-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_9718296-9905999

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_41814-T1
Valid prediction for snap_scaffold_17-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_41808-T1
Valid prediction for snap_scaffold_17-snap.1956-T1
Valid prediction for GeneMark_model.71998_t
Valid prediction for GeneMark_model.71992_t
Valid prediction for GeneMark_model.72000_t
Valid prediction for snap_scaffold_17-snap.1950-T1
Valid prediction for GeneMark_model.71984_t
Valid prediction for GeneMark_model.71964_t
Valid prediction for snap_scaffold_17-snap.1944-T1
Valid prediction for snap_scaffold_17-snap.1936-T1
Valid prediction for snap_scaffold_17-snap.1948-T1
Valid prediction for GeneMark_model.71972_t
Valid prediction for GeneMark_model.72004_t
Valid prediction for GeneMark_model.71985_t
Valid prediction for snap_scaffold_17-snap.1954-T1
Valid prediction for GeneMark_model.71973_t
Valid prediction for Augustus_model.g28043.t1
Valid prediction for Augustus_model.g28044.t1
Valid prediction for GeneMark_model.71974_t
Valid prediction for GeneMark_model.71987_t
Valid prediction for GeneMark_model.72002_t
Valid prediction for Augustus_model.g28038.t1
Valid prediction for Augustus_model.g28036.t1
Valid prediction for GeneMark_model.71968_t
Valid prediction for snap_scaffold_17-snap.1934-T1
Valid prediction for GeneMark_model.71990_t
Valid prediction for snap_scaffold_17-snap.1935-T1
Valid prediction for GeneMark_model.71961_t
Valid prediction for GlimmerHMM_glimmerT_41810-T1
Valid prediction for GeneMark_model.72011_t
Valid prediction for snap_scaffold_17-snap.1930-T1
Valid prediction for GeneMark_model.71997_t
Valid prediction for snap_scaffold_17-snap.1939-T1
Valid prediction for GeneMark_model.72010_t
Valid prediction for GeneMark_model.71982_t
Valid prediction for snap_scaffold_17-snap.1945-T1
Valid prediction for snap_scaffold_17-snap.1952-T1
Valid prediction for snap_scaffold_17-snap.1943-T1
Valid prediction for GeneMark_model.71966_t
Valid prediction for GlimmerHMM_glimmerT_41815-T1
Valid prediction for GeneMark_model.71979_t
Valid prediction for GeneMark_model.71970_t
Valid prediction for GlimmerHMM_glimmerT_41819-T1
Valid prediction for GeneMark_model.71988_t
Valid prediction for snap_scaffold_17-snap.1942-T1
Valid prediction for snap_scaffold_17-snap.1940-T1
Valid prediction for GeneMark_model.71976_t
Valid prediction for snap_scaffold_17-snap.1951-T1
Valid prediction for Augustus_model.g28040.t1
Valid prediction for GlimmerHMM_glimmerT_41811-T1
Valid prediction for GeneMark_model.71994_t
Valid prediction for snap_scaffold_17-snap.1938-T1
Valid prediction for GeneMark_model.71969_t
Valid prediction for snap_scaffold_17-snap.1931-T1
Valid prediction for GlimmerHMM_glimmerT_41818-T1
Valid prediction for snap_scaffold_17-snap.1932-T1
Valid prediction for GeneMark_model.71963_t
Valid prediction for GeneMark_model.72008_t
Valid prediction for snap_scaffold_17-snap.1961-T1
Valid prediction for snap_scaffold_17-snap.1947-T1
Valid prediction for GeneMark_model.71959_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for CodingQuarry_transcript_22095-T1
Valid prediction for CodingQuarry_transcript_22093-T1
Valid prediction for GeneMark_model.71962_t
Valid prediction for snap_scaffold_17-snap.1957-T1
Couldn't classify 150183, 150364
Couldn't classify 157039, 157160
Sorry, prediction pasa_asmbl_19241.p1 fails validation.
(CTC)	 CT	150183-150364	GT	GGG
(ATG)	 AG	150606-150720	GT	ATG
(ATG)	 AG	152789-152915	GT	TGG
(CTG)	 AG	153296-153446	GT	GGG
(CGT)	 AG	153718-153904	GT	ACG
(GAG)	 AG	154919-154964	GT	AGG
(CCA)	 AG	157039-157160	GG	CAG
add_exon() Sorry, pasa_asmbl_19241.p1 150606-150720-initial-1 is invalid.
-recovered pasa_asmbl_19241.p1, initial, 150606, 150720
-recovered pasa_asmbl_19241.p1, initial, 152789, 152915
-recovered pasa_asmbl_19241.p1, internal, 150606, 150720
-recovered pasa_asmbl_19241.p1, internal, 152789, 152915
-recovered pasa_asmbl_19241.p1, internal, 153296, 153446
-recovered pasa_asmbl_19241.p1, internal, 153718, 153904
-recovered pasa_asmbl_19241.p1, internal, 154919, 154964
Valid prediction for GeneMark_model.71996_t
Couldn't classify 143152, 143467
Couldn't classify 145580, 145644
Sorry, prediction pasa_asmbl_19574.p1 fails validation.
(AGG)	 AA	143152-143467	GT	TGG
(GCA)	 AG	145580-145644	TG	TAT
Valid prediction for Augustus_model.g28034.t1
Valid prediction for CodingQuarry_transcript_22100-T1
Valid prediction for Augustus_model.g28046.t1
Valid prediction for snap_scaffold_17-snap.1968-T1
Valid prediction for GeneMark_model.71981_t
Valid prediction for GeneMark_model.71958_t
Valid prediction for GlimmerHMM_glimmerT_41816-T1
Valid prediction for GeneMark_model.72005_t
Valid prediction for GlimmerHMM_glimmerT_41820-T1
Valid prediction for pasa_asmbl_19255.p1
Valid prediction for snap_scaffold_17-snap.1953-T1
Couldn't classify 23576, 23633
Couldn't classify 25891, 25992
Sorry, prediction pasa_asmbl_19264.p1 fails validation.
(AAG)	 TC	23576-23633	GT	GGG
(ACT)	 AG	24431-24496	GT	TAG
(GTG)	 AG	24588-24662	GT	AGG
(AAA)	 AG	24763-24831	GT	CGG
(GTC)	 AG	25538-25671	GT	TGG
(AGT)	 AG	25891-25992	AA	AGA
-recovered pasa_asmbl_19264.p1, internal, 24431, 24496
-recovered pasa_asmbl_19264.p1, internal, 24588, 24662
-recovered pasa_asmbl_19264.p1, internal, 24763, 24831
-recovered pasa_asmbl_19264.p1, internal, 25538, 25671
Valid prediction for GeneMark_model.72001_t
Valid prediction for pasa_asmbl_19253.p1
Valid prediction for GeneMark_model.71989_t
Couldn't classify 179939, 180095
Sorry, prediction pasa_asmbl_19237.p1 fails validation.
(GAC)	 AC	179939-180095	GT	AGG
(AGA)	 AG	180252-180332	GT	AGG
(CCA)	 AG	180445-180572	CC	GAC
-recovered pasa_asmbl_19237.p1, terminal, 180445, 180572
-recovered pasa_asmbl_19237.p1, internal, 180252, 180332
Valid prediction for GeneMark_model.72009_t
Valid prediction for GlimmerHMM_glimmerT_41817-T1
Valid prediction for GeneMark_model.71993_t
Valid prediction for CodingQuarry_transcript_22098-T1
Valid prediction for GlimmerHMM_glimmerT_41824-T1
Valid prediction for GeneMark_model.72007_t
Valid prediction for GeneMark_model.71967_t
Valid prediction for CodingQuarry_transcript_22092-T1
Valid prediction for GlimmerHMM_glimmerT_41823-T1
Valid prediction for snap_scaffold_17-snap.1941-T1
Valid prediction for HiQ_model.g28045.t1
Valid prediction for snap_scaffold_17-snap.1946-T1
Valid prediction for Augustus_model.g28050.t1
Valid prediction for GlimmerHMM_glimmerT_41806-T1
Valid prediction for Augustus_model.g28049.t1
Valid prediction for CodingQuarry_transcript_22088-T1
Valid prediction for GeneMark_model.71965_t
Valid prediction for GlimmerHMM_glimmerT_41821-T1
Valid prediction for GlimmerHMM_glimmerT_41812-T1
Valid prediction for GeneMark_model.71995_t
Valid prediction for GeneMark_model.71978_t
Valid prediction for snap_scaffold_17-snap.1965-T1
Valid prediction for snap_scaffold_17-snap.1966-T1
Valid prediction for GeneMark_model.71983_t
Valid prediction for snap_scaffold_17-snap.1958-T1
Valid prediction for Augustus_model.g28052.t1
Valid prediction for GeneMark_model.71960_t
Valid prediction for HiQ_model.g28035.t1
Couldn't classify 171141, 171299
Sorry, prediction pasa_asmbl_19238.p1 fails validation.
(AGC)	 CT	171141-171299	GT	AGG
(TTT)	 AG	172725-172876	GT	AAG
(GGC)	 AG	173117-173274	GT	GAG
(CTG)	 AG	173881-174143	GT	AGG
(ACC)	 AG	174423-174581	GT	AGG
(TTT)	 AG	174718-174952	GT	CGG
(GGA)	 AG	175167-175306	GT	AGG
(GTA)	 AG	175498-175581	GT	AGG
(ATG)	 AG	175677-175792	GT	GGG
(CTT)	 AG	176083-176266	GT	CGG
(ACC)	 AG	176534-176680	AG	AAA
-recovered pasa_asmbl_19238.p1, initial, 175677, 175792
-recovered pasa_asmbl_19238.p1, terminal, 173117, 173274
-recovered pasa_asmbl_19238.p1, terminal, 176534, 176680
-recovered pasa_asmbl_19238.p1, internal, 172725, 172876
-recovered pasa_asmbl_19238.p1, internal, 173117, 173274
-recovered pasa_asmbl_19238.p1, internal, 173881, 174143
-recovered pasa_asmbl_19238.p1, internal, 174423, 174581
-recovered pasa_asmbl_19238.p1, internal, 174718, 174952
-recovered pasa_asmbl_19238.p1, internal, 175167, 175306
-recovered pasa_asmbl_19238.p1, internal, 175498, 175581
-recovered pasa_asmbl_19238.p1, internal, 175677, 175792
-recovered pasa_asmbl_19238.p1, internal, 176083, 176266
Valid prediction for GeneMark_model.72012_t
Valid prediction for GlimmerHMM_glimmerT_41813-T1
Valid prediction for snap_scaffold_17-snap.1933-T1
Valid prediction for Augustus_model.g28041.t1
Valid prediction for GeneMark_model.71977_t
Couldn't classify 150719, 150720
Couldn't classify 152791, 152915
Sorry, prediction CodingQuarry_transcript_22089-T1 fails validation.
(ATG)	 CC	150719-150720	GT	ATG
(GAA)	 AT	152791-152915	GT	TGG
(CTG)	 AG	153296-153446	GT	GGG
(CGT)	 AG	153718-153904	GT	ACG
(GAG)	 AG	154919-154964	GT	AGG
(CCA)	 AG	157039-157166	GA	AAG
-recovered CodingQuarry_transcript_22089-T1, terminal, 157039, 157166
-recovered CodingQuarry_transcript_22089-T1, internal, 153296, 153446
-recovered CodingQuarry_transcript_22089-T1, internal, 153718, 153904
-recovered CodingQuarry_transcript_22089-T1, internal, 154919, 154964
Valid prediction for GeneMark_model.71971_t
Valid prediction for CodingQuarry_transcript_22099-T1
Couldn't classify 46961, 47087
Couldn't classify 47479, 47587
Sorry, prediction CodingQuarry_transcript_22094-T1 fails validation.
(ATG)	 AT	45218-45368	GT	AGG
(CCA)	 AG	46961-47087	CA	TCC
(AGG)	 GT	47479-47587	GT	GCG
(AGG)	 AG	47717-47811	GT	AGG
(ACA)	 AG	48310-48322	TC	AAT
-recovered CodingQuarry_transcript_22094-T1, initial, 45218, 45368
-recovered CodingQuarry_transcript_22094-T1, terminal, 48310, 48322
-recovered CodingQuarry_transcript_22094-T1, internal, 47717, 47811
Valid prediction for GlimmerHMM_glimmerT_41809-T1
Valid prediction for snap_scaffold_17-snap.1949-T1
Valid prediction for snap_scaffold_17-snap.1963-T1
Valid prediction for HiQ_model.g28048.t1
Valid prediction for HiQ_model.g28047.t1
Couldn't classify 64105, 64485
Sorry, prediction pasa_asmbl_19250.p1 fails validation.
(TTT)	 TT	64105-64485	GC	GAG
Valid prediction for pasa_asmbl_19252.p1
Valid prediction for snap_scaffold_17-snap.1969-T1
Valid prediction for CodingQuarry_transcript_22097-T1
Valid prediction for GeneMark_model.72003_t
Valid prediction for GeneMark_model.71991_t
Couldn't classify 37085, 37198
Sorry, prediction pasa_asmbl_19259.p2 fails validation.
(CAC)	 AT	37085-37198	GT	AGG
(GTG)	 AG	37323-37380	GT	GGG
(CAC)	 AG	37475-37771	GT	CGG
(GTC)	 AG	37861-38153	AA	GAA
-recovered pasa_asmbl_19259.p2, terminal, 37861, 38153
-recovered pasa_asmbl_19259.p2, internal, 37323, 37380
-recovered pasa_asmbl_19259.p2, internal, 37475, 37771
Valid prediction for GlimmerHMM_glimmerT_41807-T1
Valid prediction for GeneMark_model.71999_t
Valid prediction for CodingQuarry_transcript_22090-T1
Valid prediction for snap_scaffold_17-snap.1960-T1
Valid prediction for GeneMark_model.72006_t
Valid prediction for snap_scaffold_17-snap.1937-T1
Valid prediction for snap_scaffold_17-snap.1962-T1
Valid prediction for snap_scaffold_17-snap.1964-T1
Valid prediction for GeneMark_model.71986_t
Valid prediction for GeneMark_model.71975_t
Valid prediction for GlimmerHMM_glimmerT_41822-T1
Valid prediction for Augustus_model.g28051.t1
Valid prediction for snap_scaffold_17-snap.1955-T1
Valid prediction for Augustus_model.g28042.t1
Valid prediction for snap_scaffold_17-snap.1967-T1
Valid prediction for snap_scaffold_17-snap.1970-T1
Valid prediction for pasa_asmbl_19571.p1
Valid prediction for HiQ_model.g28037.t1
Valid prediction for Augustus_model.g28039.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13030, rend_intergenic: 11025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15502, rend_intergenic: 13680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29189, rend_intergenic: 25954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40791, rend_intergenic: 29711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50649, rend_intergenic: 41575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69345, rend_intergenic: 59891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82372, rend_intergenic: 71835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92959, rend_intergenic: 83902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97033, rend_intergenic: 93717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117608, rend_intergenic: 111651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119423, rend_intergenic: 118346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124237, rend_intergenic: 120876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187704
-exon list size: 723


building trellis

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62.3    
62.5    
62.6    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.6    
63.7    
63.9    
64.0    
64.1    
64.3    
64.4    
64.6    
64.7    
64.8    
65.0    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 13030, rend_intergenic: 11025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15502, rend_intergenic: 13680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29189, rend_intergenic: 25954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40791, rend_intergenic: 29711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50649, rend_intergenic: 41575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69345, rend_intergenic: 59891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82372, rend_intergenic: 71835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92959, rend_intergenic: 83902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97033, rend_intergenic: 93717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117608, rend_intergenic: 111651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119423, rend_intergenic: 118346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124237, rend_intergenic: 120876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support