使用hisat2-build对基因组建索引时遇到如下报错:
Error: Encountered internal HISAT2 exception (#1)
Command: hisat2-build --wrapper basic-0 -p 8 --ss splicesites.tsv --exon exons.tsv Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.1.ht2" file written during aborted indexing attempt.
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.2.ht2" file written during aborted indexing attempt.
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.3.ht2" file written during aborted indexing attempt.
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.4.ht2" file written during aborted indexing attempt.
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.5.ht2" file written during aborted indexing attempt.
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.6.ht2" file written during aborted indexing attempt.
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.7.ht2" file written during aborted indexing attempt.
Deleting "Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.8.ht2" file written during aborted indexing attempt.
报错原因时参考基因组较大,导致建索引失败,可以使用--large-index解决,命令如下:
hisat2-build --large-index -p 8 --ss splicesites.tsv --exon exons.tsv Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel
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