bam_header_read EOF marker is absent. The input is probably truncated.
これも海外から見る人が多そうなので英語も書いておこう。
$ samtools index foo.sorted.bam [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). Segmentation fault (core dump)
.bamファイルが壊れているらしい。
.samはまともなはずなのにいつからこうなったか。
What broke foo.sorted.bam?
I compared the bam files before and after sorting.
$samtools flagstat foo.bam 8000000 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 7910957 + 0 mapped (98.89%:-nan%) 8000000 + 0 paired in sequencing 4000000 + 0 read1 4000000 + 0 read2 7859822 + 0 properly paired (98.25%:-nan%) 7899729 + 0 with itself and mate mapped 11228 + 0 singletons (0.14%:-nan%) 15109 + 0 with mate mapped to a different chr 14075 + 0 with mate mapped to a different chr (mapQ>=5) $samtools flagstat foo.sorted.bam [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_flagstat_core] Truncated file? Continue anyway. 0 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 0 + 0 mapped (-nan%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
Sorting process would have had trouble.
Although the cause of this phenomenon is still unclear, resorting bam fixed this trouble.
どうもsortのときに問題が起きているらしいな。sortのログを見ても特におかしなことは起きていないのだけれども。
結局sortをかけ直したらなおった。
$samtools sort foo.bam foo.sorted $ samtools flagstat foo.sorted.bam 8000000 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 7910957 + 0 mapped (98.89%:-nan%) 8000000 + 0 paired in sequencing 4000000 + 0 read1 4000000 + 0 read2 7859822 + 0 properly paired (98.25%:-nan%) 7899729 + 0 with itself and mate mapped 11228 + 0 singletons (0.14%:-nan%) 15109 + 0 with mate mapped to a different chr 14075 + 0 with mate mapped to a different chr (mapQ>=5)
