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I've used Bowtie2-build to make 2 indexes of the same genome (mm9). The first index uses all default settings for Bowtie2-build. The second index uses custom settings that should hopefully make the alignment process faster:
--bmaxdivn 2 instead of 4
--dvc 256 instead of 1024
--offrate 2 instead of 5
--ftabchars 14 instead of 10
Both indexes build successfully. The default index aligns successfully. When I try to do the same alignment but using the custom index I get an error:
and then,
Then Bowtie2 exits. What what does this error message mean?
[Edit] I made another index using:
--bmaxdivn 3
--dvc 256
--offrate 3
--ftabchars 12
And it seems to be working (it is currently aligning). So either the particular custom settings I used in the first one caused the problem, or something went wrong during the build process. I will try remaking the first custom index.
--bmaxdivn 2 instead of 4
--dvc 256 instead of 1024
--offrate 2 instead of 5
--ftabchars 14 instead of 10
Both indexes build successfully. The default index aligns successfully. When I try to do the same alignment but using the custom index I get an error:
Code:
"Error reading _offs[] array: 4092, 2620353516"
Code:
"Error: Encountered internal Bowtie 2 exception (#1)"
[Edit] I made another index using:
--bmaxdivn 3
--dvc 256
--offrate 3
--ftabchars 12
And it seems to be working (it is currently aligning). So either the particular custom settings I used in the first one caused the problem, or something went wrong during the build process. I will try remaking the first custom index.
