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BWA - Samse command


Hi Dong,

I am using your program in conjunction with the TASSEL 3 Genotyping By Sequencing Pipeline, which requires the command 'samse' to convert an .sai file to a .sam file. The example command is:

bwa samse referenceSequence/rice.fa mergedTagCounts/myAlignedMasterTags.sai mergedTagCounts/myMasterTags.cnt.fq > mergedTagCounts/myAlignedMasterTags.sam

When I use this command, windows notifies that: 'BWA.exe has stopped working - a problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available'.

So, I just wanted to check - was the program written such that the samse command is available? Any other thoughts on why this might happen? Sorry if these are really naive questions.

Thanks for your help,


Athiappan wrote Apr 24, 2014 at 9:23 AM

Hi Dong/Lisa,

Am also facing the same problem. Have you got any update or solution for this problem.

Please help me in this regards.


LisaL wrote Apr 24, 2014 at 5:24 PM

Hi Athi/Dong,

No, I haven't been able to resolve the issue yet. I've written to the TASSEL Google Group to see if anyone there has any thoughts, but no response yet (just posted yesterday).

I have tried giving the full path for each file and am still getting the same error.

A couple of additional observations:

The .sam file is produced but is much smaller in size (7,760 KB versus the 51,580 KB sai file) and does not contain all of the required info. For example, each line contains the following info only:
@SQ SN:contig00001 LN:2281
@SQ SN:contig00002 LN:5330

One thing that seems strange is that during the indexing step there are only 5 additional files produced (.amb, .ann, .bwt, .pac, .sa). The files .rsa, .rpac, .rbwt are missing. Not sure if these files are necessary, but the Tassel documentation indicates that they will be produced.

Are you getting these same results?

I've searched for other programs to try to directly convert .sai files to .sam files, to try to sidestep the issue (assuming that the .sai file that has been produced is ok to convert), but nothing found to date.

Please let me know if you find a solution.


xied75 wrote Apr 28, 2014 at 10:07 PM

Hi, Lisa and Athi,

Thanks for reporting this issue here.

This is probably due to the difference between versions of BWA. Other people has reported similar behaviour.

The version you download from here has been around for a long time and has been used for real large projects, it's highly unlikely to have any bugs left.

Normally I would suggest you to try run this same command with a Linux machine (on the same version of BWA), if that runs without problem, then it'll confirm the bug in the Windows version; Otherwise, please also try the latest version on Linux.

Currently I have a plan to update the BWA to the latest version; In the meantime, according to a user suggestion, it's possible to compile the latest BWA source with Cygwin 64 bit on Windows, if you managed to get it work, please let me know. :)