[phylocom-user] Phylocom input files

Lim yjlim8 at gmail.com
Wed May 19 21:25:04 PDT 2010


Hi,
I'd greatly appreciate if someone can help me figure out what's wrong
with my input files!

The sample data is in txt format (attached), and the final line has a
return character.  The newick tree file has a semicolon at the end,
and the taxa names do not begin with a number.  However, I'm getting
the error message:

File `likelihood.txt' has unix newlines
Bus error

Thanks!
Seara Lim
MSc student
University of British Columbia
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HA1C	2	a33_ascoAtheli
HA1D	1	a33_ascoAtheli
HA1E	1	a33_ascoAtheli
HA1F	4	a33_ascoAtheli
HA2B	2	a33_ascoAtheli
HA2C	1	a33_ascoAtheli
HA3C	4	a33_ascoAtheli
HA3D	5	a33_ascoAtheli
HA3A	1	a32_ascoAtheli
HA2C	1	a85_Atheliacea
HA3C	6	a85_Atheliacea
HA3C	1	a83_Atheliacea
HA3B	1	a87_Atheliacea
HA3C	8	a77_cfChamonix
C9_4	3	a100_cfDermSLUB
HA1E	2	a100_cfDermSLUB
HA2A	2	a100_cfDermSLUB
HA3A	2	a100_cfDermSLUB
HA3D	1	a22_cfHelicoon
HA1D	1	a23_cfHelicoon
HA3A	1	a10_cfMagnapor
HA2B	1	a37_Cgeophilum
HA2C	1	a37_Cgeophilum
C26_2	1	a36_Cgeophilum
C26_4	1	a36_Cgeophilum
C9_1	2	a36_Cgeophilum
HA2C	2	a36_Cgeophilum
N11_2	1	a36_Cgeophilum
N11_3	4	a36_Cgeophilum
N18_1	2	a36_Cgeophilum
OCHB3	1	a36_Cgeophilum
OCHC2	1	a36_Cgeophilum
P31_2	1	a36_Cgeophilum
HA1E	2	a38_Cgeophilum
HA2B	1	a38_Cgeophilum
HA3A	1	a38_Cgeophilum
HA3C	2	a38_Cgeophilum
HA3D	1	a38_Cgeophilum
HA1E	6	a78_Chamonixia
HA1D	1	a63_Clavulinac
HA1F	1	a63_Clavulinac
OCHA5	1	a63_Clavulinac
OCHB4	2	a63_Clavulinac
HA3A	1	a62_Clavulinac
HA1C	2	a97_CortECUBC1
OCHB4	3	a97_CortECUBC1
OCHC2	11	a101_CortECUBC9
HA3D	1	a88_Corticiace
HA1F	2	a108_Cortinariu
HA2A	1	a108_Cortinariu
HA1C	2	a106_Cortinariu
HA1D	3	a106_Cortinariu
HA2E	1	a106_Cortinariu
HA1E	2	a98_Cortinariu
HA2E	3	a99_Cortinariu
HA3A	1	a99_Cortinariu
HA2C	2	a96_Cortinariu
HA2E	1	a94_Cortinariu
HA1D	3	a102_Cortinariu
HA1C	1	a95_CortSLUBC2
HA2A	2	a95_CortSLUBC2
HA2C	1	a95_CortSLUBC2
HA2E	9	a95_CortSLUBC2
OCHC1	7	a95_CortSLUBC2
OCHC3	7	a95_CortSLUBC2
C9_4	2	a105_CortSLUBC2
HA3D	3	a105_CortSLUBC2
OCHB1	1	a105_CortSLUBC2
P31_3	3	a105_CortSLUBC2
N30_4	9	a131_CortSWUBC7
P1_3	5	a131_CortSWUBC7
P1_4	4	a131_CortSWUBC7
P31_1	3	a131_CortSWUBC7
P31_3	2	a131_CortSWUBC7
P31_4	5	a131_CortSWUBC7
HA1E	4	a66_Craterellu
C21_1	1	a109_DermSLUBC1
C21_3	9	a109_DermSLUBC1
C21_4	1	a109_DermSLUBC1
C26_1	1	a109_DermSLUBC1
C26_3	2	a109_DermSLUBC1
C26_4	1	a109_DermSLUBC1
C9_1	6	a109_DermSLUBC1
C9_3	20	a109_DermSLUBC1
C9_4	6	a109_DermSLUBC1
HA2A	1	a109_DermSLUBC1
N18_2	11	a109_DermSLUBC1
N30_1	2	a109_DermSLUBC1
N30_3	1	a109_DermSLUBC1
P1_3	3	a109_DermSLUBC1
P20_1	2	a109_DermSLUBC1
P20_2	7	a109_DermSLUBC1
P20_3	1	a109_DermSLUBC1
P20_4	3	a109_DermSLUBC1
P31_4	2	a109_DermSLUBC1
C21_1	5	a35_DQ474324Cg
C21_2	2	a35_DQ474324Cg
C26_1	4	a35_DQ474324Cg
C26_2	9	a35_DQ474324Cg
C26_4	2	a35_DQ474324Cg
C9_1	3	a35_DQ474324Cg
C9_4	3	a35_DQ474324Cg
N11_1	3	a35_DQ474324Cg
N11_2	4	a35_DQ474324Cg
N11_3	6	a35_DQ474324Cg
N11_4	12	a35_DQ474324Cg
N18_1	5	a35_DQ474324Cg
N30_1	10	a35_DQ474324Cg
N30_2	5	a35_DQ474324Cg
N30_3	4	a35_DQ474324Cg
N30_4	2	a35_DQ474324Cg
P1_1	1	a35_DQ474324Cg
P1_2	1	a35_DQ474324Cg
P1_3	7	a35_DQ474324Cg
P1_4	6	a35_DQ474324Cg
P20_1	3	a35_DQ474324Cg
P20_3	7	a35_DQ474324Cg
P20_4	1	a35_DQ474324Cg
P31_1	1	a35_DQ474324Cg
P31_2	6	a35_DQ474324Cg
P31_3	2	a35_DQ474324Cg
P31_4	5	a35_DQ474324Cg
C21_2	9	a67_DQ474425Ct
C9_2	23	a67_DQ474425Ct
N18_1	16	a67_DQ474425Ct
N18_3	15	a67_DQ474425Ct
N30_2	11	a67_DQ474425Ct
P1_2	18	a67_DQ474425Ct
P20_1	17	a67_DQ474425Ct
P31_4	8	a67_DQ474425Ct
C21_1	1	a73_DQ474688Pi
C21_2	5	a73_DQ474688Pi
C21_3	4	a73_DQ474688Pi
C21_4	1	a73_DQ474688Pi
C26_1	3	a73_DQ474688Pi
C26_2	1	a73_DQ474688Pi
C26_4	9	a73_DQ474688Pi
C9_4	4	a73_DQ474688Pi
N11_1	9	a73_DQ474688Pi
N11_3	11	a73_DQ474688Pi
N11_4	1	a73_DQ474688Pi
N30_1	2	a73_DQ474688Pi
N30_2	8	a73_DQ474688Pi
N30_3	5	a73_DQ474688Pi
N30_4	2	a73_DQ474688Pi
OCHC1	4	a73_DQ474688Pi
P1_1	5	a73_DQ474688Pi
P1_2	2	a73_DQ474688Pi
P1_3	5	a73_DQ474688Pi
P1_4	6	a73_DQ474688Pi
P20_3	1	a73_DQ474688Pi
P31_1	16	a73_DQ474688Pi
P31_4	2	a73_DQ474688Pi
C26_2	3	a71_DQ474694Pc
C26_2	5	a70_DQ474727Pi
N11_1	1	a70_DQ474727Pi
N11_3	1	a70_DQ474727Pi
N18_2	1	a70_DQ474727Pi
N30_1	2	a70_DQ474727Pi
P20_3	2	a70_DQ474727Pi
P31_2	1	a70_DQ474727Pi
C21_3	6	a40_DQ474751Tr
P1_3	1	a40_DQ474751Tr
OCHA3	1	a40_DQ474751Tr
N11_1	1	a40_DQ474751Tr
N11_4	5	a40_DQ474751Tr
N30_2	1	a40_DQ474751Tr
N18_4	2	a135_DQ481671Co
C21_1	6	a133_DQ481674Co
C26_1	14	a133_DQ481674Co
C9_4	4	a133_DQ481674Co
P20_4	6	a133_DQ481674Co
P1_4	3	a115_DQ481676Co
C9_4	1	a123_DQ481677Co
N11_3	1	a130_DQ481678Co
C26_3	1	a138_DQ481681Co
N18_4	11	a129_DQ481685Co
P1_4	1	a119_DQ481693Co
P20_4	4	a119_DQ481693Co
P31_1	1	a119_DQ481693Co
P31_2	2	a112_DQ481717Co
P31_3	1	a112_DQ481717Co
P31_4	1	a114_DQ481722Co
C21_1	4	a132_DQ481723Co
N18_4	7	a132_DQ481723Co
P1_3	1	a122_DQ481725Co
P20_3	1	a122_DQ481725Co
P31_2	2	a122_DQ481725Co
P31_4	1	a122_DQ481725Co
N18_4	1	a137_DQ481741Co
P20_2	3	a120_DQ481762Co
P1_1	1	a116_DQ481804Co
C26_4	2	a127_DQ481832Co
C9_3	2	a127_DQ481832Co
N18_3	8	a127_DQ481832Co
P20_2	8	a127_DQ481832Co
C9_4	1	a136_DQ481834Co
N30_1	5	a136_DQ481834Co
P31_2	1	a136_DQ481834Co
N11_1	2	a118_DQ481838Co
P1_2	1	a118_DQ481838Co
P31_3	2	a118_DQ481838Co
C21_4	21	a124_DQ481839Co
N30_4	7	a134_DQ481841Co
C21_2	9	a117_DQ481852Co
C21_3	2	a117_DQ481852Co
C9_4	1	a117_DQ481852Co
P20_4	1	a117_DQ481852Co
P31_4	1	a113_DQ481858Co
C9_1	3	a125_DQ481964cf
C9_1	3	a68_DQ481970Cl
N11_2	6	a68_DQ481970Cl
P31_3	1	a68_DQ481970Cl
N11_4	1	a44_DQ481982Hy
C26_1	1	a29_DQ481983as
P31_2	1	a31_DQ481984as
N18_1	1	a30_DQ481985as
P31_1	2	a126_DQ481998Ru
P20_3	1	a121_DQ482000Th
N18_2	11	a128_DQ482016Ts
P1_2	1	a128_DQ482016Ts
P1_3	1	a128_DQ482016Ts
P1_4	4	a128_DQ482016Ts
N18_2	2	a43_DQ482025Ty
P1_3	1	a43_DQ482025Ty
P31_1	2	a43_DQ482025Ty
P31_2	7	a43_DQ482025Ty
C26_4	2	a7_DQ497921Me
C9_3	1	a7_DQ497921Me
P20_2	1	a7_DQ497921Me
C26_2	1	a4_DQ497922Ma
C26_4	1	a4_DQ497922Ma
P31_2	1	a4_DQ497922Ma
C26_4	1	a1_DQ497937Pe
N30_4	1	a3_DQ497940He
P31_1	1	a3_DQ497940He
C26_4	2	a3_DQ497940He
N18_2	1	a3_DQ497940He
P20_2	1	a3_DQ497940He
P20_3	1	a5_DQ497942Ma
P31_2	2	a5_DQ497942Ma
C26_4	1	a8_DQ497945Me
N11_3	1	a8_DQ497945Me
N18_2	1	a8_DQ497945Me
C21_1	1	a28_DQ497949as
C26_2	1	a28_DQ497949as
C9_1	5	a28_DQ497949as
P31_3	2	a28_DQ497949as
P20_1	1	a9_DQ497950He
C26_2	1	a2_DQ497966He
P20_2	1	a2_DQ497966He
N11_4	1	a27_DQ497972Ch
P20_3	1	a25_DQ497976He
N11_4	1	a6_DQ497978Lv
N30_4	1	a6_DQ497978Lv
C21_1	1	a24_DQ497979Pe
C26_1	1	a24_DQ497979Pe
N30_1	1	a24_DQ497979Pe
OCHA2	1	a24_DQ497979Pe
HA1C	2	a15_ElaphomycS
HA2A	2	a15_ElaphomycS
OCHA2	13	a65_EU057081Cr
OCHA3	21	a65_EU057081Cr
OCHA5	5	a65_EU057081Cr
OCHB1	14	a65_EU057081Cr
OCHB3	14	a65_EU057081Cr
OCHB4	10	a65_EU057081Cr
OCHC2	9	a65_EU057081Cr
OCHC6	18	a65_EU057081Cr
OCHB1	2	a64_EU057082Cr
OCHB1	4	a76_EU057083Bo
OCHC3	2	a76_EU057083Bo
OCHB3	2	a34_EU057084as
OCHB4	2	a34_EU057084as
OCHB1	1	a79_EU057085Ch
OCHA2	1	a59_EU057086Th
OCHA1	1	a103_EU057090Co
OCHA5	4	a103_EU057090Co
OCHC3	2	a42_EU057092La
OCHC1	1	a110_EU057093Co
OCHB3	1	a107_EU057095Co
OCHB1	1	a56_EU057098Ru
OCHB3	1	a56_EU057098Ru
OCHB4	2	a56_EU057098Ru
C26_3	18	a46_EU057099La
N30_3	11	a46_EU057099La
OCHA1	7	a46_EU057099La
OCHB1	2	a46_EU057099La
P31_2	2	a46_EU057099La
OCHA1	2	a55_EU057100Ru
OCHA2	3	a52_EU057103Ru
OCHA5	3	a52_EU057103Ru
OCHA5	1	a58_EU057106Ru
OCHB6	10	a58_EU057106Ru
OCHC3	3	a92_EU057108Le
OCHA5	1	a104_EU057109Co
OCHB1	1	a104_EU057109Co
OCHB6	5	a69_EU057111Pi
OCHC3	2	a69_EU057111Pi
OCHA1	3	a90_EU057112Le
OCHC1	7	a90_EU057112Le
OCHC3	1	a90_EU057112Le
OCHA1	2	a60_EU057113Ps
OCHC3	1	a80_EU057114Co
OCHA1	2	a45_EU057115Al
C21_1	1	a61_EU057117Co
OCHC1	1	a61_EU057117Co
OCHC3	1	a61_EU057117Co
OCHA3	1	a48_EU057119Ru
OCHA5	2	a48_EU057119Ru
OCHA1	1	a72_EU057120Pi
OCHC2	2	a72_EU057120Pi
OCHC3	3	a72_EU057120Pi
OCHC6	3	a91_EU057121Le
OCHB3	2	a84_EU057123At
OCHB6	1	a111_EU057124Co
OCHA1	1	a39_EU057125Cg
OCHA2	3	a39_EU057125Cg
OCHB1	1	a39_EU057125Cg
OCHC6	4	a39_EU057125Cg
OCHA2	6	a86_EU057126At
OCHA3	1	a86_EU057126At
OCHA5	2	a86_EU057126At
OCHB3	1	a86_EU057126At
OCHB6	6	a86_EU057126At
OCHA1	5	a26_EU669213Ot
HA2B	2	a93_Galerinafi
N11_1	4	a93_Galerinafi
N11_4	3	a93_Galerinafi
N18_4	1	a93_Galerinafi
P20_3	1	a93_Galerinafi
C9_1	2	a18_Helotiales
HA2A	1	a18_Helotiales
HA2B	1	a18_Helotiales
OCHA5	1	a18_Helotiales
P31_1	1	a18_Helotiales
P31_2	2	a18_Helotiales
P31_3	4	a18_Helotiales
C21_1	2	a16_Helotiales
HA2E	1	a16_Helotiales
N11_3	1	a16_Helotiales
N11_4	1	a16_Helotiales
P31_3	1	a16_Helotiales
HA3B	1	a17_Helotiales
C26_2	1	a47_Lactariusp
C26_4	5	a47_Lactariusp
C9_2	4	a47_Lactariusp
C9_3	1	a47_Lactariusp
C9_4	1	a47_Lactariusp
HA2A	3	a47_Lactariusp
N11_2	14	a47_Lactariusp
N18_3	3	a47_Lactariusp
N30_1	1	a47_Lactariusp
N30_2	2	a47_Lactariusp
OCHA2	1	a47_Lactariusp
OCHA2	1	a47_Lactariusp
OCHB4	2	a47_Lactariusp
OCHB6	2	a47_Lactariusp
OCHC2	3	a47_Lactariusp
OCHC3	1	a47_Lactariusp
P1_1	16	a47_Lactariusp
P1_2	1	a47_Lactariusp
P1_3	2	a47_Lactariusp
P20_2	5	a47_Lactariusp
P20_3	5	a47_Lactariusp
P31_3	7	a47_Lactariusp
HA2B	1	a11_Magnaporth
HA2C	1	a13_Magnaporth
OCHC1	1	a13_Magnaporth
HA1D	2	a12_Magnaporth
HA1E	2	a12_Magnaporth
HA1F	3	a12_Magnaporth
HA2C	3	a12_Magnaporth
HA2E	1	a12_Magnaporth
HA3A	3	a12_Magnaporth
HA1F	1	a20_Mvariabili
HA2C	1	a20_Mvariabili
HA2E	1	a20_Mvariabili
HA2C	1	a21_Mvariabili
HA3B	1	a21_Mvariabili
HA3D	2	a21_Mvariabili
OCHB4	1	a21_Mvariabili
HA1F	2	a19_Mvariabili
HA2C	1	a19_Mvariabili
HA1C	1	a14_Phialophor
HA1D	1	a14_Phialophor
HA1F	1	a14_Phialophor
HA2A	1	a14_Phialophor
HA2B	1	a14_Phialophor
HA2C	1	a14_Phialophor
HA3A	1	a14_Phialophor
HA3C	1	a14_Phialophor
HA3D	1	a14_Phialophor
HA1D	4	a74_PilodermaS
HA1F	3	a74_PilodermaS
HA2B	2	a74_PilodermaS
HA2B	4	a75_PilodermaS
HA2C	2	a75_PilodermaS
HA3D	1	a49_Russulaaff
HA1E	4	a50_Russuladec
HA3B	10	a50_Russuladec
HA1C	14	a53_Russulaocc
HA3A	3	a53_Russulaocc
HA3C	3	a53_Russulaocc
HA3B	1	a54_RussulaSLU
HA1D	4	a57_RussulaSLU
HA1F	5	a57_RussulaSLU
HA2A	8	a57_RussulaSLU
HA2C	1	a57_RussulaSLU
HA2E	2	a57_RussulaSLU
HA3D	2	a57_RussulaSLU
HA2B	10	a51_Russulaxer
HA2C	6	a51_Russulaxer
HA2E	3	a51_Russulaxer
HA3A	12	a51_Russulaxer
HA3D	6	a51_Russulaxer
HA2C	3	a41_Tricholoma
HA3B	8	a89_Tylosporaa
HA2E	1	a82_Tylosporaf
HA3B	2	a81_Tylosporaf
HA3C	2	a81_Tylosporaf
HA3D	1	a81_Tylosporaf
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