Samtools error: fail to open file XXX_sorted.bam.0000

[dena.dinesh]

Hi,

I have a bam files and I want to sort them. i used the following command

samtools sort control_1.bam -f control_1_sorted.bam

It produces temporary files and later when trying to merge them it throws an error "No such file or directory
[bam_merge_core] fail to open file control_1_sorted.bam.0000"

Please guide me to solve it.

[mastal]

Usage: samtools sort [options...] [in.bam]

try writing your command as:
samtools sort -f control_1_sorted.bam control_1.bam

[WhatsOEver]

"-f" is a legacy option and just not needed anymore.

just use

samtools sort control_1.bam control_1_sorted

to get a coordinate-sorted file named control_1_sorted.bam

if you want to have the same file sorted by names, use

samtools sort -n control_1.bam control_1_sorted

[dpryan]

For what it's worth, I too prefer the "legacy" format when dealing only with BAM files. The new sort command format takes twice as long to type, since you have to specify the output format and the prefix.

[WhatsOEver]

@dpryan: You are seriously complaining about typing speed? In that case I would go for scripting it. With a short script name it will be the shortest possible solution

bamFile=$1
sortBam="${bamFile%.*}_sorted"

samtools sort $bamFile $sortBam

[dpryan]

That's the legacy format The new format would be

samtools sort -O bam -T tmp input.bam > output.bam

Of course that'd be scripted with a bunch of files, but with even then if you're only dealing with BAM then the legacy format is slightly quicker to type.

Now I wonder if I ever submitted a pull request on how -T and -O are documented and set...

[WhatsOEver]

oh... yes... of course... looks like my mind is already on the weekend

[dpryan]

I know the feeling Schönes Wochenende!