example data core dumped

[yuanw-18]

Hi, Dr Song,

Thanks for your wonderful tool. I meet an error when run the example(guideline zea & sorghum).

wget ftp://ftp.ensemblgenomes.org/pub/plants/release-34/gff3/zea_mays/Zea_mays.AGPv4.34.gff3.gz gunzip Zea_mays.AGPv4.34.gff3.gz wget ftp://ftp.ensemblgenomes.org/pub/plants/release-34/fasta/zea_mays/dna/Zea_mays.AGPv4.dna.toplevel.fa.gz gunzip Zea_mays.AGPv4.dna.toplevel.fa.gz wget ftp://ftp.ensemblgenomes.org/pub/plants/release-49/fasta/sorghum_bicolor/dna/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa.gz gunzip Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa.gz

anchorwave gff2seq -r Zea_mays.AGPv4.dna.toplevel.fa -i Zea_mays.AGPv4.34.gff3 -o cds.fa minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa cds.fa > cds.sam minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 Zea_mays.AGPv4.dna.toplevel.fa cds.fa > ref.sam /usr/bin/time anchorwave proali -i Zea_mays.AGPv4.34.gff3 -as cds.fa -r Zea_mays.AGPv4.dna.toplevel.fa -a cds.sam -ar ref.sam
-s Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa -n anchors -e 2 -R 1 -Q 2
-o alignment.maf -f alignment.f.maf -w 38000 -fa3 200000 > log 2>&1

The last command error. log is following

AVX512 is enabled anchor.loganchor.loganchor.logterminate called after throwing an instance of 'std::invalid_argument' what(): stoi ***/anaconda3/bin/anchorwave: line 23: 234357 Aborted (core dumped) "${EXE}_avx512" "$@" 146.88user 9.91system 2:46.03elapsed 94%CPU (0avgtext+0avgdata 3589872maxresident)k 0inputs+0outputs (0major+2247729minor)pagefaults 0swaps

Do you have any idea about this error? Thanks!

wang

[baoxingsong]

Hi, thanks for trying AnchorWave. Looks like AnchorWave does not parse the two sam files correctly. Would you like to try again from the very beginning? Or could you share those two sam files, please? Baoxing