Hello,
I am trying to run samtools on Linux to process BAM files from the
high-coverage sequencing of the Denisovan genome.
When I run mpileup, I get a failed assertion very quickly.
$ time samtools mpileup -C50 -uf human_g1k_v37.fasta T_hg19_1000g.bam
> /dev/null
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
samtools: bam_plcmd.c:162: group_smpl: Assertion `q' failed.
Aborted
real 0m55.997s
user 0m55.631s
sys 0m0.324s
Can someone help me with what I am doing wrong, or what is the cause
of the failed assertion?
Thank you very much,
Carolyn
P.S.
The BAM file I am using can be found at
http://cdna.eva.mpg.de/denisova/alignments/T_hg19_1000g.bam
The alignment FASTA file I am using can be found at
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
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