How to convert sra-lite format to fastq?

[maubp]

I'm not 100% sure how memmap works on the Mac, but it sounds like you should have enough RAM to load the whole file into memory (assuming no other memory hungry applications are running at the same time). Can you find a smaller example to test?

[seb567]

I have to download and convert files to test Ray, the assembler I am working on (see a thread elsewhere on this forum).

My take on sratoolkit (I use /software/sratoolkit.2.0b4-2-centos_linux64/):

It is slow, but it works. My guess is that data are compressed, using something like LIBBZ2 (it is just a guess). That explains the compression ratio as well as the slowness.

[boiseb01@ls30 MyShortReadArchive]$ ldd /software/sratoolkit.2.0b4-2-centos_linux64/fastq-dump
linux-vdso.so.1 => (0x00007fff361ff000)
libdl.so.2 => /lib64/libdl.so.2 (0x00000033f5a00000)
libz.so.1 => /lib64/libz.so.1 (0x00000033f6600000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x0000003403e00000)
libm.so.6 => /lib64/libm.so.6 (0x00000033f5600000)
libc.so.6 => /lib64/libc.so.6 (0x00000033f5200000)
/lib64/ld-linux-x86-64.so.2 (0x00000033f4e00000)

Binaries are linked against libz and libbz2, but the slowness indicates that they probably rely on libbz2.

[tbusch0000]

How much RAM do you have, and how big is SRR070499.lite.sra?

I have 6GB RAM and the file is 3.5 GB

[maubp]

Received error message: "memory exhausted while constructing memory map within file system module - failed to open 'SRR070499.lite.sra'"

How much RAM do you have, and how big is SRR070499.lite.sra?

[tbusch0000]

My guess is you download a 64bit Linux binary, which won't work on the Mac.

Thanks, they've only just released the mac binaries. It will execute now, but gives the error message above.

[maubp]

I downloaded the precompiled toolkit for 64-bit architecture onto my macbookpro running snow leopard and tried to run the fastq-dump executable from the terminal, and get the error message "cannot execute binary file".

My guess is you download a 64bit Linux binary, which won't work on the Mac.

[tbusch0000]

I just noticed they released a new MacOSX beta package.

I downloaded that one and entered in the terminal $./fastq-dump -A SRP000910 -D SRR070499.lite.sra

Received error message: "memory exhausted while constructing memory map within file system module - failed to open 'SRR070499.lite.sra'"

[SongLi]

Although I can get their CentOS 64bit running, it's realy slow, take about 10hrs to unpack one file. I am also interested to know more about this new SRA-tools.

[tbusch0000]

I am trying to dump sra-lite (sequence read archive) files to fastq format. On the NCBI Sequence Read Archive site it states:

...users are asked download runs of interest and execute dumps into the desired format using the SRA SDK toolkit available at http://www.ncbi.nlm.nih.gov/Traces/s...are&s=software

I downloaded the precompiled toolkit for 64-bit architecture onto my macbookpro running snow leopard and tried to run the fastq-dump executable from the terminal, and get the error message "cannot execute binary file".

Any guidance would be much appreciated!