Mosaik Aligner Error
Hello,
I am trying to align a set of 454 reads to a Reference Genome using the Mosaik Aligner. But when I run
../MosaikAligner -in ./r.dat -ia ref.dat -out Aligned.dat -m unique -mmp 0.15
I get the following output:
ERROR: Could not open for reading.
What am I doing wrong? Thanks in advance.
1 answer
For anyone having the same problem, here is the solution I found:
../MosaikAligner -in ./r.dat -ia ref.dat -out Aligned_ACAC.dat -m unique -mmp 0.15 -annpe ../pe.ann -annse ../se.ann
The point is in letting the program know where the respective paired-end and single-end protocols are. These come with Mosaik.
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Are the input files available and readable in the directory you are running this command from?
Yes they are
Do you have the necessary permissions on the files?
Yes - I have all permissions
Nevermind, problem solved