Error in ParseAllGap

[mzahm]

Hi,

TGSGapFiller (commit 72694a3) fails at step ParseAllGap of TGSGapCandidate. I ran this command line:

TGSGapFiller.sh  \
        --scaff   assembly.fa \
        --reads   ONT.trim.filter.fq.gz \
        --output  assembly_gapclosing \
        --pilon   /usr/local/bioinfo/src/Pilon/pilon-v1.22/pilon-1.22.jar \
    --pilon_mem 64G \
        --ngs     short_reads.fq \
        --samtool /usr/local/bioinfo/src/samtools/samtools-1.9/samtools \
        --java    /tools/java/jre1.8.0_45/bin/java

I have this error:

/usr/local/bioinfo/src/TGSGapFiller/TGSGapFiller-72694a3/TGSGapFiller.sh : ligne 366 :  1579 Abandon                 $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

When I look to the assembly_gapclosing.cand.log file it ends with:

TGSGapCandidate INFO    CET 2109/11/15  11:41:16    :   LoadPAF finish. used wall clock : 1801 seconds, cpu time : 1800.460083 seconds
TGSGapCandidate INFO    CET 2109/11/15  11:41:16    :   LoadScaffInfo start now ... 
TGSGapCandidate INFO    CET 2109/11/15  11:41:33    :   LoadScaffInfo finish. used wall clock : 17 seconds, cpu time : 17.280001 seconds
TGSGapCandidate INFO    CET 2109/11/15  11:41:33    :   ParseAllGap start now ... 
terminate called after throwing an instance of 'std::out_of_range'
  what():  map::at

Do you have any solution to solve this?

Thanks

[cchd0001]

Could you please provide a little test data that can reproduce this error ?

[mzahm]

Sorry for the late reply. I do not have test data but I found the problem. The input file of --reads parameter has to be in fasta format not in fastq format.