Terminate called after throwing an instance of 'std::out_of_range' what(): map::at

[alexvasilikop]

Hello when I try to run TGS-GapCloser using the following command I get a (core dumped) crash. $ tgsgapcloser --scaff $assembly --reads $ONT_READS --output $output --thread 10 --racon /home/lege/anaconda3/envs/TGS_GapCloser/bin/racon

. . INFO : Checking basic args & env end.

INFO : Step 1 , run TGSSeqSplit to split scaffolds into contigs.

INFO : Step 1 , done .

INFO : Step 2 , run TGSCandidate ...

• 2.1 , run minmap2 to map contig into tgs-reads.
• 2.2 , run TGSGapCandidate to choose candidate region seqs. /home/lege/anaconda3/envs/TGS_GapCloser/bin/tgsgapcloser: line 374: 24174 Aborted (core dumped) $Candidate --ont_reads_a $TGS_READS --contig2ont_paf $OUT_PREFIX.sub.paf --candidate_max 10 --candidate_shake_filter --candidate_merge < $TMP_INPUT_SCAFF_INFO > $OUT_PREFIX.ont.fasta 2> $OUT_PREFIX.cand.log ###############################################################################

After checking $OUT_PREFIX.cand.log I see the following error: ###################################################################### .. 3782 1 4460 1 4521 1 6170 1 7955 1 8504 1 11943 1

TGSGapCandidate INFO CET 2022/5/20 14:25:19 : LoadPAF finish. used wall clock : 15 seconds, cpu time : 14.460800 seconds TGSGapCandidate INFO CET 2022/5/20 14:25:19 : LoadScaffInfo start now ... TGSGapCandidate INFO CET 2022/5/20 14:25:19 : LoadScaffInfo finish. used wall clock : 0 seconds, cpu time : 0.134522 seconds TGSGapCandidate INFO CET 2022/5/20 14:25:19 : ParseAllGap start now ... terminate called after throwing an instance of 'std::out_of_range' what(): map::at ####################################################################################

What might be the problem? Thanks

[alexvasilikop]

The mistake was cause by providing the reads into fastq instead of fasta format