rfci.pl notes

For large families, it is recommended you login to a node with at least 64G of RAM (bsub -M 64000M -q research -Is $SHELL). The overlap check requires a lot of RAM. There may be other steps that require a lot of RAM as well.

Table of running times for commits (rfci.pl) (compiled 10/22:

acc

family id

seed #seq

full #seq

rfci.pl flags*

runtime

RF00177

SSU_rRNA_bacteria

99

37125

-i coding -i overlap

17 min

RF01960

SSU_rRNA_eukarya

90

39618

-i coding -i overlap

9 min

RF02540

LSU_rRNA_archaea

91

48683

-i coding -i overlap

23 min

RF02542

SSU_rRNA_microsporidia

46

35934

-i coding -i overlap

11 min

RF02543

LSU_rRNA_eukarya

88

54013

-i coding -i overlap

7 min

RF03064

RAGATH-18

1420

1771

9 min

  • -i spell -i missing -preseed also used for all above rfci.pl commands

Miscellaneous notes:

Jiffy script that loads info to RfamLive: /homes/nawrocki/git/Rfam/rfam-family-pipeline/Rfam/Scripts/jiffies/update_seed_dependent_tables_for_family.pl

Note this is only a local file not in the git repo.

Code that updates the RfamLive tables is here:

Rfam/Schemata/{RfamLive,RfamDB}/ResultSet/Taxonomy.pm Rfam/Schemata/{RfamLive,RfamDB}/ResultSet/SeedRegion.pm Rfam/Schemata/{RfamLive,RfamDB}/ResultSet/Rfamseq.pm Rfam/Schemata/{RfamLive,RfamDB}/ResultSet/RnacentralMatch.pm