Mosaik Aligner Error

Question

[JW]

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.

[GenoMax]

Are the input files available and readable in the directory you are running this command from?

[JW]

Yes they are

[Ram]

Do you have the necessary permissions on the files?

[JW]

Yes - I have all permissions

[JW]

Nevermind, problem solved

Answer 1

[JW]

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.

[Ram]

You can accept your own solution. That will mark this question as solved.