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 <dilkash_ghaz...@persistent.com> Sent: 14 September 2021 15:03 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 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_v1sn000000/merged_bam/AssayDev_F28556.A5a_1_RNA_v1_copy_of_OCAv3_GX5_DNA_RNA_w5.0.2_K8ONC_K8ONC/merged.bam > s3://ddn-datamanagement-staging/thor_v1sn000000/merged_sam/header.sam -bash: s3://ddn-datamanagement-staging/thor_v1sn000000/merged_sam/header.sam: No such file or directory -----Original Message----- From: Andrew Whitwham <a...@sanger.ac.uk> Sent: Tuesday, September 14, 2021 7:26 PM To: Dilkash Ghazala <dilkash_ghaz...@persistent.com> 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 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 <dilkash_ghaz...@persistent.com> Sent: 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 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 Building dependency tree Reading state information... Done E: Version '1.13' for 'samtools' was not found Can you please tell me the version I should use here. Thanks. -----Original Message----- From: Andrew Whitwham <a...@sanger.ac.uk> Sent: Tuesday, September 14, 2021 1:53 PM To: Dilkash Ghazala <dilkash_ghaz...@persistent.com> 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 Ghazala <dilkash_ghaz...@persistent.com> Sent: 13 September 2021 19:00 To: samtools-help@lists.sourceforge.net Subject: [Samtools-help] Samtools write files to S3 bucket [EXT] 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 add this functionality ? Thanks for your help. Regards, Dilkash Ghazala DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
