Question about reading BAM file in S3 bucket

getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

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Question about reading BAM file in S3 bucket #55

Closed gujjas closed 3 years ago

gujjas commented 3 years ago

Hi,

I would like to know if RNA-SeQC supports reading BAM files from AWS S3 bucket?

Thanks

agraubert commented 3 years ago

RNA-SeQC will not automatically parse s3 or gs urls and read from buckets, however it does support streaming so a command like

rnaseqc annotation.gtf <(aws s3 cp s3://alignment.bam) ...

should work

gujjas commented 3 years ago

Thank you so much, Aaron. I'll try your command to see if it works.

On a slightly different note, I am having issues installing the tool - using git clone or downloading the source file, I get the error below:

collect2: error: ld returned 1 exit status
make: *** [rnaseqc] Error 1

[rnaseqc-2.4.0]$ gcc --version
gcc (GCC) 5.5.0

Can you please help. Thanks

agraubert commented 3 years ago

Is there any more to that error message?

gujjas commented 3 years ago

make.error.txt

Hi Aaron,

I've attached the error file for your reference. Please let me know if you need anything else.

Thanks Shar

agraubert commented 3 years ago

If you're compiling from source, try opening the makefile and setting ABI to 0. make clean && make should work then.

Alternatively, you can download our precompiled binaries for most versions of RNA-SeQC or use our docker image: gcr.io/broad-cga-aarong-gtex/rnaseqc

gujjas commented 3 years ago

Hi Aaron,

Thank you so much for the reply. Editing the makefile did not work, however the precompiled binary for linux seems to be working. Using the command you had shared earlier on collapsed gene level gtf file - giving me this error:

./rnaseqc.v2.4.0.linux ../gencode.v25.genes.gtf <(aws s3 cp s3://s3bucketname/PROJ-123/test.bam) test

usage: aws [options] <command> <subcommand> [<subcommand> ...] [parameters]
To see help text, you can run:

  aws help
  aws <command> help
  aws <command> <subcommand> help
aws: error: the following arguments are required: paths
BAM file shares no contigs with GTF

Thanks for helping. Shar

agraubert commented 3 years ago

Sorry, I'm not super familiar with the aws CLI. Here's an edited version that should work:

rnaseqc annotation.gtf <(aws s3 cp s3://alignment.bam - ) ...

gujjas commented 3 years ago

Thank you so much. It works!

agraubert commented 3 years ago

Glad to hear! Let me know if you have any additional issues