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Old 06-02-2014, 03:07 AM   #54
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Originally Posted by Thias View Post
Hello Brian,

I need someone to give me a broad hint. I have already successfully indexed some eukaryotic genomes with BBMAP. But one PhD student in our lab has sequenced a custom shRNA library and I just wanted to use my usual aligner and just lower k-mer size. But it claims that it cannot read the FASTA with the reference sequences, although it is there. It there a lower limit of scaffold sizes (or a special parameter which I didn't set) which may cause BBMAP to abort with that error or is really the FASTA file somehow corrupted?

java -da -Xmx32g -cp /home/z/zepper/software/bbmap/current/ align2.BBMap build=1 overwrite=true match=long fastareadlen=500 ref=/mnt/HPC/zepper-tmp/Pia/reference/sh_sequences/shRNAs.fa path=/mnt/HPC/zepper-tmp/Pia/reference/sh_sequences/bbmap_index build=1 threads=4 -Xmx32g midpad=2000 k=5 minscaf=5
Executing align2.BBMap [build=1, overwrite=true, match=long, fastareadlen=500, ref=/mnt/HPC/zepper-tmp/Pia/reference/sh_sequences/shRNAs.fa, path=/mnt/HPC/zepper-tmp/Pia/reference/sh_sequences/bbmap_index, build=1, threads=4, -Xmx32g, midpad=2000, k=5, minscaf=5]
Perhaps because you are using both ref= and path= options?

Since you have pre-built the BBMap index you can just use path= to point to the indexes.
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