samtool sort

Question

[jiahui]

my command :

bowtie2 -x Guy11 -1 Guy11_FDSW210137750-1r_1.clean.fq.gz -2 Guy11_FDSW210137750-1r_2.clean.fq.gz | samtools sort -O bam -@ 5 -o Guy11.bam

and then it got error sort: invalid option -- 'O' open: No such file or directory [bam_sort_core] fail to open file bam Can people help me ?

Answer 1

[Pierre Lindenbaum]

I suspect your version of samtools is just too old. What is the output of

 samtools 2>&1 | grep Version

?

[jiahui]

you are right! I used conda to install samtools and success!