[galaxy-dev] Error sorting tophat accepted hits BAM file by name

Wed, 17 Feb 2016 11:46:12 -0800

Hi Guys,

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"

[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
skype: amos_raphenya
 

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