Error when merging base space alignment with colour space alignment

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What steps will reproduce the problem?

1. Creating the .dat files

# Build binary from consensus
MosaikBuild -fr scaffolds.fna -oa scaffolds.dat

# Create jump database for consensus
MosaikJump -ia scaffolds.dat -out saffolds_15.dat -hs 15

# Build binary from consensus in colour space
MosaikBuild -fr scaffolds.fna -cs -oa scaffolds_cs.dat

# Build binaries from 454 reads
MosaikBuild -fr 1.TCA.454Reads.fna -fq 1.TCA.454Reads.qual -out
454reads.dat -st 454

# Build binary from SOLiD reads
MosaikBuild -fr solid.csfasta -fq solid.qual -out solidreads.dat -st solid

2. Aligning 454 and SOLiD reads

MosaikAligner -in 454reads.dat  -out 454reads_aligned.dat -ia scaffolds.dat
-hs 15 -mmp 0.05 -mhp 100 -act 55  -p 2 -j scaffolds_15.dat -bw 51
MosaikSort -in 454reads_aligned.dat  -out 454reads_sorted.dat

MosaikAligner -in solid_reads.dat  -out solid_reads_aligned.dat -ibs
scaffolds.dat -ia scaffolds_cs.dat -hs 15 -mm 4 -mhp 100 -act 25  -p 2
MosaikSort -in solid_reads_aligned.dat  -out solid_reads_sorted.dat 

3. Merging alignments
MosaikMerge -in 454reads_sorted.dat -in solid_reads_sorted.dat -out
all_reads_sorted.dat

What is the expected output? What do you see instead?

The expected output from the merging in step 3 is a .dat file with the two
alignments merged. Instead I see the following error message: "ERROR: Found
an inconsistency in the reference sequences. Merged alignment archives must
share the same subset of reference sequences."

What version of the product are you using? On what operating system?

I'm using version 1.0.1388 in Linux RHEL5, 64 bit.

Please provide any additional information below.

I also started a thread about this on seqanswers, but so far no reply:
http://seqanswers.com/forums/showthread.php?t=5112

Original issue reported on code.google.com by jakub.we...@imbim.uu.se on 14 May 2010 at 9:48