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Old 06-02-2014, 08:40 AM   #56
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707


That specific error is triggered by:

File f=new File(reference);
if(!f.exists() || !f.isFile() || !f.canRead()){

So according to Java, either it does not exist, is not a file, or cannot be read. Perhaps the permissions are wrong, or the metadata on the file is wrong? It triggered before even looking inside the file, so the data is probably not corrupted.

You could technically do this:

cat /mnt/HPC/zepper-tmp/Pia/reference/sh_sequences/shRNAs.fa |
java -da -Xmx32g -cp /home/z/zepper/software/bbmap/current/ align2.BBMap build=1 overwrite=true match=long fastareadlen=500 ref=stdin.fa path=/mnt/HPC/zepper-tmp/Pia/reference/sh_sequences/bbmap_index build=1 threads=4 -Xmx32g midpad=2000 k=5 minscaf=5

...which would circumvent Java trying to read the file. But I'd like to hear if you discover anything odd about the file permissions or metadata (like if it claims to be a directory, or something).
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