PAMLX - input file error

Avik Ray

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Feb 28, 2019, 9:54:57 PM2/28/19

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Hello all,

Can anyone please help to find out the error? I can not run PAMLX with the attached infiles created with ALTER and READSEQ sequence converter. I was trying to figure out the 'unrecognised character X', but failed.

Many thanks in advance.

--------

the below message obtained when the sequence conversion done with ALTER (infile_Alter.phy)

ns = 87 ls = 3918

Reading sequences, interlaved format..

Reading seq # 1: B008

Reading seq # 2: AACATTTTCT GATTTTCAGT ACTCTCTGAA AACTACTATT

Reading seq # 3: TTAGGGCTTT ATCCATAGGC TACCGACCAA TGCTAGCAAA TAGCAC

Reading seq # 4: TGTGTTATAT GAGCAGAGCT ATTGGCTAGT TTGTTCATCC CTGTTA

Reading seq # 5: ACGAG

Reading seq # 6: TAGAAGA AATGATAAAG GATCCATTTG GAAGAAGGAA GAGACTTTG

Reading seq # 7: CATTTCACTT TCTGTTGTTC GCATAATTTA GTCTGAGGTT GGAATG

Reading seq # 8: T

Reading seq # 9: T GGTCCGAGAA

Reading seq #10: TATAGTGTTG TCTAGGTTTG TATCATGCTA GTCTTTCTAT CTAGTG

Reading seq #11: GCACAAGTAT TTTTACATGC TAGCTTATTC GTGTTCTCAT TTTCTC

Reading seq #12: AACAAAGC

/Applications/paml4.8/bin/codeml running...

err: unrecognised character X at 2120 seq 12 block 1.

/Applications/paml4.8/bin/codeml finished

--------------------------------

the below message obtained when the sequence conversion done with ALTER (infile_READSEQ.phy)

ns = 87 ls = 3918

Reading sequences, interlaved format..

Reading seq # 1: B008

Reading seq # 2: GGCCGGCGTG GTGCGTTGCT TGATGCTGAC GGATAGGTGG GGAGGG

Reading seq # 3: GGGAGGCGAT GGAGTTCGGG AACGGCGGGT CCTCCTCGTC GGAGCG

Reading seq # 4: GCGGCGGCGG AGGGGGCGAC GCTGGCGAGA CAGGGTTCGG TGTATT

Reading seq # 5: GACGTTCGAC GAGTTCCAGA GCGCGCTCGC TGGTGGCGGC GGCGGC

Reading seq # 6: GTGGTGGAAG CGGGTTCGGG AAGGACTTCG GCTCCATGAA CATGGA

Reading seq # 7: CTGCTCCGGA GCATCTGGAC CGCGGAGGAG AGCCAGGCCA TGGCCT

Reading seq # 8: CTCTGGCTCC GCCGCGGGGG TGGGCGTGGC CGTGGGGGCG CCGCCG

Reading seq # 9: CGCTGCAGCG CCAGGGCTCG CTCACCCTGC CCCGCACGCT CAGCGC

Reading seq #10: ACGGTGGACG AGGTATGGCG CAACCTTGTG CGCGACGAGC CACCGC

Reading seq #11: GGGGGCGGCG GATGGCGGCG ATATGCCACC CCAGCGGCAG TCGACC

Reading seq #12: GGGAGATGAC CCTGGAGGAG TTCTTGGTCA GAGCCGGCGT GGTCCG

Reading seq #13: AATCCACCCG CTGCGCCGCC CCCCGTTCCC CCGCCAATGC CGCCGC

Reading seq #14: AGTCCCGGTG GTCCCCAAGA CCACTGCCTT CTTGGGAAAC TTCCCC

Reading seq #15: CCAACGATGC CGGCGCGGCG GCGCTGGGCT TTGCGCCGCT CGGCAT

Reading seq #16: GATCCAGCCT TGGGCAATGG CCTGATGCCC AGGGCAGTGC CAGTGG

Reading seq #17: GCCTGGCGCC GCCGTCGCTA TGCAAACAGC GGTGAACCAG TTTGAT

Reading seq #18: GCGATAAGGG GAACAGCGAC CTGTCATCGC CGACGGAGCC AATGCC

Reading seq #19: TCCTTCGAAG GGTTGGTGAG GGGGAGAAGG AACGGTGGCG GAGTAG

Reading seq #20: AGTGGTGGAG AGGAGGCAGA GGAGGATGAT CAAGAACAGG GAGTCC

Reading seq #21: CGAGATCCCG CGCGCGCAAG CAGGTCTTAA ACTCTAAATT CTTTGT

Reading seq #22: ATTATGCATC TATTGCTATT GGAACCATTC TGTGAGAGTG CCAAGT

Reading seq #23: GAGCCTACCT CAAAATAAGA TGATAGAAAT ACTATTGGCA GTAACT

Reading seq #24: TTACTGGAGT TTCCCATGGC ATGCTAATCT TAGCAACTAT AATCAA

Reading seq #25: TGTGTTATAT GAGCAGAGCT GTTGGCTAGT TTGTTCATCC CTGTTA

Reading seq #26: TTTTGTTTAA AAGCAGATAA TTTCATCAAA TTTCCTGTCT TGCTAA

Reading seq #27: TTCCTTATTG GAAAAGGCTT ACACATTGGA ATTGGAAGCT GAAGTT

Reading seq #28: AACTCAAGGA GATGAACAAG GAATTGGAGA GGAAACAGGT TTCTTT

Reading seq #29: CAAACTCTGT TGTAGAATGT TGAATGGACT ATTAGCACAT GATTAA

Reading seq #30: GTTTTAATTA TTACAAACTT GACAAATGGA TATATTTGAT ATTTTA

Reading seq #31: AACTTCTATA TAGAAAGTTT TCCCACGAAA CACACCGTTT AGCGGT

Reading seq #32: AAAGCGTGCT AACGGAAACT GAGGTAAAAT TTGTATAGTC TCCTTT

Reading seq #33: ATAAAGAACA AGGCCTACTT TTAGTATAGT CTCCTTAAGA AGGATT

Reading seq #34: CTGCTGTTCT AAAACTCGTA GCTTCAGTTC TTAAACCCCA GTATTA

Reading seq #35: CTTTGCTTCT CTGTTCATGT TCATGACATC AGAGGGTTCA AACAGG

Reading seq #36: ACTATGACTT GCTCTTTCGA AGTAATGCAT ATGTTTCTCA GAAACA

Reading seq #37: CCATTGTGTC CAACATTGAG TTTCTCTTTT AGAATAATCT TCCAAT

Reading seq #38: CTGCAGTAAT AGTTTCAATT CCTTGTCTAG GAAGAAAATT TTTTTC

Reading seq #39: CTGACATGAT GCCAACAGCC CTGTTGCCTA CGTACACAAA ACGCAT

Reading seq #40: CCCAGCTTGC ACTTCTTATA AATGATTGGT GAACATGTCG GTAAAT

Reading seq #41: GCTCAAGTAT CATACTTGAA GTTTATCATT TTTATAGAC- TTTTTT

Reading seq #42: TTCCAGTCTA TGCGGAAAGC ATGCAATCAA CCATCTATTA TTACAA

Reading seq #43: TTAGGGCTTT ATCCATAGGC TACCGACCAA TGCTAGCAAA TAGCAC

Reading seq #44: TTACAGAATT CAAAGTTTGG ATATGCTCAT AGCGTACTCC TTTGAG

Reading seq #45: CTGATATTTT CTTTTTCTTC CATCTTGCAG GCAGATATCA TGGAAA

Reading seq #46: GAAAAATGAG GTAATTGCTT TCGTCGTTTG TTTATGTCAA ATGTGT

Reading seq #47: TTGACACTTT TCTCTGTTTT TACAGTTACA ACTATAATAA ATGTCA

Reading seq #48: AACGCTATGT GCTGTCTGCT TAATTTTTTA CTATGTTTTT AGCTTA

Reading seq #49: CATTTCACTT TCTGTTGTTC GCATAATTTA GTCTGAGGTT GGAATG

Reading seq #50: ATGTGCATTT GTGGGACAAA TGCTTCAATA CTTACAAGTT ACAACA

Reading seq #51: TATTTCGCAC ATGTAAACTT TGCATTCTCT TTCAGGTTAT TGCCTA

Reading seq #52: TGCTATCTTC CAGTTCGTTT GTTGAATTGT TGTCCATTCT TTTTGT

Reading seq #53: AAACATTTAT TTTTAGGTGT TATGCTTCTT GTATTCATTA CATGAA

Reading seq #54: AATCTAGGTC ATTTGCTGCT TTCAGTTAAA ACCCTTGCTT CTCATT

Reading seq #55: GCACAAGTAT TTTTACATGC TAGCTTATTC GTGTTCTCAT TTTCTC

Reading seq #56: GTAGACTACT TTTTATCTCG TGTGTTTTTC ATGGCACTAT ATGATG

Reading seq #57: TTTTTTTGAC ATAATATATG ATGGAATTTT TATTAATTCT TCTTTC

Reading seq #58: ATCAAACCAT CTCATATTAA TTTGGTAATT TGTGGAATCC AGTCC-

Reading seq #59: TCCTTATTTT GGTGTGGATT GTGCTCATTT CTAAGAACAG AGTAGT

Reading seq #60: TAGCTGCAGA ATTTCTTTAT TTCTGGTATA TTTACATATG GTTAGC

Reading seq #61: TTTCATGAAA AACATTTTCT GATTTTCAGT ACTCTCTGAA AACTAC

Reading seq #62: ATGGTACAAT GTTATTTGCA GTTTTTCTCG AGCCAATATC TCCCAA

Reading seq #63: TGGAGAAAAA ATTACTTAGT GATTAGCATT ATTATCCAAA TCATAG

Reading seq #64: TTGAGCGTCG ACTCTTGCAA AATTCAACTT CCAGTACCAT ACCATT

Reading seq #65: TCAGTATTCA GCGAACCTGC TTGTCAG-AA AAAAAGTGTG GAACGG

Reading seq #66: TTTATCGTAT TTTACCTGTG TAACTGCTTA AATTTTGTTT CACTGC

Reading seq #67: AGGTAGAAGA AATGATAAAG GATCCATTTG GAAGAAGGAA GAGACT

Reading seq #68: TTGCGAAGAA CACTGACTGG TCCCTGGTGA TGACGAGTGG TCGATG

Reading seq #69: GCAAATTCCC ACCTTCATCA GCGACTGTGC ATAATTTAAT CTGTTG

Reading seq #70: CCAATGGTGG ACGAACTTGT GCTTGATTAA TCTTCTAGTT TCATTT

Reading seq #71: TGCTAGCTGA TTCTGAGAAG GCTTCCAAAA CTGACATGTA GATTAT

Reading seq #72: AGACGAATGA AGCTGTCAGA ACAACTTCCT GTAATCCTTG AGAAAA

Reading seq #73: TATAGTGTTG TCTAGGTTTG TATCATGCTA GTCTTTCTAT CTAGTG

Reading seq #74: ACCCTAGAGA CCAGACATCT TGGATGAGTT CAGAGGTCGA TTTAAG

Reading seq #75: TCATGGGGAC CAAGAATCAT ACTGCAACCT GCCTGATGAC TAGCTA

Reading seq #76: AGGTAGTATG TAGCAATATC TGATATCTGT ACCTGCTTCC TGAAGT

Reading seq #77: ATTGTTATCT AGTGTATCTG ATATCTAGCG TGTAAACTGT AAAGGA

Reading seq #78: AAGCAGACCT AGTTCTCAAG AAAAAAAA-G TATAAGCAGA CCTACT

Reading seq #79: GCTTATAAGC CTGTTACT

Reading seq #80: B013

Reading seq #81: GGCCGGCGTG GTGCGTTGCT TGATGCTGAC GGATAGGTGG GGAGGG

Reading seq #82: GGGAGGCGAT GGAGTTCGGG AACGGCGGGT CCTCCTCGTC GGAGCG

Reading seq #83: GCGGCGGCGG AGGGGGCGAC GCTGGCGAGA CAGGGTTCGG TGTATT

Reading seq #84: GACGTTCGAC GAGTTCCAGA GCGCGCTCGC TGGTGGCGGC GGCGGC

Reading seq #85: GTGGTGGAAG CGGGTTCGGG AAGGACTTCG GCTCCATGAA CATGGA

Reading seq #86: CTGCTCCGGA GCATCTGGAC CGCGGAGGAG AGCCAGGCCA TGGCCT

Reading seq #87: CTCTGGCTCC GCCGCGGGGG TGGGCGTGGC CGTGGGGGCG CCGCCG

block 1: 50 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 0 50 4 4 4 4 4 4 4

block 2: 100 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54 22 55 54 54 54 54 54 54 50 100 54 54 54 54 54 54 54

block 3: 150 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 104 72 105 104 104 104 104 104 104 72 105 104 104 104 104 104 104 100 150 104 104 104 104 104 104 104

block 4: 200 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 154 122 155 154 154 154 154 154 154 122 155 154 154 154 154 154 154 122 155 154 154 154 154 154 154 150 200 154 154 154 154 154 154 154

block 5: 250 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 204 172 205 204 204 204 204 204 204 172 205 204 204 204 204 204 204 172 205 204 204 204 204 204 204 172 205 204 204 204 204 204 204 200 250 204 204 204 204 204 204 204

block 6: 300 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 254 222 255 254 254 254 254 254 254 222 255 254 254 254 254 254 254 222 255 254 254 254 254 254 254 222 255 254 254 254 254 254 254 222 255 254 254 254 254 254 254 250 300 254 254 254 254 254 254 254

block 7: 350 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 304 272 305 304 304 304 304 304 304 272 305 304 304 304 304 304 304 272 305 304 304 304 304 304 304 272 305 304 304 304 304 304 304 272 305 304 304 304 304 304 304 272 305 304 304 304 304 304 304 300 350 304 304 304 304 304 304 304

block 8: 400 354 354 354 354 354 354 354 354 354 354 354 354 354 354 354 354 354 354 354 354 354 322 355 354 354 354 354 354 354 322 355 354 354 354 354 354 354 322 355 354 354 354 354 354 354 322 355 354 354 354 354 354 354 322 355 354 354 354 354 354 354 322 355 354 354 354 354 354 354 322 355 354 354 354 354 354 354 350 400 354 354 354 354 354 354 354

block 9: 450 404 404 404 404 404 404 404 404 404 404 404 404 404 372 405 404 404 404 404 404 404 372 405 404 404 404 404 404 404 372 405 404 404 404 404 404 404 372 405 404 404 404 404 404 404 372 405 404 404 404 404 404 404 372 405 404 404 404 404 404 404 372 405 404 404 404 404 404 404 372 405 404 404 404 404 404 404 400 450 404 404 404 404 404 404 404

block 10: 500 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 422 455 454 454 454 454 454 454 450 500 454 454 454 454 454 422 455

block 11: 550 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 504 472 505 504 504 504 504 504 472 501 550 504 504 504 504 504 472 505

block 12: 600 554 554 554 554 554 522 555 554 554 554 554 554 554 522 555 554 554 554 554 554 554 522 555 554 554 554 554 554 554 522 555 554 554 554 554 554 554 522 555 554 554 554 554 554 554 522 555 554 554 554 554 554 554 522 555 554 554 554 554 554 554 522 555 554 554 554 554 554 522 523 555 554 554 554 554 554 522 551 600 554 554 554 554 554 522 555

block 13: 650 604 604 604 604 604 572 605 604 604 604 604 604 604 572 605 604 604 604 604 604 604 572 605 604 604 604 604 604 604 572 605 604 604 604 604 604 604 572 605 604 604 604 604 604 604 572 605 604 604 604 604 604 604 572 605 604 604 604 604 604 572 573 605 604 604 604 604 604 572 573 605 604 604 604 604 604 572 601 650 604 604 604 604 604 572 605

block 14: 700 654 654 654 654 654 622 655 654 654 654 654 654 654 622 655 654 654 654 654 654 654 622 655 654 654 654 654 654 654 622 655 654 654 654 654 654 654 622 655 654 654 654 654 654 654 622 655 654 654 654 654 654 622 623 655 654 654 654 654 654 622 623 655 654 654 654 654 654 622 623 655 654 654 654 654 654 622 651 700 654 654 654 654 654 622 655

block 15: 750 704 704 704 704 704 672 705 704 704 704 704 704 704 672 705 704 704 704 704 704 704 672 705 704 704 704 704 704 704 672 705 704 704 704 704 704 704 672 705 704 704 704 704 704 672 673 705 704 704 704 704 704 672 673 705 704 704 704 704 704 672 673 705 704 704 704 704 704 672 673 705 704 704 704 704 704 672 701 750 704 704 704 704 704 672 705

block 16: 800 754 754 754 754 754 722 755 754 754 754 754 754 754 722 755 754 754 754 754 754 754 722 755 754 754 754 754 754 754 722 755 754 754 754 754 754 722 723 755 754 754 754 754 754 722 723 755 754 754 754 754 754 722 723 755 754 754 754 754 754 722 723 755 754 754 754 754 754 722 723 755 754 754 754 754 754 722 751 800 754 754 754 754 754 722 755

block 17: 850 804 804 804 804 804 772 805 804 804 804 804 804 804 772 805 804 804 804 804 804 804 772 805 804 804 804 804 804 772 773 805 804 804 804 804 804 772 773 805 804 804 804 804 804 772 773 805 804 804 804 804 804 772 773 805 804 804 804 804 804 772 773 805 804 804 804 804 804 772 773 805 804 804 804 804 804 772 801 850 804 804 804 804 804 772 805

/Applications/paml4.8/bin/codeml running...

err: unrecognised character X at 774 seq 23 block 18.

/Applications/paml4.8/bin/codeml finished

infile_Alter.phy

infile_READSEQ.phy

Avik Ray

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Feb 28, 2019, 10:03:21 PM2/28/19

to PAML discussion group

Sorry, forgot to mention was running codeml and the following are codeml.ctl files.

Thanks.

codeml.ctl.tmp

Ziheng

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Mar 21, 2019, 3:06:37 PM3/21/19

to PAML discussion group

The sequence alignment file has errors. The program reads the first sequence name correctly, which is B008.
But it read some sequence as the name of the second sequence, and so on.
Perhaps look at some example files in the package to get familiar with the file format.
Ziheng

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