-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_8159871-8310061

-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 pasa_asmbl_28814.p1
Valid prediction for snap_scaffold_21-snap.1745-T1
Valid prediction for GlimmerHMM_glimmerT_49397-T1
Valid prediction for GeneMark_model.85490_t
Valid prediction for snap_scaffold_21-snap.1756-T1
Valid prediction for GeneMark_model.85494_t
Valid prediction for snap_scaffold_21-snap.1749-T1
Valid prediction for GlimmerHMM_glimmerT_49396-T1
Valid prediction for pasa_asmbl_28812.p1
Valid prediction for Augustus_model.g33134.t1
Valid prediction for GlimmerHMM_glimmerT_49383-T1
Valid prediction for Augustus_model.g33124.t1
Valid prediction for CodingQuarry_transcript_32599-T1
Valid prediction for Augustus_model.g33143.t1
Valid prediction for GeneMark_model.85501_t
Valid prediction for snap_scaffold_21-snap.1737-T1
Valid prediction for GeneMark_model.85489_t
Valid prediction for CodingQuarry_transcript_32601-T1
Valid prediction for GeneMark_model.85487_t
Valid prediction for Augustus_model.g33139.t1
Valid prediction for GlimmerHMM_glimmerT_49391-T1
Valid prediction for CodingQuarry_transcript_32611-T1
Valid prediction for GeneMark_model.85485_t
Valid prediction for snap_scaffold_21-snap.1755-T1
Valid prediction for CodingQuarry_transcript_32608-T1
Valid prediction for Augustus_model.g33120.t1
Valid prediction for CodingQuarry_transcript_32609-T1
Valid prediction for GeneMark_model.85510_t
Valid prediction for Augustus_model.g33137.t1
Valid prediction for snap_scaffold_21-snap.1742-T1
Valid prediction for snap_scaffold_21-snap.1759-T1
Valid prediction for GeneMark_model.85506_t
Couldn't classify 10145, 10263
Couldn't classify 10598, 10765
Sorry, prediction CodingQuarry_transcript_32598-T1 fails validation.
(ATG)	 AT	7134-7410	GT	AGG
(CAG)	 AG	7612-7669	GT	AAG
(CAA)	 AG	7828-7883	GT	AGG
(AGC)	 AG	8001-8127	GT	GGG
(GAA)	 AG	8244-8346	GT	GAG
(GCC)	 AG	8470-8547	GT	AGG
(GTA)	 AG	8706-8805	GT	AGG
(GTG)	 AG	8901-9043	GT	TGG
(CTG)	 AG	9165-9371	GT	TGG
(GTG)	 AG	9558-9670	GT	AGG
(GTC)	 AG	9807-9940	GT	AGG
(AGG)	 AG	10145-10263	GG	GAG
(GAA)	 CT	10598-10765	GT	TGG
(GAT)	 AG	11069-11179	GT	ATG
(TTC)	 AG	11442-11529	GT	GGG
(GCC)	 AG	11777-11867	GT	ATG
(GAC)	 AG	11994-12129	GT	AGG
(GCT)	 AG	12407-12496	GT	CCG
(CTG)	 AG	12606-12727	GT	GCG
(AAA)	 AG	12994-13012	GC	GAG
-recovered CodingQuarry_transcript_32598-T1, initial, 7134, 7410
-recovered CodingQuarry_transcript_32598-T1, terminal, 12994, 13012
-recovered CodingQuarry_transcript_32598-T1, internal, 7612, 7669
-recovered CodingQuarry_transcript_32598-T1, internal, 7828, 7883
-recovered CodingQuarry_transcript_32598-T1, internal, 8001, 8127
-recovered CodingQuarry_transcript_32598-T1, internal, 8244, 8346
-recovered CodingQuarry_transcript_32598-T1, internal, 8470, 8547
-recovered CodingQuarry_transcript_32598-T1, internal, 8706, 8805
-recovered CodingQuarry_transcript_32598-T1, internal, 8901, 9043
-recovered CodingQuarry_transcript_32598-T1, internal, 9165, 9371
-recovered CodingQuarry_transcript_32598-T1, internal, 9558, 9670
-recovered CodingQuarry_transcript_32598-T1, internal, 9807, 9940
-recovered CodingQuarry_transcript_32598-T1, internal, 11069, 11179
-recovered CodingQuarry_transcript_32598-T1, internal, 11442, 11529
-recovered CodingQuarry_transcript_32598-T1, internal, 11777, 11867
-recovered CodingQuarry_transcript_32598-T1, internal, 11994, 12129
-recovered CodingQuarry_transcript_32598-T1, internal, 12407, 12496
-recovered CodingQuarry_transcript_32598-T1, internal, 12606, 12727
-recovered CodingQuarry_transcript_32598-T1, internal, 12994, 13012
Valid prediction for GeneMark_model.85499_t
Valid prediction for snap_scaffold_21-snap.1732-T1
Valid prediction for Augustus_model.g33130.t1
Valid prediction for GeneMark_model.85513_t
Valid prediction for GlimmerHMM_glimmerT_49379-T1
Valid prediction for HiQ_model.g33122.t1
Valid prediction for CodingQuarry_transcript_32610-T1
Valid prediction for snap_scaffold_21-snap.1736-T1
Valid prediction for snap_scaffold_21-snap.1738-T1
Couldn't classify 115495, 115629
Sorry, prediction pasa_asmbl_28817.p1 fails validation.
(ACA)	 AC	115495-115629	GT	GAG
(ACA)	 AG	115891-116041	GT	CGG
(AGG)	 AG	116260-116384	GT	GGG
(GCT)	 AG	116525-116671	CA	AAC
-recovered pasa_asmbl_28817.p1, terminal, 116525, 116671
-recovered pasa_asmbl_28817.p1, internal, 115891, 116041
-recovered pasa_asmbl_28817.p1, internal, 116260, 116384
Valid prediction for snap_scaffold_21-snap.1733-T1
Valid prediction for HiQ_model.g33125.t1
Valid prediction for HiQ_model.g33121.t1
Valid prediction for GlimmerHMM_glimmerT_49384-T1
Valid prediction for GlimmerHMM_glimmerT_49392-T1
Valid prediction for GlimmerHMM_glimmerT_49374-T1
Valid prediction for GeneMark_model.85488_t
Valid prediction for snap_scaffold_21-snap.1743-T1
Valid prediction for snap_scaffold_21-snap.1754-T1
Valid prediction for Augustus_model.g33128.t1
Valid prediction for GeneMark_model.85514_t
Valid prediction for snap_scaffold_21-snap.1763-T1
Valid prediction for GlimmerHMM_glimmerT_49388-T1
Couldn't classify 20297, 20307
Sorry, prediction pasa_asmbl_28809.p1 fails validation.
(TAC)	 AC	20297-20307	GT	AGG
(GAC)	 AG	20527-20605	GT	AGG
(GTC)	 AG	20838-20981	GT	CGG
(GCA)	 AG	21410-21544	GT	CTG
(TAT)	 AG	21822-21919	GT	AGG
(GTA)	 AG	22157-22298	GT	GGG
(GTC)	 AG	22421-22499	GT	GGG
(CAA)	 AG	22591-22656	GT	TGG
(GGG)	 AG	22894-22962	GT	AGG
(GCT)	 AG	23155-23363	TT	GAT
-recovered pasa_asmbl_28809.p1, terminal, 23155, 23363
-recovered pasa_asmbl_28809.p1, internal, 20527, 20605
-recovered pasa_asmbl_28809.p1, internal, 20838, 20981
-recovered pasa_asmbl_28809.p1, internal, 21410, 21544
-recovered pasa_asmbl_28809.p1, internal, 21822, 21919
-recovered pasa_asmbl_28809.p1, internal, 22157, 22298
-recovered pasa_asmbl_28809.p1, internal, 22421, 22499
-recovered pasa_asmbl_28809.p1, internal, 22591, 22656
-recovered pasa_asmbl_28809.p1, internal, 22894, 22962
Valid prediction for Augustus_model.g33138.t1
Valid prediction for GlimmerHMM_glimmerT_49390-T1
Valid prediction for snap_scaffold_21-snap.1734-T1
Valid prediction for GlimmerHMM_glimmerT_49377-T1
Valid prediction for GlimmerHMM_glimmerT_49386-T1
Valid prediction for GlimmerHMM_glimmerT_49373-T1
Valid prediction for GeneMark_model.85517_t
Valid prediction for GlimmerHMM_glimmerT_49371-T1
Valid prediction for snap_scaffold_21-snap.1740-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49370-T1
Valid prediction for GeneMark_model.85493_t
Valid prediction for pasa_asmbl_28820.p1
Valid prediction for GeneMark_model.85511_t
Valid prediction for CodingQuarry_transcript_32607-T1
Valid prediction for GeneMark_model.85496_t
Valid prediction for snap_scaffold_21-snap.1750-T1
Valid prediction for GeneMark_model.85502_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: -)Couldn't classify 6665, 6692
Sorry, prediction pasa_asmbl_27941.p1 fails validation.
(TTC)	 CA	6665-6692	GT	TGG
(GTC)	 AG	6791-6867	GT	AGG
(GTG)	 AG	7298-7372	GT	CAG
(ATC)	 AG	7762-7875	GT	AAG
(GGC)	 AG	8302-8414	GT	AGG
(CCC)	 AG	8549-8649	GT	AGG
(ATG)	 AG	9003-9112	CA	AAC
-recovered pasa_asmbl_27941.p1, terminal, 9003, 9112
-recovered pasa_asmbl_27941.p1, internal, 6791, 6867
-recovered pasa_asmbl_27941.p1, internal, 7298, 7372
-recovered pasa_asmbl_27941.p1, internal, 7762, 7875
-recovered pasa_asmbl_27941.p1, internal, 8302, 8414
-recovered pasa_asmbl_27941.p1, internal, 8549, 8649
Valid prediction for GeneMark_model.85515_t
Valid prediction for GlimmerHMM_glimmerT_49381-T1
Valid prediction for HiQ_model.g33142.t1
Valid prediction for GeneMark_model.85504_t
Valid prediction for GeneMark_model.85495_t
Valid prediction for GeneMark_model.85492_t
Valid prediction for snap_scaffold_21-snap.1761-T1
Valid prediction for pasa_asmbl_27936.p1
Valid prediction for snap_scaffold_21-snap.1757-T1
Valid prediction for CodingQuarry_transcript_32612-T1
Valid prediction for GeneMark_model.85519_t
Couldn't classify 69951, 70364
Sorry, prediction pasa_asmbl_27929.p1 fails validation.
(GGT)	 CA	69951-70364	GT	AGG
(GTC)	 AG	70564-70728	GT	AGG
(GAG)	 AG	70924-71445	AC	AGA
-recovered pasa_asmbl_27929.p1, terminal, 70924, 71445
-recovered pasa_asmbl_27929.p1, internal, 70564, 70728
Valid prediction for CodingQuarry_transcript_32613-T1
Valid prediction for snap_scaffold_21-snap.1748-T1
Valid prediction for CodingQuarry_transcript_32603-T1
Valid prediction for GeneMark_model.85497_t
Valid prediction for Augustus_model.g33129.t1
Valid prediction for pasa_asmbl_27939.p1
Valid prediction for GeneMark_model.85486_t
Valid prediction for GlimmerHMM_glimmerT_49394-T1
Valid prediction for snap_scaffold_21-snap.1752-T1
Couldn't classify 81185, 81297
Sorry, prediction CodingQuarry_transcript_32605-T1 fails validation.
(ATG)	 TC	79716-79925	GT	AGG
(AAT)	 AG	80079-80149	GT	AAG
(GAG)	 AG	80240-80295	GT	ACG
(TTG)	 AG	80385-80455	GT	AGG
(GAC)	 AG	80737-80853	GT	AGG
(TCA)	 AG	80958-81014	GT	AGG
(AAC)	 AG	81185-81297	CT	ACC
(GTA)	 AG	81515-81518	TT	AAT
-recovered CodingQuarry_transcript_32605-T1, initial, 79716, 79925
add_exon() Sorry, CodingQuarry_transcript_32605-T1 80079-80149-terminal-2 is invalid.
-recovered CodingQuarry_transcript_32605-T1, terminal, 80079, 80149
-recovered CodingQuarry_transcript_32605-T1, terminal, 81515, 81518
-recovered CodingQuarry_transcript_32605-T1, internal, 80079, 80149
-recovered CodingQuarry_transcript_32605-T1, internal, 80240, 80295
-recovered CodingQuarry_transcript_32605-T1, internal, 80385, 80455
-recovered CodingQuarry_transcript_32605-T1, internal, 80737, 80853
-recovered CodingQuarry_transcript_32605-T1, internal, 80958, 81014
Couldn't classify 27379, 27420
Sorry, prediction pasa_asmbl_27933.p1 fails validation.
(ATG)	 AA	26737-26794	GT	AGG
(GTG)	 AG	26949-27145	GT	AGG
(GTT)	 AG	27379-27420	TA	AGT
-recovered pasa_asmbl_27933.p1, initial, 26737, 26794
-recovered pasa_asmbl_27933.p1, internal, 26949, 27145
Valid prediction for HiQ_model.g33127.t1
Valid prediction for pasa_asmbl_27931.p1
Couldn't classify 52769, 53006
Couldn't classify 53034, 53107
Sorry, prediction CodingQuarry_transcript_32606-T1 fails validation.
(ATG)	 AG	49761-49826	GT	AGG
(GTG)	 AG	50017-50141	GT	AGG
(TTC)	 AG	50691-50751	GT	CAG
(GTA)	 AG	50837-50980	GT	ATG
(GTG)	 AG	51397-51498	GT	AGG
(GTA)	 AG	51671-51827	GT	AGG
(GGC)	 AG	52146-52288	GT	AGG
(GTG)	 AG	52459-52512	GT	AGG
(CTG)	 AG	52769-53006	AT	GAA
(GCG)	 GA	53034-53107	CA	GAC
-recovered CodingQuarry_transcript_32606-T1, initial, 49761, 49826
-recovered CodingQuarry_transcript_32606-T1, internal, 49761, 49826
-recovered CodingQuarry_transcript_32606-T1, internal, 50017, 50141
-recovered CodingQuarry_transcript_32606-T1, internal, 50691, 50751
-recovered CodingQuarry_transcript_32606-T1, internal, 50837, 50980
-recovered CodingQuarry_transcript_32606-T1, internal, 51397, 51498
-recovered CodingQuarry_transcript_32606-T1, internal, 51671, 51827
-recovered CodingQuarry_transcript_32606-T1, internal, 52146, 52288
-recovered CodingQuarry_transcript_32606-T1, internal, 52459, 52512
Valid prediction for GeneMark_model.85516_t
Valid prediction for snap_scaffold_21-snap.1760-T1
Valid prediction for CodingQuarry_transcript_32600-T1
Valid prediction for GeneMark_model.85507_t
Valid prediction for pasa_asmbl_27924.p1
Valid prediction for CodingQuarry_transcript_32604-T1
Valid prediction for HiQ_model.g33131.t1
Valid prediction for CodingQuarry_transcript_32602-T1
Valid prediction for HiQ_model.g33141.t1
Valid prediction for pasa_asmbl_27926.p1
Valid prediction for GlimmerHMM_glimmerT_49378-T1
Valid prediction for snap_scaffold_21-snap.1744-T1
Valid prediction for snap_scaffold_21-snap.1739-T1
Valid prediction for snap_scaffold_21-snap.1741-T1
Valid prediction for snap_scaffold_21-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_49375-T1
Valid prediction for Augustus_model.g33135.t1
Valid prediction for GeneMark_model.85503_t
Valid prediction for GeneMark_model.85505_t
Valid prediction for snap_scaffold_21-snap.1751-T1
Valid prediction for HiQ_model.g33136.t1
Valid prediction for snap_scaffold_21-snap.1753-T1
Valid prediction for pasa_asmbl_27917.p1
Valid prediction for Augustus_model.g33140.t1
Valid prediction for GlimmerHMM_glimmerT_49398-T1
Valid prediction for GlimmerHMM_glimmerT_49382-T1
Valid prediction for GeneMark_model.85518_t
Valid prediction for GlimmerHMM_glimmerT_49380-T1
Valid prediction for GeneMark_model.85498_t
Valid prediction for GlimmerHMM_glimmerT_49393-T1
Valid prediction for HiQ_model.g33126.t1
Valid prediction for snap_scaffold_21-snap.1747-T1
Valid prediction for GlimmerHMM_glimmerT_49395-T1
Valid prediction for snap_scaffold_21-snap.1746-T1
Valid prediction for GlimmerHMM_glimmerT_49385-T1
Valid prediction for Augustus_model.g33123.t1
Valid prediction for GeneMark_model.85500_t
Valid prediction for GlimmerHMM_glimmerT_49372-T1
Valid prediction for GeneMark_model.85491_t
Couldn't classify 28089, 28119
Sorry, prediction pasa_asmbl_27932.p1 fails validation.
(GCT)	 CA	28089-28119	GT	AGG
(GGA)	 AG	28316-28419	GT	GGG
(GTC)	 AG	28591-28710	GT	AGG
(GAG)	 AG	28879-29047	GT	CGG
(GAC)	 AG	29236-29316	GT	AAG
(AGC)	 AG	29673-29795	GT	TGG
(GTT)	 AG	29932-30092	AC	GAA
-recovered pasa_asmbl_27932.p1, terminal, 29932, 30092
-recovered pasa_asmbl_27932.p1, internal, 28316, 28419
-recovered pasa_asmbl_27932.p1, internal, 28591, 28710
-recovered pasa_asmbl_27932.p1, internal, 28879, 29047
-recovered pasa_asmbl_27932.p1, internal, 29236, 29316
-recovered pasa_asmbl_27932.p1, internal, 29673, 29795
Valid prediction for GeneMark_model.85512_t
Valid prediction for GlimmerHMM_glimmerT_49387-T1
Valid prediction for HiQ_model.g33133.t1
Valid prediction for GeneMark_model.85509_t
Valid prediction for HiQ_model.g33132.t1
Valid prediction for snap_scaffold_21-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_49389-T1
Valid prediction for GlimmerHMM_glimmerT_49376-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 44125, rend_intergenic: 41498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87279, rend_intergenic: 83612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108126, rend_intergenic: 104137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119687, rend_intergenic: 117715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133868, rend_intergenic: 131050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150191
-exon list size: 537


building trellis

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58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 44125, rend_intergenic: 41498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87279, rend_intergenic: 83612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108126, rend_intergenic: 104137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119687, rend_intergenic: 117715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133868, rend_intergenic: 131050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support