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SAMtools bam_sort_core truncated file.

fizwitfizwit Fred Hutch Cancer Research CenterMember

using samtools-1.3.1
getting error about bgzf reads

samtools sort -n -m 4G --threads 4 -o out.bam xxx_hg19_Illumina_gdc_realn.bam

[E::inflate_block] inflate failed: invalid distance too far back
[E::bgzf_read_block] inflate_block error -1
[E::bgzf_read] bgzf_read_block error -1 after 234 of 439 bytes
[bam_sort_core] truncated file. Aborting.

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