arriba
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Published
20 hours ago •
suhrig
suhrig
Segmentation fault on Re-aligning chimeric reads to filter fusions
Hello,
I have an error Segmentation fault when I run arriba v2.4.0. I tried to debug with gdb.
Below, you can find all the logs.
(gdb) run -x /data/sample.bam -o /data/sample_arriba_standard.tsv -O /data/sample_arriba_discarded_standard.tsv -a /data/GRCh37.fa -g /data/ensembl.gtf.gz -b /data/blacklist.tsv.gz -u
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[2023-06-02T11:55:46] Launching Arriba 2.4.0
[2023-06-02T11:55:46] Loading assembly from '/data/GRCh37.fa'
[2023-06-02T11:55:54] Loading annotation from '/data/ensembl.gtf.gz'
[2023-06-02T11:55:57] Reading chimeric alignments from '/data/sample.bam' (total=WARNING: 236 SAM records were malformed and ignored
16969)
[2023-06-02T11:55:58] Marking multi-mapping alignments (marked=4156)
[2023-06-02T11:55:58] Detecting strandedness (no)
[2023-06-02T11:55:58] Annotating alignments
[2023-06-02T11:55:58] Filtering duplicates (remaining=16969)
[2023-06-02T11:55:58] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=16961)
[2023-06-02T11:55:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=16961)
[2023-06-02T11:55:58] Filtering viral contigs with expression lower than the top 5 (remaining=16961)
[2023-06-02T11:55:58] Filtering viral contigs with less than 5% coverage (remaining=16961)
[2023-06-02T11:55:58] Estimating fragment length WARNING: not enough chimeric reads to estimate mate gap distribution, using default values
[2023-06-02T11:55:58] Filtering read-through fragments with a distance <=10000bp (remaining=15815)
[2023-06-02T11:55:58] Filtering inconsistently clipped mates (remaining=15685)
[2023-06-02T11:55:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=15670)
[2023-06-02T11:55:58] Filtering fragments with small insert size (remaining=15446)
[2023-06-02T11:55:58] Filtering alignments with long gaps (remaining=15446)
[2023-06-02T11:55:58] Filtering fragments with both mates in the same gene (remaining=15444)
[2023-06-02T11:55:58] Filtering fusions arising from hairpin structures (remaining=15110)
[2023-06-02T11:55:58] Filtering reads with a mismatch p-value <=0.01 (remaining=2292)
[2023-06-02T11:55:58] Filtering reads with low entropy (k-mer content >=60%) (remaining=1850)
[2023-06-02T11:55:58] Finding fusions and counting supporting reads (total=WARNING: some fusions were subsampled, because they have more than 300 supporting reads
1983)
[2023-06-02T11:55:58] Merging adjacent fusion breakpoints (remaining=1980)
[2023-06-02T11:55:58] Filtering multi-mapping fusions by alignment score and read support (remaining=1795)
[2023-06-02T11:55:58] Estimating expected number of fusions by random chance (e-value)
[2023-06-02T11:55:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1749)
[2023-06-02T11:55:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1696)
[2023-06-02T11:55:58] Filtering fusions with <2 supporting reads (remaining=62)
[2023-06-02T11:55:58] Filtering fusions with an e-value >=0.3 (remaining=50)
[2023-06-02T11:55:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=51)
[2023-06-02T11:55:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=37)
[2023-06-02T11:55:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=15)
[2023-06-02T11:55:58] Searching for fusions with spliced split reads (remaining=15)
[2023-06-02T11:55:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=13)
[2023-06-02T11:55:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=13)
[2023-06-02T11:55:58] Searching for fusions with >=4 spliced events (remaining=13)
[2023-06-02T11:55:58] Filtering blacklisted fusions in '/data/blacklist.tsv.gz' (remaining=WARNING: unknown gene or malformed range: 2:87565634-87566158 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:87565634-87566158 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:87565634-87566158 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:91679087-91679734 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:91679087-91679734 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:91679087-91679734 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:92005797-92006650 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:92005797-92006650 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:92005797-92006650 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:97712325-97712628 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:97712325-97712628 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:97712325-97712628 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:97716466-97716765 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:97716466-97716765 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:97716466-97716765 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:97725682-97726152 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:97725682-97726152 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:97725682-97726152 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:97987331-97987617 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:97987331-97987617 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:97987331-97987617 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:97996726-97997025 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:97996726-97997025 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:97996726-97997025 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:98000864-98001167 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:98000864-98001167 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:98000864-98001167 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:98018364-98018640 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:98018364-98018640 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:98018364-98018640 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:98024520-98024800 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:98024520-98024800 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:98024520-98024800 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:98037725-98038028 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:98037725-98038028 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:98037725-98038028 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:98041867-98042166 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:98041867-98042166 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:98041867-98042166 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:98051276-98051562 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:98051276-98051562 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:98051276-98051562 14 106053226-107288019
WARNING: unknown gene or malformed range: 2:114163973-114164486 22 22380474-23922495
WARNING: unknown gene or malformed range: 2:114163973-114164486 2 89156674-90458671
WARNING: unknown gene or malformed range: 2:114163973-114164486 14 106053226-107288019
WARNING: unknown gene or malformed range: 8:48114067-48114520 22 22380474-23922495
WARNING: unknown gene or malformed range: 8:48114067-48114520 2 89156674-90458671
WARNING: unknown gene or malformed range: 8:48114067-48114520 14 106053226-107288019
WARNING: unknown gene or malformed range: 9:69777099-69777953 22 22380474-23922495
WARNING: unknown gene or malformed range: 9:69777099-69777953 2 89156674-90458671
WARNING: unknown gene or malformed range: 9:69777099-69777953 14 106053226-107288019
WARNING: unknown gene or malformed range: 9:70394238-70395090 22 22380474-23922495
WARNING: unknown gene or malformed range: 9:70394238-70395090 2 89156674-90458671
WARNING: unknown gene or malformed range: 9:70394238-70395090 14 106053226-107288019
WARNING: unknown gene or malformed range: 10:42680787-42681239 22 22380474-23922495
WARNING: unknown gene or malformed range: 10:42680787-42681239 2 89156674-90458671
WARNING: unknown gene or malformed range: 10:42680787-42681239 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20169919-20170354 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20169919-20170354 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20169919-20170354 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20178035-20178471 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20178035-20178471 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20178035-20178471 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20192909-20193370 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20192909-20193370 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20192909-20193370 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20209093-20209115 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20209093-20209115 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20209093-20209115 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20210050-20210068 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20210050-20210068 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20210050-20210068 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20211158-20211188 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20211158-20211188 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20211158-20211188 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20213655-20213685 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20213655-20213685 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20213655-20213685 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20216406-20216422 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20216406-20216422 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20216406-20216422 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:20844768-20845194 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:20844768-20845194 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:20844768-20845194 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:21215823-21215845 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:21215823-21215845 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:21215823-21215845 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:21216780-21216798 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:21216780-21216798 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:21216780-21216798 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:21217888-21217918 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:21217888-21217918 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:21217888-21217918 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:21220377-21220407 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:21220377-21220407 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:21220377-21220407 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:21223129-21223145 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:21223129-21223145 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:21223129-21223145 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:22448382-22448819 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:22448382-22448819 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:22448382-22448819 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:22466058-22466493 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:22466058-22466493 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:22466058-22466493 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:22472918-22473353 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:22472918-22473353 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:22472918-22473353 14 106053226-107288019
WARNING: unknown gene or malformed range: 15:22482836-22483268 22 22380474-23922495
WARNING: unknown gene or malformed range: 15:22482836-22483268 2 89156674-90458671
WARNING: unknown gene or malformed range: 15:22482836-22483268 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:32046174-32046647 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:32046174-32046647 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:32046174-32046647 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:32070405-32070693 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:32070405-32070693 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:32070405-32070693 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:32077386-32077679 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:32077386-32077679 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:32077386-32077679 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:32859034-32859477 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:32859034-32859477 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:32859034-32859477 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:32914763-32915215 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:32914763-32915215 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:32914763-32915215 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:32926395-32926857 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:32926395-32926857 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:32926395-32926857 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:32989782-32990212 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:32989782-32990212 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:32989782-32990212 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33006369-33006826 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33006369-33006826 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33006369-33006826 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33013654-33013942 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33013654-33013942 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33013654-33013942 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33020496-33020941 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33020496-33020941 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33020496-33020941 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33605231-33605684 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33605231-33605684 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33605231-33605684 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33629681-33630128 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33629681-33630128 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33629681-33630128 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33661363-33661819 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33661363-33661819 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33661363-33661819 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33740804-33741266 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33740804-33741266 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33740804-33741266 14 106053226-107288019
WARNING: unknown gene or malformed range: 16:33752443-33752887 22 22380474-23922495
WARNING: unknown gene or malformed range: 16:33752443-33752887 2 89156674-90458671
WARNING: unknown gene or malformed range: 16:33752443-33752887 14 106053226-107288019
WARNING: unknown gene or malformed range: 18:3394887-3395310 22 22380474-23922495
WARNING: unknown gene or malformed range: 18:3394887-3395310 2 89156674-90458671
WARNING: unknown gene or malformed range: 18:3394887-3395310 14 106053226-107288019
WARNING: unknown gene or malformed range: 21:10862622-10863067 22 22380474-23922495
WARNING: unknown gene or malformed range: 21:10862622-10863067 2 89156674-90458671
WARNING: unknown gene or malformed range: 21:10862622-10863067 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:17385109-17385586 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:17385109-17385586 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:17385109-17385586 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:17395125-17395871 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:17395125-17395871 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:17395125-17395871 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:17402333-17403063 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:17402333-17403063 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:17402333-17403063 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:17406842-17407334 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:17406842-17407334 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:17406842-17407334 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:17414411-17414893 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:17414411-17414893 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:17414411-17414893 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:25833273-25833790 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:25833273-25833790 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:25833273-25833790 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:32595906-32596221 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:32595906-32596221 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:32595906-32596221 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:32752663-32752975 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:32752663-32752975 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:32752663-32752975 14 106053226-107288019
WARNING: unknown gene or malformed range: 22:32772669-32773122 22 22380474-23922495
WARNING: unknown gene or malformed range: 22:32772669-32773122 2 89156674-90458671
WARNING: unknown gene or malformed range: 22:32772669-32773122 14 106053226-107288019
8)
[2023-06-02T11:56:01] Filtering fusions with anchors <=23nt (remaining=6)
[2023-06-02T11:56:01] Filtering end-to-end fusions with low support (remaining=5)
[2023-06-02T11:56:01] Filtering fusions with no coverage around the breakpoints (remaining=2)
[2023-06-02T11:56:01] Indexing gene sequences
[2023-06-02T11:56:01] Filtering genes with >=30% identity (remaining=2)
[2023-06-02T11:56:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers
Program received signal SIGSEGV, Segmentation fault.
std::_Hashtable<unsigned int, std::pair<unsigned int const, std::vector<int, std::allocator<int> > >, std::allocator<std::pair<unsigned int const, std::vector<int, std::allocator<int> > > >, std::__detail::_Select1st, std::equal_to<unsigned int>, std::hash<unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::_M_find_before_node (__code=55405, __k=<optimized out>, __bkt=55405, this=0x55557a64a2b8) at /usr/include/c++/11/bits/hashtable.h:1827
1827 _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal,
(gdb) bt
#0 std::_Hashtable<unsigned int, std::pair<unsigned int const, std::vector<int, std::allocator<int> > >, std::allocator<std::pair<unsigned int const, std::vector<int, std::allocator<int> > > >, std::__detail::_Select1st, std::equal_to<unsigned int>, std::hash<unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::_M_find_before_node (__code=55405, __k=<optimized out>, __bkt=55405, this=0x55557a64a2b8) at /usr/include/c++/11/bits/hashtable.h:1827
#1 std::_Hashtable<unsigned int, std::pair<unsigned int const, std::vector<int, std::allocator<int> > >, std::allocator<std::pair<unsigned int const, std::vector<int, std::allocator<int> > > >, std::__detail::_Select1st, std::equal_to<unsigned int>, std::hash<unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::_M_find_node (__c=55405, __key=<optimized out>, __bkt=55405, this=0x55557a64a2b8) at /usr/include/c++/11/bits/hashtable.h:810
#2 std::_Hashtable<unsigned int, std::pair<unsigned int const, std::vector<int, std::allocator<int> > >, std::allocator<std::pair<unsigned int const, std::vector<int, std::allocator<int> > > >, std::__detail::_Select1st, std::equal_to<unsigned int>, std::hash<unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::find (__k=<optimized out>, this=0x55557a64a2b8) at /usr/include/c++/11/bits/hashtable.h:1610
#3 std::unordered_map<unsigned int, std::vector<int, std::allocator<int> >, std::hash<unsigned int>, std::equal_to<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<int, std::allocator<int> > > > >::find (__x=<optimized out>, this=0x55557a64a2b8) at /usr/include/c++/11/bits/unordered_map.h:880
#4 align (score=score@entry=0, read_sequence="AGCTGCAGCAGCTGCCCAGGCAGCAGCCGTGGCAGGAAACATCCCTGGCCCAGGATCAGTAGGTGGAATAGCTCCAGCTATCA", read_pos=read_pos@entry=0, contig_sequence=...,
gene_pos=gene_pos@entry=48494088, gene_start=gene_start@entry=48494088, gene_end=48584813, kmer_index=std::unordered_map with 93825612994296 elements = {...}, kmer_length=8 '\b',
splice_sites=std::set with 9 elements = {...}, min_score=66, max_deletions=1) at source/filter_mismappers.cpp:96
#5 0x00005555555c64aa in align_both_strands (read_sequence="AGCTGCAGCAGCTGCCCAGGCAGCAGCCGTGGCAGGAAACATCCCTGGCCCAGGATCAGTAGGTGGAATAGCTCCAGCTATCA", read_length=100, max_mate_gap=200,
breakpoints_on_same_contig=true, alignment_start=48603063, alignment_end=48603145, kmer_indices=std::vector of length 15, capacity 15 = {...}, assembly=std::unordered_map with 24 elements = {...},
exon_annotation_index=..., splice_sites_by_gene=std::unordered_map with 1 element = {...}, genes=..., kmer_length=8 '\b', min_align_fraction=<optimized out>) at source/filter_mismappers.cpp:210
#6 0x00005555555c70b7 in filter_mismappers (fusions=std::unordered_map with 16920 elements = {...}, kmer_indices=std::vector of length 15, capacity 15 = {...}, kmer_length=kmer_length@entry=8 '\b',
assembly=std::unordered_map with 24 elements = {...}, exon_annotation_index=..., max_mismapper_fraction=<optimized out>, max_mate_gap=max_mate_gap@entry=200) at source/filter_mismappers.cpp:292
#7 0x0000555555569e17 in main (argc=<optimized out>, argv=<optimized out>) at source/arriba.cpp:564
Do you know why I have this error ?
Thank you
