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Kalign produces seg fault when doing MSA #1

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William-Gibson-ig opened this issue Dec 8, 2021 · 0 comments
Open

Kalign produces seg fault when doing MSA #1

William-Gibson-ig opened this issue Dec 8, 2021 · 0 comments

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@William-Gibson-ig
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During IG detect, kalign will be used to perform MSA on fasta files. The input fasta files contain a reference fasta, a hap1 fasta, and a hap2 fasta. The seg fault occurs when one of the fastas has a single nucleotide. See the example fasta and run kalign on it.
kalign -i chr7_142765800_142767176_seg-fault.txt -f clu -o chr7_142765800_142767176.clu
chr7_142765800_142767176_seg-fault.txt

Unsure what causes a single nucleotide fasta in the fasta file.
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@William-Gibson-ig