root1@root1-HP-Compaq-Elite-8300-MT:~/Documents/MODPIPE/demo$ ${MODPIPE}/main/AddSeqMP.py --conf_file modpipe.conf --sequence_file test.fsa
root1@root1-HP-Compaq-Elite-8300-MT:~/Documents/MODPIPE/demo$ ${MODPIPE}/main/ModPipe.pl --conf_file /home/root1/Documents/MODPIPE/demo/modpipe.conf --sequence_id 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW --hits_mode 1100 --score_by_tsvmod OFF 
MPLib::MPModules::GetProfile__M> No profile found for sequence
MPLib::MPModules::GetProfile__M>    Seqid  : 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW
MPLib::MPModules::GetProfile__M>    Profile: /home/root1/Documents/MODPIPE/demo/data/7ba/7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW/sequence/7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW-uniprot90.prf
MPLib::MPModules::GetProfile__M> Will calculate a new profile
MPLib::MPModules::GetProfile__M> Calculating profile for sequence: 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW
HitsSeqSeq.py__M> MODELLER Runtime: 4.59
HitsSeqSeq.py__M> No. of iterations: 1
HitsSeqSeq.py__M> Chi2 fit of distributions: 0.0612
HitsSeqSeq.py__M> KS-Stat for the distributions: 0.0109
HitsSeqSeq.py__M> Found 16 hits for 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW (Seq-Seq)
HitsSeqSeq.py__M>       Input   : 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW.fsa
HitsSeqSeq.py__M>       Database: pdb_95.hdf5
main::ProcessAliBPSS__M> Total number of templates to process: 16
Failed alignment is:
>P1;7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW
sequence:7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW:30::249::7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW:Seq-Seq (1000)::
KVKDAEDQL-------GARVGYIELD-LNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGR
RIHYSQNDLVK--Y--SPVTEK--HLT--D--GMTVREL---------CSAAITMTD-----NTAANLLL
TT-IGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMA---TTLRKLLTGELLT--LAS
RQQLIDWMEADKVAGPLLRSALPAGWFIADKSG-----A-GERGSR---GIIA-AL-GP
*
>P1;1alq
structureX:1alq:.::.::1alq:Seq-Seq (1000)::
ELNDLEKKY-------NAHIGVYALD-TKSGKEVK-FNSDKRFAYASTSKAINSAILLEQVP--YNKLNK
KVHINKDDIVA--Y--SPILEK--YVG--K--DITLKAL---------IEASMTYSD-----NTANNKII
KE-IGGIKKVKQRLKELGDKVTNPVRYEIELNYYSPKSKKDTSTPAAFG---KTLNKLIANGKLS--KEN
KKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQ----A-ITYASR---NDVA-FV-YP
*
Traceback (most recent call last):
  File "/home/root1/Documents/MODPIPE/src/int/HitsSeqSeq.py", line 294, in <module>
    main()
  File "/home/root1/Documents/MODPIPE/src/int/HitsSeqSeq.py", line 290, in main
    process_hits(env, hits, target_code, opts, 'SEQSEQ')
  File "/home/root1/Documents/MODPIPE/src/int/HitsSeqSeq.py", line 270, in process_hits
    a = hit.get_modeling_alignment()
  File "/home/root1/Documents/MODPIPE/lib/python/modpipe/fold_assignment.py", line 80, in get_modeling_alignment
    return _read_alignment(self.env, [target, template])
  File "/home/root1/Documents/MODPIPE/lib/python/modpipe/fold_assignment.py", line 97, in _read_alignment
    a = modeller.alignment(env, file=tmpfile, allow_alternates=True)
  File "/home/root1/Documents/MODPIPE/ext/mod/modlib/modeller/alignment.py", line 21, in __init__
    self.append(**vars)
  File "/home/root1/Documents/MODPIPE/ext/mod/modlib/modeller/alignment.py", line 80, in append
    allow_alternates)
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not match that in PDB file:        2  /home/root1/Documents/MODPIPE/demo/db/pdb/pdb1alq.ent (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q).
MPLib::MPModules::GetHits100__E> Failed to calculate sequence/sequence hits: 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW
MPLib::MPModules::GetHits100__E> /home/root1/Documents/MODPIPE/src/HitsSeqSeq.py --custom_tag Seq-Seq (1000) --pdb_repository /home/root1/Documents/MODPIPE/demo/db/pdb --hitfile_name 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW-seqseq.hits --e_value 1 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW.fsa pdb_95.hdf5
ModPipe.pl__E> Failed to get Seq-Seq hits: 7ba4f5e16b3a568fb3b527a668d15f6cMSIKIKHW