Merging alignments in mosaik - problems

[454andSolid]

Hi! I'm having trouble merging alignments in colour space (SOLiD) and base space (454) in Mosaik (version 1.0.1388). This is what I have done:

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## 1. Build Mosaik binary files from SOLiD reads, 454 reads and  consensus

# 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. Map 454 reads to consensus
>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

# then sort
>MosaikSort -in 454reads_aligned.dat  -out 454reads_sorted.dat


################
## 3. Map SOLiD reads to consensus
>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

# then sort
>MosaikSort -in solid_reads_aligned.dat  -out solid_reads_sorted.dat 


################
## 4. Merge alignments from 2. and 3.
>MosaikMerge -in 454reads_sorted.dat -in solid_reads_sorted.dat -out all_reads_sorted.dat

The last step is where I run into problems. I get "ERROR: Found an inconsistency in the reference sequences. Merged alignment archives must share the same subset of reference sequences."

Any advice? Is there a bug somewhere or am I just doing something wrong?

/Jakub