Samtools index and sambamba-depth error?

Question

[MobiusT]

I have the following script

samtools index dataset01.bam
basename dataset01.bam
f="$(basename -- dataset01.bam)"
sambamba depth base -L genomic.bed dataset01.bam > ./read_depths/"$f.txt"

I run this script with a whole genome dataset and after that is gives the following error.

samtools index: failed to create or write index
dataset001.bam
sambamba-depth: All files must be coordinate-sorted

What can be the reason for this and it takes more than half a day running so any help could save my time.

I use a conda environment and use the following versions

• sambamba=0.6.6=2
• samtools=1.7=1

[Pierre Lindenbaum]

samtools index: failed to create or write index

you first have to find why samtools failed at this point: is the bam sorted on coordinate ? is the directory writeable ? etc....