Dear all,
indexing works without problems on Ubuntu 12.04, but not on Ubuntu 12.10, or Fedora 17. The issue therefore seems to really be distribution specific.

Thanks for help and suggestions!
All the best,

2012/10/15 Uebe, Steffen <>

Hi Aleš,


I have run into the same problem. While we (that is, even Nils) were unable to pinpoint the exact source of the problem, it did not occur on all distributions.


I normally do the computationally intensive stuff on a 48-core machine running CentOS 5; this is where I get the same error message.


I’ve also built bfast on my 8-core desktop PC under OpenSuSE 12 – here, the indexing completes without errors. So I ran the indexing step on my desktop machine and all other jobs on the 48-core box.


Even if that should fail, there are probably quite a few people out there with indexed hg19 genomes (I was using bfast for Arabidopsis data, so I’m afraid I can’t help here), which they would likely be willing to share.




Steffen Uebe



Dr. rer. nat. Steffen Uebe

Humangenetisches Institut

Universitätsklinikum Erlangen

Tel. +49-9131-85-26101

Fax +49-9131-85-23232


Von: Aleš Maver []
Gesendet: Montag, 15. Oktober 2012 10:08
Betreff: [Bfast-help] Error during BFAST indexing step


Dear bfast-help mailing list,

I have been trying to index human genome fasta file using bfast and I have been getting a new error during indexing step.


I would normally use this command for indexing:

bfast index -f hg19.fa -w 14 -m 1111111111111111 -n 16 -i 1


Soon after running this command, I get the following error:

Sorting by thread...

1.805 percent complete************************************************************

In function "RGIndexMergeHelperFromDiskGetNext_8": Fatal Error[ReadFileError]. Message: Could not read in buffer.

1.806 percent completeThe file stream error was:: Bad file descriptor

 ***** Exiting due to errors *****



I could perform this task previously without errors. I am quite sure the problem is somehow related to file permissions and the program fails when trying to read the .bfast.tmp* temporary files. I have been trying to fix this with setting the default system-wide umask, but I was still unable to make program run normally. 


I would be grateful for any hint regarding this issue and I wish you all a good day!

Ales Maver, MD
Institute of Medical Genetics, Department of Obstetrics and Gynaecology
UMC Ljubljana
Šlajmerjeva 3
SI-1000 Ljubljana
E-mail: ales.maver((@))