[Seqan-dev] rabema_prepare_sam "File must be sorted by query name."

[Uwe Appelt <uappelt@clcbio.com>]

Hi guys,

I've got a small problem in Rabema: I am preparing another gold standard 
for a Rabema benchmark and received the following error msg:

./razers3 -v -tc 32 -of sam -rr 100 -i 90 -m 1000000 -ds -o 
./output0.sam ./hg19.fa ./input.fastq
[load of outputs]
./rabema_prepare_sam ./output0.sam > ./output.sam

ERROR: 16A7I:4:100 succeeds 16A7I:49:92 in SAM file.
File must be sorted by query name.

Seems like razers3 and rabema_prepare_sam are somehow out of sync with 
respect to their sorting code (maybe it's just the multi-threading in 
razers3 that sometimes results in slightly "unordered" output of mapping 
results)? The Trunk-checkout is, however, already a week old, so I might 
have to re-run everything. Before doing so, I wanted to ask for advice 
here, because re-running razers3 will take 4 days. Any ideas or suggestions?

Thanks in advance,
Uwe