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gdanetzk diane-r thexiyang mariabeamer sminot

maliampi's Issues

RFAM blocking access to CM

RFAM is now blocking direct download to the 16S SSU covariance matrix, causing the refpkg workflow to fail.

ObtainCM references hardcoded path

It looks like the ObtainCM references a hard-coded file path (/cmalign/data/SSU_rRNA_bacteria.cm refpkg.cm).

Would it be possible to parameterize this for users who cannot add files to their root directory?

Vsearch segfault

Depending on processor (e.g. newer AMD) vsearch will segfault.

Update README.md with new manifest column names

In the README.md, the column names for read 1 and read 2 are listed as read__1 and read__2, but it appears that the code has been updated to use R1 and R2. It appears that the README.md should be updated to reflect this new file format.

Thanks!

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