jgolob / maliampi Goto Github PK

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!

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

Dear author team,

This is a marvelous work! I can try the test data on my personal computer locally, but now I need to run meta-analysis on the linux server. We use PBS as the scheduler. Could you please give an example config file? I can't run it successfully by simply setting process.executor = 'pbs'.

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?

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