mpileup on 300 BAM files

[tejajo]

I have seen similar posts on this forum, but I continue getting "segmentation fault" every time I start mpileup on my BAM files. I have about 300 BAM files from Exome sequencing of high depth.

samtools-0.1.18/samtools mpileup -BEDf ref/hg19.fa -d 200 -q 20 -r chr2 -b bamFiles > mpileups/kirc.exome.q20.chr2.m.pileup

[bam_header_read] EOF marker is absent. The input is probably truncated.

[bam_header_read] EOF marker is absent. The input is probably truncated.
Segmentation fault

What is the solution ?
Thanks.

[jebowers]

Segmentation faults are often due to insufficient memory in the computer. The sorting process requests too much memory based on the size of the files involved. Try a more powerful computer.

[maubp]

Have you checked if this warning from samtools is actually true? It can happen if a BAM file is only partially copied for example.

[bam_header_read] EOF marker is absent. The input is probably truncated.

Corrupt data could easily be causing the segmentation fault.

Note there is a bug in samtools 0.1.19 where this warning can appear by mistake when using Unix pipes - https://github.com/samtools/samtools/issues/18