File for psipred not found! Generating from scratch instead.
picking fragments with options:
            add_pdbs_to_vall: 
                       chain: 0
                     cleanup: 1
exclude_homologs_by_pdb_date: 0
                           f: pep00.fasta
                   fastafile: pep00.fasta
                       frags: 1
                        homs: 1
                          id: pep0
                n_candidates: 1000
                     n_frags: 200
             old_name_format: 0
                      porter: 0
                  porterfile: 
                     psipred: 1
                 psipredfile: 
                      rundir: /shared/home/payal/Calpains/Peptide_Docking
                       runid: pep00
                         sam: 0
                     samfile: 
                 torsion_bin: 0
--------------------------------------------------------------------------------

running psiblast for sequence: pep00.fasta
[blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

[blastpgp] WARNING: a standard checkpoint file should have extension ".chk".

[blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

[blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

Error: expected creation of pep00.200.9mers after running '/home/lyna/rosetta_workshop/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/fragment_picker.static.linuxgccrelease @pep00_picker_cmd_size9.txt -j 1'!