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Old 04-16-2012, 10:58 PM   #5
scami
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Location: italy

Join Date: Sep 2010
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Hi there,

so let me get this clear. When you write:

Now, it only reports that the alignments are okay for each batch of 131072, so if I take out that block of reads, it continues until it hit something else!


you mean that you cut the file containing the reads starting from line 131072 and until the end? And you got the same error?

Generally the "segmentation default" error happens (at least in C and C++) when one of the following problems occur (among other):
1) the software is trying to open a file that does not exist. This is not our case since all the files are recognised and open
2) the available memory is not sufficient for the process to terminate
3) Some variable is used to store a value that is retrieved from a file but for some reason the retrieved value is too big to fit in the amount of memory available for that variable.

If all the reads are ok then point 3 should not happen. In order to verify that point 2 is not happening I would split the file containing the reads in sub-files 131072 line long, launch the alignment and see whether the software fails again.

let me know whether this suggestion has been of any help
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