-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_8407064-8626466

-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 Augustus_model.g25845.t1
Valid prediction for GlimmerHMM_glimmerT_38697-T1
Valid prediction for GlimmerHMM_glimmerT_38701-T1
Valid prediction for Augustus_model.g25832.t1
Valid prediction for pasa_asmbl_16402.p2
Valid prediction for snap_scaffold_16-snap.1564-T1
Valid prediction for snap_scaffold_16-snap.1548-T1
Valid prediction for Augustus_model.g25844.t1
Valid prediction for CodingQuarry_transcript_20033-T1
Valid prediction for CodingQuarry_transcript_20035-T1
Valid prediction for CodingQuarry_transcript_20036-T1
Valid prediction for Augustus_model.g25825.t1
Valid prediction for snap_scaffold_16-snap.1571-T1
Valid prediction for snap_scaffold_16-snap.1574-T1
Valid prediction for HiQ_model.g25837.t1
Valid prediction for CodingQuarry_transcript_20037-T1
Valid prediction for GlimmerHMM_glimmerT_38698-T1
Valid prediction for GlimmerHMM_glimmerT_38705-T1
Valid prediction for pasa_asmbl_16397.p1
Valid prediction for GlimmerHMM_glimmerT_38706-T1
Valid prediction for pasa_asmbl_16400.p1
Valid prediction for snap_scaffold_16-snap.1545-T1
Valid prediction for Augustus_model.g25840.t1
Valid prediction for snap_scaffold_16-snap.1539-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g25838.t1
Couldn't classify 9900, 9980
Sorry, prediction pasa_asmbl_16391.p1 fails validation.
(GTG)	 CT	9900-9980	GT	AGG
(GTG)	 AG	10061-10295	GT	AGG
(GCC)	 AG	10401-10513	TT	GAT
add_exon() Sorry, pasa_asmbl_16391.p1 10061-10295-terminal-3 is invalid.
-recovered pasa_asmbl_16391.p1, terminal, 10061, 10295
-recovered pasa_asmbl_16391.p1, terminal, 10401, 10513
-recovered pasa_asmbl_16391.p1, internal, 10061, 10295
Valid prediction for GlimmerHMM_glimmerT_38688-T1
Valid prediction for snap_scaffold_16-snap.1576-T1
Valid prediction for GlimmerHMM_glimmerT_38696-T1
Valid prediction for pasa_asmbl_16393.p1
Valid prediction for GlimmerHMM_glimmerT_38699-T1
Valid prediction for Augustus_model.g25841.t1
Valid prediction for snap_scaffold_16-snap.1572-T1
Valid prediction for GlimmerHMM_glimmerT_38686-T1
Valid prediction for snap_scaffold_16-snap.1540-T1
Couldn't classify 210059, 210093
Couldn't classify 213493, 213599
Sorry, prediction pasa_asmbl_16425.p1 fails validation.
(GAG)	 TG	210059-210093	GT	AGG
(GTT)	 AG	210283-210372	GT	AAG
(CCT)	 AG	210794-210850	GT	ACG
(GTC)	 AG	211408-211471	GT	TGG
(CCT)	 AG	212487-212561	GT	CAG
(GAG)	 AG	212668-212812	GT	AGG
(GCA)	 AG	213493-213599	AA	AGA
add_exon() Sorry, pasa_asmbl_16425.p1 212668-212812-terminal-3 is invalid.
-recovered pasa_asmbl_16425.p1, terminal, 212668, 212812
-recovered pasa_asmbl_16425.p1, internal, 210283, 210372
-recovered pasa_asmbl_16425.p1, internal, 210794, 210850
-recovered pasa_asmbl_16425.p1, internal, 211408, 211471
-recovered pasa_asmbl_16425.p1, internal, 212487, 212561
-recovered pasa_asmbl_16425.p1, internal, 212668, 212812
Valid prediction for snap_scaffold_16-snap.1573-T1
Valid prediction for CodingQuarry_transcript_20031-T1
Valid prediction for Augustus_model.g25836.t1
Valid prediction for snap_scaffold_16-snap.1560-T1
Valid prediction for CodingQuarry_transcript_20039-T1
Valid prediction for snap_scaffold_16-snap.1578-T1
Valid prediction for GlimmerHMM_glimmerT_38679-T1
Valid prediction for GlimmerHMM_glimmerT_38694-T1
Couldn't classify 148550, 148680
Sorry, prediction pasa_asmbl_16403.p1 fails validation.
(GGA)	 GT	148550-148680	GT	CTG
(AAT)	 AG	149004-149097	GT	AGG
(GAG)	 AG	149380-149646	AA	AAA
-recovered pasa_asmbl_16403.p1, terminal, 149380, 149646
-recovered pasa_asmbl_16403.p1, internal, 149004, 149097
Valid prediction for CodingQuarry_transcript_20032-T1
Valid prediction for snap_scaffold_16-snap.1577-T1
Valid prediction for HiQ_model.g25842.t1
Valid prediction for HiQ_model.g25843.t1
Valid prediction for snap_scaffold_16-snap.1559-T1
Valid prediction for snap_scaffold_16-snap.1566-T1
Valid prediction for snap_scaffold_16-snap.1553-T1
Couldn't classify 72290, 72477
Sorry, prediction pasa_asmbl_16395.p1 fails validation.
(CGT)	 AG	72290-72477	GT	AAG
(GAA)	 AG	74398-74487	GT	AAG
(TGC)	 AG	75842-75884	GT	GGG
(ATC)	 AG	77324-77446	GT	AGG
(CAA)	 AG	77704-77826	GT	ATG
(CCT)	 AG	78418-78513	GT	AGG
(TGG)	 AG	80098-80199	GT	AGG
(CCC)	 AG	80300-80461	GT	AGG
(ATC)	 AG	80714-80811	GT	AGG
(TGT)	 AG	80918-81053	GT	AGG
(ATC)	 AG	81290-81412	GT	AGG
(CTT)	 AG	81592-81693	GT	AGG
(ATC)	 AG	81891-81944	CC	AAC
-recovered pasa_asmbl_16395.p1, terminal, 81891, 81944
-recovered pasa_asmbl_16395.p1, internal, 72290, 72477
-recovered pasa_asmbl_16395.p1, internal, 74398, 74487
-recovered pasa_asmbl_16395.p1, internal, 75842, 75884
-recovered pasa_asmbl_16395.p1, internal, 77324, 77446
-recovered pasa_asmbl_16395.p1, internal, 77704, 77826
-recovered pasa_asmbl_16395.p1, internal, 78418, 78513
-recovered pasa_asmbl_16395.p1, internal, 80098, 80199
-recovered pasa_asmbl_16395.p1, internal, 80300, 80461
-recovered pasa_asmbl_16395.p1, internal, 80714, 80811
-recovered pasa_asmbl_16395.p1, internal, 80918, 81053
-recovered pasa_asmbl_16395.p1, internal, 81290, 81412
-recovered pasa_asmbl_16395.p1, internal, 81592, 81693
Valid prediction for CodingQuarry_transcript_20038-T1
Valid prediction for pasa_asmbl_16407.p1
Valid prediction for HiQ_model.g25829.t1
Valid prediction for snap_scaffold_16-snap.1544-T1
Valid prediction for GlimmerHMM_glimmerT_38681-T1
Valid prediction for snap_scaffold_16-snap.1546-T1
Valid prediction for GlimmerHMM_glimmerT_38690-T1
Valid prediction for snap_scaffold_16-snap.1575-T1
Valid prediction for HiQ_model.g25839.t1
Valid prediction for GlimmerHMM_glimmerT_38700-T1
Valid prediction for snap_scaffold_16-snap.1551-T1
Couldn't classify 67641, 67991
Sorry, prediction pasa_asmbl_16394.p1 fails validation.
(GCT)	 AG	67641-67991	GT	TGG
-recovered pasa_asmbl_16394.p1, internal, 67641, 67991
Valid prediction for CodingQuarry_transcript_20030-T1
Valid prediction for HiQ_model.g25830.t1
Valid prediction for GlimmerHMM_glimmerT_38704-T1
Valid prediction for snap_scaffold_16-snap.1563-T1
Valid prediction for pasa_asmbl_16416.p1
Valid prediction for Augustus_model.g25835.t1
Valid prediction for GlimmerHMM_glimmerT_38684-T1
Valid prediction for Augustus_model.g25846.t1
Valid prediction for GlimmerHMM_glimmerT_38702-T1
Valid prediction for snap_scaffold_16-snap.1550-T1
Valid prediction for snap_scaffold_16-snap.1555-T1
Valid prediction for GlimmerHMM_glimmerT_38703-T1
Valid prediction for GlimmerHMM_glimmerT_38678-T1
Valid prediction for GlimmerHMM_glimmerT_38692-T1
Couldn't classify 214641, 214782
Couldn't classify 215803, 215886
Sorry, prediction pasa_asmbl_16426.p1 fails validation.
(GCC)	 TG	214641-214782	GT	GGG
(AGA)	 AG	214952-215079	GT	GGG
(GGT)	 AG	215561-215686	GT	AGG
(GAG)	 AG	215803-215886	AG	AGA
-recovered pasa_asmbl_16426.p1, internal, 214952, 215079
-recovered pasa_asmbl_16426.p1, internal, 215561, 215686

-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 snap_scaffold_16-snap.1565-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1552-T1
Valid prediction for snap_scaffold_16-snap.1541-T1
Valid prediction for Augustus_model.g25831.t1
Valid prediction for Augustus_model.g25828.t1
Couldn't classify 132739, 133239
Sorry, prediction pasa_asmbl_17244.p1 fails validation.
(GTG)	 GC	132739-133239	AC	AGA
Valid prediction for snap_scaffold_16-snap.1543-T1
Valid prediction for snap_scaffold_16-snap.1554-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1581-T1
Couldn't classify 201733, 201783
Couldn't classify 202486, 202677
Sorry, prediction pasa_asmbl_17520.p2 fails validation.
(ACT)	 AG	201733-201783	GT	CAG
(CTT)	 AG	202235-202342	GT	AGG
(CCC)	 AG	202486-202677	GC	ACG
-recovered pasa_asmbl_17520.p2, internal, 201733, 201783
-recovered pasa_asmbl_17520.p2, internal, 202235, 202342
-recovered pasa_asmbl_17520.p2, internal, 202486, 202677
Couldn't classify 116862, 116930
Sorry, prediction pasa_asmbl_17245.p1 fails validation.
(CCA)	 CT	116862-116930	GT	TGG
(ATT)	 AG	117086-117542	GT	GGG
(GGC)	 AG	117754-117852	GT	CGG
(GGA)	 AG	118223-118313	GT	AGG
(GGA)	 AG	118503-118726	GT	AGG
(CTC)	 AG	118914-119156	GT	CGG
(ATG)	 AG	119335-119433	GT	AGG
(GCC)	 AG	119588-119781	GT	AGG
(GTG)	 AG	119976-120150	GT	GGG
(GTC)	 AG	120224-120380	GT	AGG
(GCT)	 AG	120490-120643	GT	AGG
(GTG)	 AG	120927-121038	GT	CGG
(GTC)	 AG	121158-121336	GA	GAG
add_exon() Sorry, pasa_asmbl_17245.p1 119335-119433-initial-1 is invalid.
-recovered pasa_asmbl_17245.p1, initial, 119335, 119433
-recovered pasa_asmbl_17245.p1, terminal, 121158, 121336
-recovered pasa_asmbl_17245.p1, internal, 117086, 117542
-recovered pasa_asmbl_17245.p1, internal, 117754, 117852
-recovered pasa_asmbl_17245.p1, internal, 118223, 118313
-recovered pasa_asmbl_17245.p1, internal, 118503, 118726
-recovered pasa_asmbl_17245.p1, internal, 118914, 119156
-recovered pasa_asmbl_17245.p1, internal, 119335, 119433
-recovered pasa_asmbl_17245.p1, internal, 119588, 119781
-recovered pasa_asmbl_17245.p1, internal, 119976, 120150
-recovered pasa_asmbl_17245.p1, internal, 120224, 120380
-recovered pasa_asmbl_17245.p1, internal, 120490, 120643
-recovered pasa_asmbl_17245.p1, internal, 120927, 121038
Couldn't classify 206242, 206364
Sorry, prediction pasa_asmbl_17243.p1 fails validation.
(ACG)	 AA	206242-206364	GT	CGG
(GGC)	 AG	206520-206642	GT	GGG
(ATT)	 AG	206941-207015	CA	AAC
-recovered pasa_asmbl_17243.p1, terminal, 206941, 207015
-recovered pasa_asmbl_17243.p1, internal, 206520, 206642
Valid prediction for snap_scaffold_16-snap.1557-T1
Valid prediction for snap_scaffold_16-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_38691-T1
Valid prediction for snap_scaffold_16-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_38707-T1
Valid prediction for snap_scaffold_16-snap.1580-T1
Valid prediction for Augustus_model.g25827.t1
Valid prediction for GlimmerHMM_glimmerT_38682-T1
Valid prediction for HiQ_model.g25833.t1
Valid prediction for GlimmerHMM_glimmerT_38683-T1
Valid prediction for snap_scaffold_16-snap.1556-T1
Valid prediction for snap_scaffold_16-snap.1542-T1
Valid prediction for snap_scaffold_16-snap.1570-T1
Valid prediction for Augustus_model.g25834.t1
Valid prediction for snap_scaffold_16-snap.1549-T1
Valid prediction for GlimmerHMM_glimmerT_38680-T1
Couldn't classify 114694, 114849
Couldn't classify 116420, 116490
Sorry, prediction pasa_asmbl_17248.p1 fails validation.
(AGT)	 CC	114694-114849	GT	CGG
(ACT)	 AG	115605-115711	GT	TGG
(GCT)	 AG	115905-116053	GT	AGG
(GGC)	 AG	116420-116490	AT	GGA
-recovered pasa_asmbl_17248.p1, internal, 115605, 115711
-recovered pasa_asmbl_17248.p1, internal, 115905, 116053
Valid prediction for snap_scaffold_16-snap.1569-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38695-T1
Valid prediction for GlimmerHMM_glimmerT_38685-T1
Valid prediction for snap_scaffold_16-snap.1567-T1
Valid prediction for pasa_asmbl_17247.p2
Valid prediction for GlimmerHMM_glimmerT_38687-T1
Valid prediction for snap_scaffold_16-snap.1568-T1
Valid prediction for Augustus_model.g25826.t1
Valid prediction for snap_scaffold_16-snap.1558-T1
Valid prediction for GlimmerHMM_glimmerT_38689-T1
Valid prediction for GlimmerHMM_glimmerT_38693-T1
Valid prediction for snap_scaffold_16-snap.1582-T1
Valid prediction for snap_scaffold_16-snap.1547-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23377, rend_intergenic: 12389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35468, rend_intergenic: 23824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41753, rend_intergenic: 37457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70324, rend_intergenic: 68818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76490, rend_intergenic: 71871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77783, rend_intergenic: 77247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82316, rend_intergenic: 78445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100549, rend_intergenic: 97809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125461, rend_intergenic: 123679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127458, rend_intergenic: 125881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138816, rend_intergenic: 130190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219403
-exon list size: 543


building trellis

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75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 23377, rend_intergenic: 12389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35468, rend_intergenic: 23824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41753, rend_intergenic: 37457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70324, rend_intergenic: 68818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76490, rend_intergenic: 71871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77783, rend_intergenic: 77247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82316, rend_intergenic: 78445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100549, rend_intergenic: 97809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125461, rend_intergenic: 123679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127458, rend_intergenic: 125881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138816, rend_intergenic: 130190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support