I’m getting error shown below, when sorting tophat accepted hits BAM file by name using samtools_sort version 1.0.2 (by iuc)

Program: samtools (Tools for alignments in the SAM format)

Version: 0.1.19-44428cd

Command:

samtools sort -n "../../database/files/036/dataset_36372.dat" foo 2>&1 || echo "Error running samtools sort." >&2 ; mv foo.bam "../../database/files/036/dataset_36665.dat"

stdout:

[bam_sort_core] merging from 33 files...
[bam_index_core] the alignment is not sorted (HWI-D00351:251:C80TWANXX:1:1101:1081:98020): 15-th chr > 5-th chr
[bam_index_build2] fail to index the BAM file.

stderr:

Aborted (core dumped)

Any ideas?

Amos Raphenya

Bioinformatics Software Developer

Department of Biochemistry & Biomedical Sciences

McMaster University, MDCL 2317

p: (905) 525-9140 ext: 22787

a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1

e: raphenar@mcmaster.ca

skype: amos_raphenya