I am using novoalign to do alignment, the resulting file is "test.nal" which has
195 million matches and the size is 36 GB. Next I want to transfer the test.nal into MAQ-compatible format using:
>novoalign -F ILMFQ -t120 -r0.2 -q5 -d hg19.ndx -f test_1.txt.gz test_2.gz | grep chr > test.nal
>novo2map test.nal - test.map
But the "novo2map" command failed and gave a "Segmentation Fault" error.
it turns out that the error only happens when the size of "test.nal" is bigger enough. For example, if the size of "test.nal" was ~18GB, it is OK. if it was ~24GB, it will fail. So the question is, for novo2map, the size of the novoalign result file can not exceed the size of available physical memory and swap space? Or is it a bug of novo2map? Anyone has similar experience?
Thanks,
Ying Sun
195 million matches and the size is 36 GB. Next I want to transfer the test.nal into MAQ-compatible format using:
>novoalign -F ILMFQ -t120 -r0.2 -q5 -d hg19.ndx -f test_1.txt.gz test_2.gz | grep chr > test.nal
>novo2map test.nal - test.map
But the "novo2map" command failed and gave a "Segmentation Fault" error.
it turns out that the error only happens when the size of "test.nal" is bigger enough. For example, if the size of "test.nal" was ~18GB, it is OK. if it was ~24GB, it will fail. So the question is, for novo2map, the size of the novoalign result file can not exceed the size of available physical memory and swap space? Or is it a bug of novo2map? Anyone has similar experience?
Thanks,
Ying Sun
