: [Samtools-help] Samtools write files to S3 bucket [EXT]
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: Di
03
To: Andrew Whitwham
Cc: samtools-help@lists.sourceforge.net; Sunanda Unni
Subject: RE: [Samtools-help] Samtools write files to S3 bucket [EXT]
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
Copyr
nal Message-
From: Andrew Whitwham
Sent: Tuesday, September 14, 2021 7:26 PM
To: Dilkash Ghazala
Cc: samtools-help@lists.sourceforge.net
Subject: Re: [Samtools-help] Samtools write files to S3 bucket [EXT]
Hello Dilkash,
1.10 should have s3 write. Ubuntu 20.04.3 LTS doesn't have
t: 14 September 2021 11:33
To: Andrew Whitwham
Cc: samtools-help@lists.sourceforge.net
Subject: RE: [Samtools-help] Samtools write files to S3 bucket [EXT]
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 2
Dilkash Ghazala
Cc: samtools-help@lists.sourceforge.net
Subject: Re: [Samtools-help] Samtools write files to S3 bucket [EXT]
Yes it should be, as long as you are using a modern enough version of samtools
and htslib.
Regards,
Andrew
From: Dilkash Ghazal
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
Hi,
I am using samtools to convert bam files to sam format. Both the files should
be in S3 bucket. While samtools is able to successfully read files from S3
path, it gives error while writing sam file to S3 bucket.
Is it possible to write directly to S3 using samtools ? If not, do you plan to
a
