I want to get familiar with MetaBAT binning pipeline (https://bitbucket.org/berkeleylab/metabat/wiki/Example_Large_Data). I download the dataset and try to follow the instruction like this:
- Run Ray with kmer=31 and bloom filter defaults
- run BBmap to Ray scaffolds >= 2500 bp, idfilter=90
- run megahit on unmapped reads and mates
- concatenate Ray >=2500 and megahit assemblies
My dataset is under the folder ~/data/ and I ran the command
mpiexec -n 1 Ray -k 31 -detect-sequence-files ~/data/ -o "RayOutput . In the folder "RayOutput", I found a file named "Scaffolds.fasta". I do not know whether this step is correct.
Then, I ran the command
bbmap.sh in=Scaffolds.fasta out=trial.sam idfilter=0.9 minlen=2500, but got a message like this:
Exception in thread "main" java.lang.RuntimeException: Can't find file ref/genome/1/summary.txt at fileIO.ReadWrite.getRawInputStream(ReadWrite.java:815) at fileIO.ReadWrite.getInputStream(ReadWrite.java:780) at fileIO.TextFile.open(TextFile.java:241) at fileIO.TextFile.<init>(TextFile.java:92) at dna.Data.setGenome2(Data.java:823) at dna.Data.setGenome(Data.java:769) at align2.BBMap.loadIndex(BBMap.java:306) at align2.BBMap.main(BBMap.java:31)
My operating system is Ubuntu 14,04LTS and I believe I have installed Ray and BBmap correctly. But I can't implement the second step of the instruction. I don't know where is wrong.
Could you give me any suggestions? Thanks.