Question: Using sam-dump to convert .sra to .sam file from dbGaP
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gravatar for lujie0823
3.7 years ago by
lujie08230
lujie08230 wrote:

I have downloaded .sra files under gap accession phs000552. I have configured sratoolkit following the instruction and was able to download .sra files from that project. When I tried to run sam-dump to get sam files from these .sra files, I got error messages:
> ./sam-dump /scratch/02078/jl32587/MENINGIOMA/SRR619296.sra

/scratch/02078/jl32587/MENINGIOMA/SRR619296.sam


> <error message>
> 2015-09-22T20:25:52 sam-dump.2.5.2 err: item not found while reading file - input object(s) not found

I also tried to run sam-dump to directly pull sam files:
> sam-dump SRR619137 >test.sam


> <error message>
> 2015-09-22T20:31:36 sam-dump.2.5.2 err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR619137' - Access denied - please request permission to access phs000552/DS-BDBC-NPU-MDS in dbGaP ( 403 )
> 2015-09-22T20:31:36 sam-dump.2.5.2 err: item not found while reading file - input object(s) not found

 In contrast, when I run sam-dump using the example in the documentation, it did work.
> sam-dump SRR390728

I am wondering if anyone has encountered this error and has addressed it.

Thanks!

 

software error • 2.2k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 3.7 years ago by lujie08230

Looks like this is a protected SRA file. Do you have permission to use/access it?

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by genomax67k
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