check the newly created files in a directory

ls -lrt

fix long sequence titles

cd /workdir/$USER/project3/faa

zcat GCF_000005845.2_ASM584v2_translated_cds.faa.gz |  head

zcat GCF_000005845.2_ASM584v2_translated_cds.faa.gz | sed "s/ .*//" | sed "s/>lcl|NC_000913.3_prot_/>s1" > new.faa

head -n 100 new.faa

tail -n 100 new.faa

 

use grep to examine files 

ls E*log
grep -i final E*log
grep Final E*log

 

create a batch script to process all files in a directory

cd /workdir/$USER/project3/Results_Oct06/Single_Copy_Orthologue_Sequences
ls *fa | xargs -I {} echo "mafft {} > {}.aln" > batch.sh

 

run long jobs in "screen"

screen

run shell scripts in serial

sh batch.sh

run jobs in parallel

parallel -j 4 < batch.sh