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....

[jkbonfield]

sambamba-depth: All files must be coordinate-sorted

Does this not answer your question? Your files must be sorted prior to indexing, or doing pretty much any genomic-coordinate based analysis. Samtools should give a clearer error message. It gives more information now, but it's still not crystal clear IMO. This also implies you're using an out-dated version of samtools.

Try looking at the samtools sort man page for detailed usage.