Question: Empty SAM files with sam-dump
0
gravatar for adamlangenbucher
3.6 years ago by
adamlangenbucher0 wrote:

I'm working with some .sra files from dbGaP and I'm having trouble converting them into .sam files using SRA Toolkit. I'm running Windows 7 on a 64-bit machine with 16Gb of RAM, and I'm using the newest version of SRA Toolkit (2.7.0). When I run sam-dump, it creates the output file, but finishes within a few seconds giving me an empty .sam file with a size of 0kb. The command I run is as follows:

sam-dump --output-file SRR3018199.sam SRR3018199

I've used other SRA Toolkit tools on this same machine without problems (vdb-dump, vdb-decrypt, etc.). I can convert the .sra files to .fasta or .csv files using vdb-dump, just not directly to a .sam file using sam-dump.

Has anyone seen a problem like this before?

sra sam sratoolkit • 1.5k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by adamlangenbucher0

This looks like a controlled access dataset. Does it require a sam-dump for encrypted/controlled data?

ADD REPLYlink written 3.6 years ago by genomax78k

I'm calling sam-dump within the dbGaP project workspace where I can call other functions on the controlled, decrypted data I've downloaded, including other functions within the SRA Toolkit package. I can run sam-dump effectively on another, non-controlled .sra file. Is there another conversion software I should be using for these controlled data?

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by adamlangenbucher0

I am not familiar with controlled access data so someone else would need to help. You should email SRA tech support on the side with a problem description. They are generally good about getting back in a business day or so. There have been corrupt records/files on SRA in the past that a ticket to tech support generally fixes easily.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax78k
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