problem converting bam to pileup

[crh]

Hi

We are getting an error stating the bam files are not sorted when we attempt to convert bam to pileup.

I sort the bam file, index it, then attempt to convert to pileup:

samtools sort psr1_p_deplete_s3.bam psr1_p_deplete_s3.sorted
samtools index psr1_p_deplete_s3.sorted.bam

samtools pileup -f ~/binf/seq/genome/chlre4/chlre4.fa psr1_p_deplete_s3.sorted.bam > pileup_sorted.pup
[bam_pileup_core] the input is not sorted (reads out of order)
[bam_plp_destroy] memory leak: 1. Continue anyway.

the file pileup_sorted.pup is created.

The bam file was generated by using samtools merge:
samtools merge out.bam file1.bam file2.bam

Any suggestions?

thanks
Charles