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?