Assertion failed: (fn), function gt_feature_node_iterator_new, file src/extended/feature_node_iterator.c, line 46.

[MaikaM]

Problem description

When I try running LTR-digest I get this error.

Exact command line call triggering the problem

$gt -j $NCPUS ltrdigest -pptlen 10 30 -trnas $prefix/GtRNAdb-all-tRNAs.fas -hmms /home/m.matsumoto/PfamA/Pfam-A.hmm -outfileprefix cgor_copia_LTR $prefix/copia_LTR.sorted.gff3 $prefix/copia_LTR_index > $prefix/copia_LTR_after_ltrdigest.gff3

Example minimal input triggering the problem

What GenomeTools version are you reporting an issue for (as output by gt -version)?

gt 1.5.10

Did you compile GenomeTools from source? If so, please state the make parameters used.

make with-hmmer=yes
make install prefix=/home/user/gt

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?

[satta]

Could you probably narrow down your input file copia_LTR.sorted.gff3 to an offending feature and make it available to us for debugging? We will need to reproduce the issue before we can start fixing it -- thanks!

[omar25-20]

I also get the same error ....
COMMAND:

gt -j 4 ltrdigest -outfileprefix Prunus_avium -trnas ./INPUT/tRNA_databas/plant_tRNA_cat.fa -hmms ./INPUT/Protein_database/*.hmm -seqfile ./INPUT/genomes/Prunus_avium.fa -matchdescstart < ./EDTA-1.8..2/Prunus_avium_sorted.gff3 > ./Prunus_avium_ltrdigest.gff3

OUTPUT:

Assertion failed: (fn), function gt_feature_node_iterator_new, file src/extended/feature_node_iterator.c, line 46.
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)

[omar25-20]

A preview of my sorted file:

##gff-version 3
##sequence-region CM024352.1 1 62324707
##sequence-region CM024353.1 1 46928806
##sequence-region CM024354.1 1 42862123
##sequence-region CM024355.1 1 37373756
##sequence-region CM024356.1 1 41299679
##sequence-region CM024357.1 1 42624765
##sequence-region CM024358.1 1 30632009
##sequence-region CM024359.1 1 38835769
#CM024352.1
#CM024353.1
#CM024354.1
#CM024355.1
#CM024356.1
#CM024357.1
#CM024358.1
#CM024359.1
CM024352.1 EDTA repeat_region 191737 201094 . ? . ID=repeat_region1
CM024352.1 EDTA target_site_duplication 191737 191741 . ? . Parent=repeat_region1
CM024352.1 EDTA LTR/unknown 191742 201089 . ? . ID=LTR/unknown1;Parent=repeat_region1;motif=TGCA;tsd=TCCAT;ltr_identity=0.9959;seq_number=0
CM024352.1 EDTA long_terminal_repeat 191742 193449 . ? . Parent=LTR/unknown1
CM024352.1 EDTA long_terminal_repeat 199383 201089 . ? . Parent=LTR/unknown1
CM024352.1 EDTA target_site_duplication 201090 201094 . ? . Parent=repeat_region1

CM024352.1 EDTA repeat_region 1617430 1629426 . ? . ID=repeat_region2
CM024352.1 EDTA target_site_duplication 1617430 1617434 . ? . Parent=repeat_region2
CM024352.1 EDTA LTR/Gypsy 1617435 1629421 . ? . ID=LTR/Gypsy1;Parent=repeat_region2;motif=TGCA;tsd=CCAAT;ltr_identity=1.0000;seq_number=0
CM024352.1 EDTA long_terminal_repeat 1617435 1619599 . ? . Parent=LTR/Gypsy1
CM024352.1 EDTA long_terminal_repeat 1627258 1629421 . ? . Parent=LTR/Gypsy1
CM024352.1 EDTA target_site_duplication 1629422 1629426 . ? . Parent=repeat_region2

CM024352.1 EDTA repeat_region 1946186 1956558 . ? . ID=repeat_region3
CM024352.1 EDTA target_site_duplication 1946186 1946190 . ? . Parent=repeat_region3
CM024352.1 EDTA LTR/unknown 1946191 1956553 . ? . ID=LTR/unknown2;Parent=repeat_region3;motif=TGCA;tsd=GTAAT;ltr_identity=0.9991;seq_number=0
CM024352.1 EDTA long_terminal_repeat 1946191 1948386 . ? . Parent=LTR/unknown2
CM024352.1 EDTA long_terminal_repeat 1954358 1956553 . ? . Parent=LTR/unknown2
CM024352.1 EDTA target_site_duplication 1956554 1956558 . ? . Parent=repeat_region3

CM024352.1 EDTA repeat_region 2203935 2208697 . ? . ID=repeat_region4
CM024352.1 EDTA target_site_duplication 2203935 2203938 . ? . Parent=repeat_region4
CM024352.1 EDTA LTR/Gypsy 2203939 2208693 . ? . ID=LTR/Gypsy2;Parent=repeat_region4;motif=TGCA;tsd=AATT;ltr_identity=0.9921;seq_number=0
CM024352.1 EDTA long_terminal_repeat 2203939 2204568 . ? . Parent=LTR/Gypsy2
CM024352.1 EDTA long_terminal_repeat 2208064 2208693 . ? . Parent=LTR/Gypsy2
CM024352.1 EDTA target_site_duplication 2208694 2208697 . ? . Parent=repeat_region4

CM024352.1 EDTA repeat_region 2418427 2436960 . ? . ID=repeat_region5
CM024352.1 EDTA target_site_duplication 2418427 2418431 . ? . Parent=repeat_region5
CM024352.1 EDTA LTR/unknown 2418432 2436955 . ? . ID=LTR/unknown3;Parent=repeat_region5;motif=TGCA;tsd=GAATA;ltr_identity=0.9945;seq_number=0
CM024352.1 EDTA long_terminal_repeat 2418432 2420445 . ? . Parent=LTR/unknown3
CM024352.1 EDTA long_terminal_repeat 2434948 2436955 . ? . Parent=LTR/unknown3
CM024352.1 EDTA target_site_duplication 2436956 2436960 . ? . Parent=repeat_region5

CM024352.1 EDTA repeat_region 2423283 2432123 . ? . ID=repeat_region6
CM024352.1 EDTA target_site_duplication 2423283 2423287 . ? . Parent=repeat_region6
CM024352.1 EDTA LTR/unknown 2423288 2432118 . ? . ID=LTR/unknown4;Parent=repeat_region6;motif=TGCA;tsd=GTCAC;ltr_identity=0.9988;seq_number=0
CM024352.1 EDTA long_terminal_repeat 2423288 2424944 . ? . Parent=LTR/unknown4
CM024352.1 EDTA long_terminal_repeat 2430481 2432118 . ? . Parent=LTR/unknown4
CM024352.1 EDTA target_site_duplication 2432119 2432123 . ? . Parent=repeat_region6