error Killed java $before -jar $PROG/../share/halign-stmsa.jar $after

malabz / HAlign-3

do multiple nucleotide sequence alignment fast and accurately

http://lab.malab.cn/soft/halign/

MIT License

14 stars 4 forks source link

error Killed java $before -jar $PROG/../share/halign-stmsa.jar $after #5

Open Thtcare opened 2 months ago

Thtcare commented 2 months ago

I run with command halign -o merge_genome_dna.aln -t 20 -Xmx1000g merge_genome_dna.fna that merge_genome_dna.fna contain 2 sequence that first sequence length=8,735,486 and second sequence length = 7,023,957 that error reading merge_genome_dna.fna... finished in 209 ms suffix tree: 4985 ms name: 7319 ms anti-name: 11 ms /miniconda3/envs/halign/bin/halign: line 56: 2434645 Killed java $before -jar $PROG/../share/halign-stmsa.jar $after how should i slove this problem? thank you

metaphysicser commented 1 month ago

@Thtcare , Thank you for reporting the issue.

The problem is likely due to the length of the sequences being aligned, which causes a memory overflow during the dynamic programming process. In the next version of HAlign, we are considering incorporating the Wavefront Alignment Algorithm (WFA) to address such issues. In the meantime, we recommend using WFA2-lib or other software to perform the alignment of these large sequences.

Please let us know if you have any further questions.