/scripts/01_potato_tr_evigene_IPS_commands.txt

Version 1

# MPE

##InterProScan evigene potato de-novo assembly
# interproscan.properties file change: binary.getorf.parser.filtersize=3 #(Default 12)
# precalc server lookup disabled because these are nonpublished sequences!

# pwd is _I_STRT/_S_03_stCuSTr/_A_02.3_InterProScan/scripts/
mkdir ../intermediate/
mkdir ../intermediate/Desiree_IPS
mkdir ../intermediate/PW363_IPS
mkdir ../intermediate/Rywal_IPS

# InterProScan-5.32-71.0 run on translated aa seqs without precalc queries
# we decided not to run dropsets as it is several mio sequences

#Desiree
/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--seqtype p \
-i ../../_A_01_evigene/intermediate_tr2aacds_Desiree/okayset/all.okay.aa \
--output-dir ../intermediate/Desiree_IPS \
--disable-precalc \
--formats TSV

/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--seqtype p \
-i ../../_A_01_evigene/intermediate_tr2aacds_Desiree/okayset/all.okalt.aa \
--output-dir ../intermediate/Desiree_IPS \
--disable-precalc \
--formats TSV

#PW363
/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--seqtype p \
-i ../../_A_01_evigene/intermediate_tr2aacds_PW363/okayset/all.okay.aa \
--output-dir ../intermediate/PW363_IPS \
--disable-precalc \
--formats TSV

/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--seqtype p \
-i ../../_A_01_evigene/intermediate_tr2aacds_PW363/okayset/all.okalt.aa \
--output-dir ../intermediate/PW363_IPS \
--disable-precalc \
--formats TSV

#Rywal
/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--seqtype p \
-i ../../_A_01_evigene/intermediate_tr2aacds_Rywal/all.okay.aa \
--output-dir ../intermediate/Rywal_IPS \
--disable-precalc \
--formats TSV

/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--seqtype p \
-i ../../_A_01_evigene/intermediate_tr2aacds_Rywal/all.okalt.aa \
--output-dir ../intermediate/Rywal_IPS \
--disable-precalc \
--formats TSV