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dcppc / data-stewards

Questions and answers about TOPmed, GTEx, and AGR resources.
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Access Denied on Some S3 Bucket Files #23

Closed zflamig closed 6 years ago

zflamig commented 6 years ago

Using the assumed role and attempting to access some files I get access denied, for example: s3://nih-nhlbi-datacommons/NWD156483.freeze5.v1.vcf.gz

But there are several other files in the vcf list for this project that also have the problem. I haven't checked everything yet.

If necessary I can try to provide a full list of files with this error in the future too.

Alastair-Thomson-NHLBI commented 6 years ago

My team is investigating - Can you provide a full list of files with issues?

Alastair NIH/NHLBI

zflamig commented 6 years ago

Thanks @AlastairThomson. I will get you that list by the end of the week.

Coming around to GTEx, we had similar problems with some of the RNASeq files. Noteably everything in https://github.com/dcppc/full-stacks/blob/master/gtex-rnaseq.tsv that doesn't have a data GUID assigned to it by us we were unable to access.

zflamig commented 6 years ago

Hi @AlastairThomson please see the following TSV files. Ones with missing filenames/Calcium GUIDs are files to which we did not have access. https://github.com/dcppc/full-stacks/blob/master/topmed-vcf.tsv https://github.com/dcppc/full-stacks/blob/master/topmed-vcfcsi.tsv https://github.com/dcppc/full-stacks/blob/master/topmed-cram.tsv https://github.com/dcppc/full-stacks/blob/master/topmed-crai.tsv

dzakpasuns commented 6 years ago

Hi Zac,

Resolution: Objects listed in these TSV files (TOPMed and GTEx) are now tagged for cross-account access. Please note: investigating these problems revealed some TOPMed samples do not have corresponding VCF and VCF_CSI files. Attached are listings of VCF and VCF_CSI objects that are in the s3://nih-nhlbi-datacommons bucket.

topmed-vcf-CSI-object-list.txt topmed-vcf-object-list.txt

zflamig commented 6 years ago

Thanks! Works great now.