rfsearch.pl notes

Families which require special rfsearch.pl flags:


recommended command



rfsearch.pl -ignoresm -cut_ga

too many hits otherwise, and it takes more than 1 week


rfsearch.pl -cgtailn 200

allows calibration to finish successfully, otherwise you get this error ‘Error: –gtailn =250 cannot be used, there’s only 215.000 hits per Mb in the histogram! Lower or use –tailp.’

Possible rfsearch.pl error:

ERROR unable to fetch description for JZJH011 at /homes/nawrocki/git/Rfam/rfam-family-pipeline/Rfam/Lib/Bio/Rfam/FamilyIO.pm line 2070, <RTBL> line 48.

If you see an error like this: rerun with -scpu 0. This error is due to a bug in infernal 1.1.4 (actually in easel) that was fixed in commit 8d300ef, so should be fixed in next release of infernal. https://github.com/EddyRivasLab/easel/pull/66/commits/8d300ef3899f69365be02635416333d0f30ccbe9