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:
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
Code:
################ ## 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