# /export3/home/gzwang/tools/netMHCpan-4.0/Linux_x86_64/bin/netMHCpan -p test/test.pep # Mon Jul 30 16:58:05 2018 # User: gzwang # PWD : /export3/home/gzwang/tools/netMHCpan-4.0 # Host: Linux hpc.scbit.org 2.6.32-279.14.1.el6.x86_64 x86_64 # -p 1 Use peptide input # Command line parameters set to: # [-rdir filename] /export3/home/gzwang/tools/netMHCpan-4.0/Linux_x86_64 Home directory for NetMHpan # [-syn filename] /export3/home/gzwang/tools/netMHCpan-4.0/Linux_x86_64/data/synlist.bin Synaps file # [-v] 0 Verbose mode # [-dirty] 0 Dirty mode, leave tmp dir+files # [-tdir filename] /export3/home/gzwang/tools/netMHCpan-4.0/tmp/netMHCpanXXXXXX Temporary directory (made with mkdtemp) # [-hlapseudo filename] /export3/home/gzwang/tools/netMHCpan-4.0/Linux_x86_64/data/MHC_pseudo.dat File with HLA pseudo sequences # [-hlaseq filename] File with full length HLA sequences # [-a line] HLA-A02:01 HLA allele # [-f filename] File name with input # [-w] 0 w option for webface # [-s] 0 Sort output on descending affinity # [-p] 1 Use peptide input # [-rth float] 0.500000 Rank Threshold for high binding peptides # [-rlt float] 2.000000 Rank Threshold for low binding peptides # [-l string] 8,9,10,11 Peptide length [8-11] (multiple length with ,) # [-xls] 0 Save output to xls file # [-xlsfile filename] NetMHCpan_out.xls Filename for xls dump # [-t float] -99.900002 Threshold for output # [-thrfmt filename] /export3/home/gzwang/tools/netMHCpan-4.0/Linux_x86_64/data/threshold/%s.thr.%s Format for threshold filenames # [-expfix] 0 Exclude prefix from synlist # [-version filename] /export3/home/gzwang/tools/netMHCpan-4.0/Linux_x86_64/data/version File with version information # [-inptype int] 0 Input type [0] FASTA [1] Peptide # [-listMHC] 0 Print list of alleles included in netMHCpan # [-allname filename] /export3/home/gzwang/tools/netMHCpan-4.0/Linux_x86_64/data/allelenames File with print names for alleles # [-BA] 0 Make Binding affinity prediction # NetMHCpan version 4.0 # Tmpdir made /export3/home/gzwang/tools/netMHCpan-4.0/tmp/netMHCpanjpqUfR # Input is in PEPTIDE format # Make Eluted ligand likelihood predictions HLA-A02:01 : Distance to training data 0.000 (using nearest neighbor HLA-A02:01) # Rank Threshold for Strong binding peptides 0.500 # Rank Threshold for Weak binding peptides 2.000 ----------------------------------------------------------------------------------- Pos HLA Peptide Core Of Gp Gl Ip Il Icore Identity Score %Rank Exp BindLevel ----------------------------------------------------------------------------------- 1 HLA-A*02:01 AAAWYLWEV AAAWYLWEV 0 0 0 0 0 AAAWYLWEV PEPLIST 0.4024040 0.7289 0.7426 <= WB 1 HLA-A*02:01 AAGLQDCTM AAGLQDCTM 0 0 0 0 0 AAGLQDCTM PEPLIST 0.0002320 37.6111 0.0000 1 HLA-A*02:01 AARNIVRRA AARNIVRRA 0 0 0 0 0 AARNIVRRA PEPLIST 0.0007680 24.1688 0.0000 1 HLA-A*02:01 AARPDDPTL AARPDDPTL 0 0 0 0 0 AARPDDPTL PEPLIST 0.0043920 12.2866 0.1488 1 HLA-A*02:01 AASCGGAVF AASCGGAVF 0 0 0 0 0 AASCGGAVF PEPLIST 0.0006550 25.7101 0.1492 1 HLA-A*02:01 AASKQQMLM AASKQQMLM 0 0 0 0 0 AASKQQMLM PEPLIST 0.0019590 16.9000 0.0000 1 HLA-A*02:01 AASSTHRKV AASSTHRKV 0 0 0 0 0 AASSTHRKV PEPLIST 0.0012940 19.7747 0.2717 1 HLA-A*02:01 AEALLADGL AEALLADGL 0 0 0 0 0 AEALLADGL PEPLIST 0.0013450 19.4945 0.0847 1 HLA-A*02:01 AEESLSLEA AEESLSLEA 0 0 0 0 0 AEESLSLEA PEPLIST 0.0003820 31.5294 0.0000 1 HLA-A*02:01 AEFGPWQTV AEFGPWQTV 0 0 0 0 0 AEFGPWQTV PEPLIST 0.0432370 4.1532 0.3156 ----------------------------------------------------------------------------------- Protein PEPLIST. Allele HLA-A*02:01. Number of high binders 0. Number of weak binders 1. Number of peptides 10 -----------------------------------------------------------------------------------