problem of mpileup

[Hit]

I generated a file using the command:

"samtools mpileup -m 1796 -ugf ref.fa raw.bam > raw.mpileup.output"

it worked fine. Then I tried to use bcftools to generate vcf file using:

"bcftools view -bvcg raw.mpileup.output | bcftools view - > test.var.raw.vcf".

The first lines on screen looked fine for me and the output file test.var.raw.vvf keeps increasing:

[bcfview] 100000 sites processed.
[afs] 0:99821.109 1:147.549 2:31.342
[bcfview] 200000 sites processed.
[afs] 0:99882.002 1:105.096 2:12.902

However from certain site on (I checked and it seems to be on chr1) it turned out to be this:

[bcfview] 150600000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
[bcfview] 150700000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
[bcfview] 150800000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000


and the output file, test.var.raw.vcf, was no longer changed.

Does anyone know where is wrong or did I miss something in the command line?

Thank you! Any suggestion would be greatly appreciated....

[Yilong Li]

I've had similar problems under Linux, but with different programs. During scaffolding in Velvet, the program stops progressing even though top shows that it is still fully running. Oddly enough, when I re-run Velvet using slightly different parameters, the program runs through smoothly.

Similarly, in BWT-SW alignment, writing to the output file stops (always in the same position), even though the program keeps running according to top.

Does anybody know if this is some Linux-specific issue?

[Hit]

Actually in my case, the process went to "D" (uninterruptible sleep), and I have to manually kill it.