error of samtools sort

Question

[jolin0701-dy]

I got no outputs from samtools sort.

$bowtie2 -x genome nophiX.fastq -S nophiX.sam

$samtools view -bS nophiX.sam > nophiX.bam

$samtools sort nophiX.bam nophiX.sorted

[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files

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

No outputs..

Some suggestions?

Thanks...

Answer 1

[GenoMax]

Current samtools (v.1.3) has a slightly different syntax.

$ samtools sort -o nophiX.sorted.bam nophiX.bam

Answer 2

[Daniel]

In the instructions it tells you to provide an output file:

  -o output.bam

However, I alternatively you can also use redirection arrows such as:

samtools sort accepted_hits.bam > acc_sort.bam