You need to use -o to specify the output if you want to write to s3.
samtools view -H s3://mybucket/myfile.bam -o s3://mybucket/header.sam
The '>' is only for local redirection.
Andrew
From: Dilkash Ghazala
Sent: 14 September 2021 15:03
To: Andrew Whitwh
Hi Andrew,
Please find below the command I am using and the error.
ubuntu@ip-172-31-25-43:~$ samtools --version
samtools 1.10
Using htslib 1.10.2-3
Copyright (C) 2019 Genome Research Ltd.
ubuntu@ip-172-31-25-43:~$
ubuntu@ip-172-31-25-43:~$ samtools view -H
s3://ddn-datamanagement-staging/thor_v1
Hello Dilkash,
1.10 should have s3 write. Ubuntu 20.04.3 LTS doesn't have 1.13 by default, it
only comes with Ubuntu 21.10 (Impish Indri).
Can you paste in the command line you are using and any output?
Andrew
From: Dilkash Ghazala
Sent: 14 September
I have samtools 1.10 which is failing to write to s3 path.
$ samtools --version
samtools 1.10
Using htslib 1.10.2-3
My system is "Ubuntu 20.04.3 LTS".
When I try to install the latest samtools (1.13) here, it's failing:
$ sudo apt-get install -y samtools=1.13
Reading package lists... Done
Buildi
Yes it should be, as long as you are using a modern enough version of samtools
and htslib.
Regards,
Andrew
From: Dilkash Ghazala
Sent: 13 September 2021 19:00
To: samtools-help@lists.sourceforge.net
Subject: [Samtools-help] Samtools write files to S3 b
