dbi-dump

[linp5]

Hi all!

I am running abi-dump to convert a SRA file DRR013277.sra into ABI format.
my cmd is simply:

abi-dump DRR013277.sra

but some errors were encountered :
2014-09-10T04:15:44 abi-dump.2.3.5 err: transfer unknown while reading file within file system module - system I/O error - likely broken pipe
2014-09-10T04:16:03 abi-dump.2.3.5 err: transfer unknown while reading file within file system module - system I/O error - likely broken pipe
2014-09-10T04:16:12 abi-dump.2.3.5 err: transfer unknown while reading file within file system module - system I/O error - likely broken pipe
2014-09-10T04:16:42 abi-dump.2.3.5 err: transfer unknown while reading file within file system module - system I/O error - likely broken pipe
2014-09-10T04:16:46 abi-dump.2.3.5 err: transfer unknown while reading file within file system module - system I/O error - likely broken pipe
2014-09-10T04:16:46 abi-dump.2.3.5 err: data corrupt while executing function within transform module - failed DRR013277.sra

Could anyone help me figure out what's wrong ?
Thanks a lot!

[GenoMax]

Have you tried providing full file path to DRR013277.sra (even though you may be in the directory where the file is located)? It sounds counter intuitive but works at times.

[WhatsOEver]

It rather looks to me as if something with your sra file is wrong. Are you sure the download finished successfully? How big is your file? It should be 5.646.779.371 bytes.

[linp5]

Thank you!

I have checked the file size:
-rw-rw-r-- 1 linp linp 5646779371 Sep 10 11:36 DRR013277.sra

I also tried to run the cmd using full file path.
But it failed again.

Please let me know if anyone have some opinions.
Thanks in advance!

[WhatsOEver]

Hi,
As I actually need some colorspace data for testing, I downloaded the file. Although it took the program 3h to unpack the file, no errors occurred:

/usr/local/sratoolkit.2.3.5-ubuntu64/bin/abi-dump ./DRR013277.sra 
Read 130133653 spots for ./DRR013277.sra
Written 130133653 spots for ./DRR013277.sra

Have you ever used the sratoolkit before? Did it work? What is your Linux-dist?

[linp5]

Thank you!

my linux dist is
Ubuntu 14.04 LTS (GNU/Linux 3.13.0-24-generic x86_64)

I did not use abi-dump before.

[WhatsOEver]

Thank you!

my linux dist is
Ubuntu 14.04 LTS (GNU/Linux 3.13.0-24-generic x86_64)

I did not use abi-dump before.

And you're using the pre-compiled binaries of the toolkit from here (http://ftp-trace.ncbi.nlm.nih.gov/sr...buntu64.tar.gz)?
It would be surprising - although not totally unlikely - that the toolkit doesn't work under 14.04 ... You could try to use the fastq-dumb (or any other) command from the toolkit on an appropriate file (eg https://trace.ddbj.nig.ac.jp/DRASear...?acc=SRR504687)

If this doesn't work, I would build it from source or write to the NCBI help desk and ask them if they can provide a fix.

[WhatsOEver]

I just saw that NCBI provides a small sra file to test the toolkit http://www.ncbi.nlm.nih.gov/Traces/s...&run=SRR390728

Test fastq-dumb on that file; if this doesn't work, something with your toolkit binaries is wrong

[GenoMax]

File available from SRA appears to be good (sometimes archives are corrupt at source). WhatsOEver's suggestion is the best option to check on (i.e. sratoolkit binaries being used must have some problem).