GeneMarkES log

##Input
##n	n:500	n:N50	min	N80	N50	N20	E-size	max	sum	name
##34	34	9	18562	111345	159114	321119	198500	406529	4313902	test.fa
##
##gm_es.pl test.fa --BP OFF > GenemarkES.log 2>&1


running hmm2nt.a2
74 files IN
Clusters were defined as:
 0 <= GC% <= 99
99 < GC% <= 99
99 < GC% <= 100

Parsing dna.fa.good.cod

Program complete
----------------
10 sequences found
11 dna.fa.good.ini
zero order for Ini
GC Range: (0,99)
10 sequences of length 12 used from 10
total sequences in dna.fa.good.ini
Generating model...
T    0.40 0.00 0.20 0.20 0.20 0.40 0.00 1.00 0.00 0.20 0.20 0.30
C    0.20 0.60 0.40 0.20 0.20 0.10 0.00 0.00 0.00 0.00 0.10 0.10
A    0.10 0.40 0.10 0.30 0.40 0.20 1.00 0.00 0.00 0.30 0.50 0.30
G    0.30 0.00 0.30 0.30 0.20 0.30 0.00 0.00 1.00 0.50 0.20 0.30
Done
11 lines read from dna.fa.good.ter
10 sequences obtained
1 comment lines
0 lines contained no sequence (or improperly formatted seq)
4 sequences used TAA
4 sequences used TAG
2 sequences used TGA
0 sequences did not begin with a stop codon
All lines accounted for
Done
4 dna.fa.good.taa
zero order for TAA
GC Range: (0,99)
4 sequences of length 12 used from 4
total sequences in dna.fa.good.taa
Generating model...
T    1.00 0.00 0.00 0.50 0.25 0.25 0.25 0.25 0.25 0.00 0.25 0.00
C    0.00 0.00 0.00 0.25 0.50 0.25 0.50 0.25 0.25 0.75 0.25 0.25
A    0.00 1.00 1.00 0.25 0.25 0.25 0.00 0.25 0.50 0.25 0.50 0.50
G    0.00 0.00 0.00 0.00 0.00 0.25 0.25 0.25 0.00 0.00 0.00 0.25
Done
4 dna.fa.good.tag
zero order for TAG
GC Range: (0,99)
4 sequences of length 12 used from 4
total sequences in dna.fa.good.tag
Generating model...
T    1.00 0.00 0.00 0.25 0.25 0.25 0.00 0.00 0.25 0.00 0.00 0.25
C    0.00 0.00 0.00 0.25 0.25 0.25 0.00 0.50 0.25 0.50 0.25 0.00
A    0.00 1.00 0.00 0.00 0.50 0.25 0.50 0.50 0.50 0.25 0.50 0.00
G    0.00 0.00 1.00 0.50 0.00 0.25 0.50 0.00 0.00 0.25 0.25 0.75
Done
2 dna.fa.good.tga
zero order for TGA
GC Range: (0,99)
2 sequences of length 12 used from 2
total sequences in dna.fa.good.tga
Generating model...
T    1.00 0.00 0.00 0.50 0.00 0.50 0.00 0.00 1.00 0.00 0.00 0.00
C    0.00 0.00 0.00 0.50 0.50 0.00 0.50 0.50 0.00 0.00 0.50 0.00
A    0.00 0.00 1.00 0.00 0.50 0.00 0.00 0.50 0.00 0.50 0.50 0.50
G    0.00 1.00 0.00 0.00 0.00 0.50 0.50 0.00 0.00 0.50 0.00 0.50
Done
23 dna.fa.good.don
zero order for DON
GC Range: (0,99)
22 sequences of length 9 used from 22
total sequences in dna.fa.good.don
Generating model...
T    0.05 0.18 0.32 0.00 1.00 0.27 0.18 0.32 0.45
C    0.23 0.32 0.09 0.00 0.00 0.23 0.27 0.32 0.27
A    0.32 0.36 0.36 0.00 0.00 0.00 0.50 0.23 0.18
G    0.41 0.14 0.23 1.00 0.00 0.50 0.05 0.14 0.09
Done
23 dna.fa.good.acc
zero order for ACC
GC Range: (0,99)
22 sequences of length 21 used from 22
total sequences in dna.fa.good.acc
Generating model...
T    0.18 0.27 0.27 0.27 0.32 0.09 0.36 0.36 0.09 0.27 0.18 0.32 0.23 0.18 0.23 0.14 0.41 0.14 0.00 0.00 0.23
C    0.14 0.27 0.27 0.23 0.18 0.41 0.18 0.18 0.23 0.14 0.27 0.14 0.36 0.36 0.32 0.32 0.18 0.45 0.00 0.00 0.27
A    0.27 0.36 0.09 0.36 0.41 0.27 0.32 0.32 0.36 0.36 0.32 0.32 0.18 0.23 0.32 0.36 0.18 0.14 1.00 0.00 0.18
G    0.41 0.09 0.36 0.14 0.09 0.23 0.14 0.14 0.32 0.23 0.23 0.23 0.23 0.23 0.14 0.18 0.23 0.27 0.00 1.00 0.32
Done
running hmm2nt.a2
74 files IN
Clusters were defined as:
 0 <= GC% <= 99
99 < GC% <= 99
99 < GC% <= 100

Parsing dna.fa.good.cod

Program complete
----------------
4 sequences found
5 dna.fa.good.ini
zero order for Ini
GC Range: (0,99)
4 sequences of length 12 used from 4
total sequences in dna.fa.good.ini
Generating model...
T    0.50 0.00 0.25 0.00 0.50 0.50 0.00 1.00 0.00 0.25 0.50 0.50
C    0.25 0.25 0.25 0.25 0.00 0.25 0.00 0.00 0.00 0.00 0.00 0.00
A    0.25 0.75 0.00 0.50 0.25 0.25 1.00 0.00 0.00 0.25 0.25 0.00
G    0.00 0.00 0.50 0.25 0.25 0.00 0.00 0.00 1.00 0.50 0.25 0.50
Done
5 lines read from dna.fa.good.ter
4 sequences obtained
1 comment lines
0 lines contained no sequence (or improperly formatted seq)
1 sequences used TAA
1 sequences used TAG
2 sequences used TGA
0 sequences did not begin with a stop codon
All lines accounted for
Done
1 dna.fa.good.taa
zero order for TAA
GC Range: (0,99)
1 sequences of length 12 used from 1
total sequences in dna.fa.good.taa
Generating model...
T    1.00 0.00 0.00 1.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
C    0.00 0.00 0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00
A    0.00 1.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 1.00 1.00 1.00
G    0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Done
1 dna.fa.good.tag
zero order for TAG
GC Range: (0,99)
1 sequences of length 12 used from 1
total sequences in dna.fa.good.tag
Generating model...
T    1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
C    0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 1.00 0.00
A    0.00 1.00 0.00 0.00 1.00 0.00 0.00 1.00 1.00 0.00 0.00 0.00
G    0.00 0.00 1.00 0.00 0.00 1.00 1.00 0.00 0.00 0.00 0.00 1.00
Done
2 dna.fa.good.tga
zero order for TGA
GC Range: (0,99)
2 sequences of length 12 used from 2
total sequences in dna.fa.good.tga
Generating model...
T    1.00 0.00 0.00 0.50 0.00 0.50 0.00 0.00 1.00 0.00 0.00 0.00
C    0.00 0.00 0.00 0.50 0.50 0.00 0.50 0.50 0.00 0.00 0.50 0.00
A    0.00 0.00 1.00 0.00 0.50 0.00 0.00 0.50 0.00 0.50 0.50 0.50
G    0.00 1.00 0.00 0.00 0.00 0.50 0.50 0.00 0.00 0.50 0.00 0.50
Done
14 dna.fa.good.don
zero order for DON
GC Range: (0,99)
13 sequences of length 9 used from 13
total sequences in dna.fa.good.don
Generating model...
T    0.15 0.31 0.46 0.00 1.00 0.15 0.15 0.46 0.46
C    0.08 0.46 0.23 0.00 0.00 0.23 0.46 0.38 0.38
A    0.31 0.15 0.23 0.00 0.00 0.00 0.31 0.08 0.15
G    0.46 0.08 0.08 1.00 0.00 0.62 0.08 0.08 0.00
Done
14 dna.fa.good.acc
zero order for ACC
GC Range: (0,99)
13 sequences of length 21 used from 13
total sequences in dna.fa.good.acc
Generating model...
T    0.15 0.15 0.23 0.23 0.38 0.00 0.46 0.38 0.23 0.15 0.38 0.31 0.31 0.15 0.15 0.15 0.46 0.15 0.00 0.00 0.23
C    0.15 0.46 0.46 0.08 0.38 0.46 0.08 0.15 0.38 0.38 0.38 0.08 0.31 0.54 0.31 0.31 0.23 0.38 0.00 0.00 0.23
A    0.23 0.38 0.00 0.38 0.15 0.23 0.31 0.15 0.15 0.31 0.23 0.31 0.15 0.15 0.46 0.38 0.08 0.38 1.00 0.00 0.23
G    0.46 0.00 0.31 0.31 0.08 0.31 0.15 0.31 0.23 0.15 0.00 0.31 0.23 0.15 0.08 0.15 0.23 0.08 0.00 1.00 0.31
Done
running hmm2nt.a2
74 files IN
Clusters were defined as:
 0 <= GC% <= 99
99 < GC% <= 99
99 < GC% <= 100

Parsing dna.fa.good.cod

Program complete
----------------
2 sequences found
3 dna.fa.good.ini
zero order for Ini
GC Range: (0,99)
2 sequences of length 12 used from 2
total sequences in dna.fa.good.ini
Generating model...
T    0.50 0.00 0.00 0.00 0.00 0.50 0.00 1.00 0.00 0.00 0.00 0.00
C    0.00 0.00 0.50 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
A    0.50 1.00 0.00 1.00 0.50 0.50 1.00 0.00 0.00 0.50 0.50 0.00
G    0.00 0.00 0.50 0.00 0.50 0.00 0.00 0.00 1.00 0.50 0.50 1.00
Done
3 lines read from dna.fa.good.ter
2 sequences obtained
1 comment lines
0 lines contained no sequence (or improperly formatted seq)
1 sequences used TAA
0 sequences used TAG
1 sequences used TGA
0 sequences did not begin with a stop codon
All lines accounted for
Done
1 dna.fa.good.taa
zero order for TAA
GC Range: (0,99)
1 sequences of length 12 used from 1
total sequences in dna.fa.good.taa
Generating model...
T    1.00 0.00 0.00 1.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
C    0.00 0.00 0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00
A    0.00 1.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 1.00 1.00 1.00
G    0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Done
0 dna.fa.good.tag
zero order for TAG
Use of uninitialized value $length in concatenation (.) or string at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 104.
Use of uninitialized value $length in concatenation (.) or string at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 110.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117.
GC Range: (0,99)
0 sequences of length  used from 0
total sequences in dna.fa.good.tag
Generating model...
T    
C    
A    
G    
Done
1 dna.fa.good.tga
zero order for TGA
GC Range: (0,99)
1 sequences of length 12 used from 1
total sequences in dna.fa.good.tga
Generating model...
T    1.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 0.00
C    0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
A    0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
G    0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00 1.00
Done

program runs as fast as it can
..............................
Obtaining data from the file

1 dna.fa.good.gb.don.ph0
zero order for DON 0
Use of uninitialized value $length in concatenation (.) or string at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 104, <IN> line 1.
Use of uninitialized value $length in concatenation (.) or string at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 110, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Error: unknown line format
       GC%	Intron	Accession	 (File generated at 2014/04/10 Thu 19:12:13 EDT)

GC Range: (0,99)
0 sequences of length  used from 1
total sequences in dna.fa.good.gb.don.ph0
Generating model...
T    
C    
A    
G    
Done
4 dna.fa.good.gb.don.ph1
zero order for DON 1
Error: unknown line format
       GC%	Intron	Accession	 (File generated at 2014/04/10 Thu 19:12:13 EDT)

GC Range: (0,99)
3 sequences of length 9 used from 4
total sequences in dna.fa.good.gb.don.ph1
Generating model...
T    0.67 0.33 0.67 0.00 1.00 0.00 0.33 0.00 0.33
C    0.00 0.33 0.00 0.00 0.00 0.00 0.33 0.67 0.67
A    0.00 0.00 0.33 0.00 0.00 0.00 0.00 0.33 0.00
G    0.33 0.33 0.00 1.00 0.00 1.00 0.33 0.00 0.00
Done
3 dna.fa.good.gb.don.ph2
zero order for DON 1
Error: unknown line format
       GC%	Intron	Accession	 (File generated at 2014/04/10 Thu 19:12:13 EDT)

GC Range: (0,99)
2 sequences of length 9 used from 3
total sequences in dna.fa.good.gb.don.ph2
Generating model...
T    0.00 0.00 0.50 0.00 1.00 0.50 0.50 0.50 1.00
C    0.00 0.50 0.00 0.00 0.00 0.00 0.50 0.50 0.00
A    0.50 0.50 0.50 0.00 0.00 0.00 0.00 0.00 0.00
G    0.50 0.00 0.00 1.00 0.00 0.50 0.00 0.00 0.00
Done
1 dna.fa.good.gb.acc.ph0
zero order for ACC 0
Use of uninitialized value $length in concatenation (.) or string at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 104, <IN> line 1.
Use of uninitialized value $length in concatenation (.) or string at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 110, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Use of uninitialized value $length in subtraction (-) at /home/macmanes/gm_es_bp_linux64_v2.3e/gmes/make_nt_freq.mat line 117, <IN> line 1.
Error: unknown line format
       GC%	Intron	Accession	 (File generated at 2014/04/10 Thu 19:12:13 EDT)

GC Range: (0,99)
0 sequences of length  used from 1
total sequences in dna.fa.good.gb.acc.ph0
Generating model...
T    
C    
A    
G    
Done
4 dna.fa.good.gb.acc.ph1
zero order for ACC 1
Error: unknown line format
       GC%	Intron	Accession	 (File generated at 2014/04/10 Thu 19:12:13 EDT)

GC Range: (0,99)
3 sequences of length 21 used from 4
total sequences in dna.fa.good.gb.acc.ph1
Generating model...
T    0.33 0.00 0.00 0.00 0.67 0.00 0.33 0.33 0.00 0.00 0.67 0.33 0.33 0.00 0.00 0.00 0.67 0.33 0.00 0.00 0.67
C    0.00 0.67 0.67 0.33 0.33 0.33 0.33 0.33 0.67 0.33 0.00 0.00 0.33 1.00 0.33 0.33 0.00 0.00 0.00 0.00 0.00
A    0.33 0.33 0.00 0.67 0.00 0.00 0.33 0.00 0.00 0.33 0.33 0.00 0.33 0.00 0.67 0.00 0.33 0.67 1.00 0.00 0.33
G    0.33 0.00 0.33 0.00 0.00 0.67 0.00 0.33 0.33 0.33 0.00 0.67 0.00 0.00 0.00 0.67 0.00 0.00 0.00 1.00 0.00
Done
3 dna.fa.good.gb.acc.ph2
zero order for ACC 2
Error: unknown line format
       GC%	Intron	Accession	 (File generated at 2014/04/10 Thu 19:12:13 EDT)

GC Range: (0,99)
2 sequences of length 21 used from 3
total sequences in dna.fa.good.gb.acc.ph2
Generating model...
T    0.00 0.50 0.50 0.50 0.00 0.00 0.50 1.00 0.50 0.00 0.50 0.50 1.00 0.50 0.00 0.00 0.50 0.00 0.00 0.00 0.00
C    0.00 0.00 0.50 0.00 1.00 0.50 0.00 0.00 0.00 1.00 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.50 0.00 0.00 0.00
A    0.50 0.50 0.00 0.50 0.00 0.50 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 1.00 0.00 0.50 1.00 0.00 0.00
G    0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00 0.50 0.00 0.00 0.50 0.00 0.50 0.00 0.00 0.00 0.00 0.00 1.00 1.00
Done
error reading parameter TERM_TAG_MAT
error in model file org_S3.0mtx
Error on system: prediction step