S. Kurtz, and CONTRIBUTORS
Copyright (c) 2003-2016 Center for Bioinformatics, University of Hamburg
See LICENSE file or http://genometools.org/license.html for license details.
Used compiler: cc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Compile flags: -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -Wno-unknown-pragmas -O3 -Werror
What operating system (e.g. Ubuntu, Mac OS X), OS version (e.g. 15.10, 10.11) and platform (e.g. x86_64) are you using?
Ubuntu 20.04
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