++ pwd + ORIGDIR=/usr/users/0/nigra/clustal + PID=30731 + export PID + TMPDIR=/tmp/nigra/30731 + export TMPDIR + mkdir -p /tmp/nigra/30731 + cd /tmp/nigra/30731 + cp /usr/users/0/nigra/clustal/seq.pir seq.pir + srun /home/biomed/bin/clustalw ************************************************************** ******** CLUSTAL W (1.82) Multiple Sequence Alignments ******** ************************************************************** 1. Sequence Input From Disc 2. Multiple Alignments 3. Profile / Structure Alignments 4. Phylogenetic trees S. Execute a system command H. HELP X. EXIT (leave program) Your choice: Sequences should all be in 1 file. 7 formats accepted: NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF, RSF. Enter the name of the sequence file: Sequence format is PIR Sequences assumed to be PROTEIN Sequence 1: CARP_RHICH 393 aa Sequence 2: CARP_YEAST 405 aa Sequence 3: CATD_HUMAN 412 aa Sequence 4: CHYM_BOVIN 381 aa Sequence 5: PEPA_ASPAW 394 aa ************************************************************** ******** CLUSTAL W (1.82) Multiple Sequence Alignments ******** ************************************************************** 1. Sequence Input From Disc 2. Multiple Alignments 3. Profile / Structure Alignments 4. Phylogenetic trees S. Execute a system command H. HELP X. EXIT (leave program) Your choice: ****** MULTIPLE ALIGNMENT MENU ****** 1. Do complete multiple alignment now (Slow/Accurate) 2. Produce guide tree file only 3. Do alignment using old guide tree file 4. Toggle Slow/Fast pairwise alignments = SLOW 5. Pairwise alignment parameters 6. Multiple alignment parameters 7. Reset gaps before alignment? = OFF 8. Toggle screen display = ON 9. Output format options S. Execute a system command H. HELP or press [RETURN] to go back to main menu Your choice: ********* Format of Alignment Output ********* 1. Toggle CLUSTAL format output = ON 2. Toggle NBRF/PIR format output = OFF 3. Toggle GCG/MSF format output = OFF 4. Toggle PHYLIP format output = OFF 5. Toggle NEXUS format output = OFF 6. Toggle GDE format output = OFF 7. Toggle GDE output case = LOWER 8. Toggle CLUSTALW sequence numbers = OFF 9. Toggle output order = ALIGNED 0. Create alignment output file(s) now? T. Toggle parameter output = OFF H. HELP Enter number (or [RETURN] to exit): ********* Format of Alignment Output ********* 1. Toggle CLUSTAL format output = ON 2. Toggle NBRF/PIR format output = OFF 3. Toggle GCG/MSF format output = ON 4. Toggle PHYLIP format output = OFF 5. Toggle NEXUS format output = OFF 6. Toggle GDE format output = OFF 7. Toggle GDE output case = LOWER 8. Toggle CLUSTALW sequence numbers = OFF 9. Toggle output order = ALIGNED 0. Create alignment output file(s) now? T. Toggle parameter output = OFF H. HELP Enter number (or [RETURN] to exit): ****** MULTIPLE ALIGNMENT MENU ****** 1. Do complete multiple alignment now (Slow/Accurate) 2. Produce guide tree file only 3. Do alignment using old guide tree file 4. Toggle Slow/Fast pairwise alignments = SLOW 5. Pairwise alignment parameters 6. Multiple alignment parameters 7. Reset gaps before alignment? = OFF 8. Toggle screen display = ON 9. Output format options S. Execute a system command H. HELP or press [RETURN] to go back to main menu Your choice: Enter a name for the CLUSTAL output file [seq.aln]: Enter a name for the GCG output file [seq.msf]: Enter name for new GUIDE TREE file [seq.dnd]: Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 28 Sequences (1:3) Aligned. Score: 28 Sequences (1:4) Aligned. Score: 30 Sequences (1:5) Aligned. Score: 31 Sequences (2:3) Aligned. Score: 38 Sequences (2:4) Aligned. Score: 31 Sequences (2:5) Aligned. Score: 21 Sequences (3:4) Aligned. Score: 43 Sequences (3:5) Aligned. Score: 21 Sequences (4:5) Aligned. Score: 21 Guide tree file created: [seq.dnd] Start of Multiple Alignment There are 4 groups Aligning... Group 1: Sequences: 2 Score:5833 Group 2: Sequences: 3 Score:4479 Group 3: Sequences: 4 Score:4007 Group 4: Sequences: 5 Score:3210 Alignment Score 5291 Consensus length = 431 CLUSTAL-Alignment file created [seq.aln] GCG-Alignment file created [seq.msf] CLUSTAL W (1.82) multiple sequence alignment CATD_HUMAN ---MQPSSLLPLALCLLAAPASALVRIPLHKFTSIRRTMSEVGGSVEDLIAKGPVSKYSQ CHYM_BOVIN ---MR--CLVVLLAVFALSQGTEITRIPLYKGKSLRKALKEHG-LLEDFLQK---QQYGI CARP_YEAST MFSLKALLPLALLLVSANQVAAKVHKAKIYKHELSDEMKEVTFEQHLAHLGQKYLTQFEK CARP_RHICH -----MKFTLISSCIAIAALAVAVDAAPGEKKISIPLAKNPNYKPSAKNAIQKAIAKYNK PEPA_ASPAW MVVFSKTAALVLGLSSAVSAAPAPTRKG-FTINQIARPANKTRTINLPGMYARSLAKFGG : . . . :: CATD_HUMAN AVPAVTEG--------PIPEV-LKNYM-DAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPS CHYM_BOVIN SSKYSGFG--------EVASVPLTNYL-DSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPS CARP_YEAST ANPEVVFSREHPFFTEGGHDVPLTNYL-NAQYYTDITLGTPPQNFKVILDTGSSNLWVPS CARP_RHICH HKINTSTGG--IVPDAGVGTVPMTDYGNDVEYYGQVTIGTPGKKFNLDFDTGSSDLWIAS PEPA_ASPAW TVPQSVKEA------ASKGSAVTTPQNNDEEYLTPVTVGKS--TLHLDFDTGSADLWVFS . . : :* : :*.. : : :****:::*: * CATD_HUMAN IHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGS-LSGYLSQDTVSVPCQSASSA CHYM_BOVIN IYCKSN--ACKNHQRFDPRKSSTFQNLGKPLSIHYGTGS-MQGILGYDTVTVS------- CARP_YEAST NECGSL--ACFLHSKYDHEASSSYKANGTEFAIQYGTGS-LEGYISQDTLSIG------- CARP_RHICH TLCTNCG---SRQTKYDPKQSSTYQADGRTWSISYGDGSSASGILAKDNVNLG------- PEPA_ASPAW DELPSSE---QTGHDLYTPSSSATKLSGYTWDISYGDGSSASGDVYRDTVTVG------- Press [RETURN] to continue or X to stop: ****** MULTIPLE ALIGNMENT MENU ****** 1. Do complete multiple alignment now (Slow/Accurate) 2. Produce guide tree file only 3. Do alignment using old guide tree file 4. Toggle Slow/Fast pairwise alignments = SLOW 5. Pairwise alignment parameters 6. Multiple alignment parameters 7. Reset gaps before alignment? = OFF 8. Toggle screen display = ON 9. Output format options S. Execute a system command H. HELP or press [RETURN] to go back to main menu Your choice: ************************************************************** ******** CLUSTAL W (1.82) Multiple Sequence Alignments ******** ************************************************************** 1. Sequence Input From Disc 2. Multiple Alignments 3. Profile / Structure Alignments 4. Phylogenetic trees S. Execute a system command H. HELP X. EXIT (leave program) Your choice: + cp seq.aln /usr/users/0/nigra/clustal/seq.aln + '[' 0 -eq 0 ']' + echo ' ' + echo 'Successfully copied seq.aln' Successfully copied seq.aln + echo ' ' + cp seq.msf /usr/users/0/nigra/clustal/seq.msf + '[' 0 -eq 0 ']' + echo ' ' + echo 'Successfully copied seq.msf' Successfully copied seq.msf + echo ' ' + cp seq.dnd /usr/users/0/nigra/clustal/seq.dnd + '[' 0 -eq 0 ']' + echo ' ' + echo 'Successfully copied seq.dnd' Successfully copied seq.dnd + echo ' ' + cd /usr/users/0/nigra/clustal + /bin/rm -rf /tmp/nigra/30731