notes: infernal test

notes/infernal.sh

+
+# FASTQ -> FASTA
+zcat /scratch/users/vgalata/GDB/results/preproc/metat/sr/R1.fastp.fastq.gz | sed -n '1~4s/^@/>/p;2~4p' > R1.fastp.fasta
+zcat /scratch/users/vgalata/GDB/results/preproc/metat/sr/R2.fastp.fastq.gz | sed -n '1~4s/^@/>/p;2~4p' > R2.fastp.fasta
+
+# 
+cm="/scratch/users/vgalata/GDB/dbs/infernal/Rfam.cm"
+clain="/scratch/users/vgalata/GDB/dbs/infernal/Rfam.clanin"
+date && cmscan --cpu 5 --noali --anytrunc --nohmmonly --rfam --cut_ga --fmt 2 --oclan --oskip --clanin ${clain} -o R1.fastp.out --tblout R1.fastp.tblout ${cm} R1.fastp.fasta && date