-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_1-215286

-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_42557-T1
Couldn't classify 155907, 156176
Sorry, prediction pasa_asmbl_20291.p1 fails validation.
(TCT)	 CT	155907-156176	GT	GGG
(GAC)	 AG	156314-156380	GT	CGG
(GCT)	 AG	156622-157181	GC	GAG
-recovered pasa_asmbl_20291.p1, terminal, 156622, 157181
-recovered pasa_asmbl_20291.p1, internal, 156314, 156380
-recovered pasa_asmbl_20291.p1, internal, 156622, 157181
Valid prediction for snap_scaffold_18-snap.8-T1
Valid prediction for GeneMark_model.73574_t
Valid prediction for snap_scaffold_18-snap.24-T1
Valid prediction for Augustus_model.g28457.t1
Valid prediction for Augustus_model.g28437.t1
Valid prediction for GlimmerHMM_glimmerT_42564-T1
Valid prediction for GlimmerHMM_glimmerT_42546-T1
Valid prediction for Augustus_model.g28439.t1
Valid prediction for Augustus_model.g28447.t1
Valid prediction for Augustus_model.g28462.t1
Valid prediction for snap_scaffold_18-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_42563-T1
Valid prediction for GlimmerHMM_glimmerT_42541-T1
Valid prediction for snap_scaffold_18-snap.28-T1
Valid prediction for snap_scaffold_18-snap.26-T1
Valid prediction for GeneMark_model.73577_t
Valid prediction for Augustus_model.g28445.t1
Valid prediction for snap_scaffold_18-snap.15-T1
Valid prediction for GeneMark_model.73573_t
Couldn't classify 170623, 170649
Couldn't classify 181051, 181051
Sorry, prediction pasa_asmbl_20296.p1 fails validation.
(TGG)	 CC	170623-170649	GT	AGG
(ACC)	 AG	170733-170832	GT	CAG
(ACT)	 AG	171014-171090	GT	AGG
(GTT)	 AG	171493-171609	GT	AGG
(AAG)	 AG	171728-171817	GT	GGG
(TCA)	 AG	172375-172540	GT	AGG
(CTA)	 AG	172712-172872	GT	TGG
(GCT)	 AG	173519-173644	GT	AGG
(ATT)	 AG	173745-173811	GT	AGG
(AGT)	 AG	174123-174248	GT	AGG
(ACA)	 AG	176781-176878	GT	AGG
(GTG)	 AG	178204-178299	GT	AGG
(GTC)	 AG	179038-179258	GT	GGG
(GCT)	 AG	179473-179678	GT	TGG
(AGG)	 AG	180053-180280	GT	TAG
(GGG)	 AG	180788-180917	GT	TGG
(ATG)	 AG	181051-181051	TG	GAT
add_exon() Sorry, pasa_asmbl_20296.p1 173745-173811-terminal-3 is invalid.
-recovered pasa_asmbl_20296.p1, terminal, 173745, 173811
-recovered pasa_asmbl_20296.p1, internal, 170733, 170832
-recovered pasa_asmbl_20296.p1, internal, 171014, 171090
-recovered pasa_asmbl_20296.p1, internal, 171493, 171609
-recovered pasa_asmbl_20296.p1, internal, 171728, 171817
-recovered pasa_asmbl_20296.p1, internal, 172375, 172540
-recovered pasa_asmbl_20296.p1, internal, 172712, 172872
-recovered pasa_asmbl_20296.p1, internal, 173519, 173644
-recovered pasa_asmbl_20296.p1, internal, 173745, 173811
-recovered pasa_asmbl_20296.p1, internal, 174123, 174248
-recovered pasa_asmbl_20296.p1, internal, 176781, 176878
-recovered pasa_asmbl_20296.p1, internal, 178204, 178299
-recovered pasa_asmbl_20296.p1, internal, 179038, 179258
-recovered pasa_asmbl_20296.p1, internal, 179473, 179678
-recovered pasa_asmbl_20296.p1, internal, 180053, 180280
-recovered pasa_asmbl_20296.p1, internal, 180788, 180917
Valid prediction for Augustus_model.g28460.t1
Valid prediction for snap_scaffold_18-snap.18-T1
Valid prediction for GeneMark_model.73555_t
Valid prediction for snap_scaffold_18-snap.10-T1
Valid prediction for snap_scaffold_18-snap.16-T1
Valid prediction for snap_scaffold_18-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_42542-T1
Valid prediction for GeneMark_model.73575_t
Valid prediction for GeneMark_model.73553_t
Valid prediction for GlimmerHMM_glimmerT_42553-T1
Valid prediction for snap_scaffold_18-snap.36-T1
Valid prediction for GeneMark_model.73557_t
Valid prediction for GlimmerHMM_glimmerT_42540-T1
Valid prediction for Augustus_model.g28454.t1
Valid prediction for GlimmerHMM_glimmerT_42539-T1
Couldn't classify 139282, 139408
Sorry, prediction pasa_asmbl_20286.p1 fails validation.
(AGA)	 AG	139282-139408	GT	GGG
(AAA)	 AG	139849-140023	GT	AGG
(AGA)	 AG	140512-140695	CC	AAC
-recovered pasa_asmbl_20286.p1, terminal, 140512, 140695
-recovered pasa_asmbl_20286.p1, internal, 139282, 139408
-recovered pasa_asmbl_20286.p1, internal, 139849, 140023
Valid prediction for snap_scaffold_18-snap.23-T1
Valid prediction for GeneMark_model.73554_t
Valid prediction for GlimmerHMM_glimmerT_42545-T1
Valid prediction for snap_scaffold_18-snap.25-T1
Valid prediction for snap_scaffold_18-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_42559-T1
Valid prediction for GlimmerHMM_glimmerT_42549-T1
Valid prediction for CodingQuarry_transcript_23586-T1
Valid prediction for Augustus_model.g28458.t1
Valid prediction for snap_scaffold_18-snap.27-T1
Couldn't classify 133782, 133854
Couldn't classify 135822, 135910
Sorry, prediction pasa_asmbl_20284.p1 fails validation.
(CAG)	 AG	133782-133854	GT	CAG
(TGA)	 AG	134008-134153	GT	ACG
(TGT)	 AG	135249-135367	GT	AAG
(GTT)	 AG	135541-135728	GT	CAG
(AGC)	 AG	135822-135910	GT	GTG
-recovered pasa_asmbl_20284.p1, internal, 133782, 133854
-recovered pasa_asmbl_20284.p1, internal, 134008, 134153
-recovered pasa_asmbl_20284.p1, internal, 135249, 135367
-recovered pasa_asmbl_20284.p1, internal, 135541, 135728
-recovered pasa_asmbl_20284.p1, internal, 135822, 135910
Valid prediction for snap_scaffold_18-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_42565-T1
Valid prediction for Augustus_model.g28456.t1
Couldn't classify 59721, 59879
Sorry, prediction pasa_asmbl_20279.p1 fails validation.
(ATG)	 AG	59241-59402	GT	AGG
(GTG)	 AG	59721-59879	AG	CCA
-recovered pasa_asmbl_20279.p1, initial, 59241, 59402
-recovered pasa_asmbl_20279.p1, internal, 59241, 59402
Valid prediction for GlimmerHMM_glimmerT_42543-T1
Valid prediction for Augustus_model.g28442.t1
Valid prediction for snap_scaffold_18-snap.5-T1
Couldn't classify 166387, 166471
Sorry, prediction pasa_asmbl_20292.p1 fails validation.
(ATG)	 AT	164123-164206	GT	AGG
(TCT)	 AG	164706-164787	GT	AGG
(CTG)	 AG	164963-165119	GT	CGG
(GGC)	 AG	165381-165539	GT	GAG
(GTA)	 AG	165708-165864	GT	AGG
(TAC)	 AG	166002-166091	GT	CAG
(GAG)	 AG	166188-166282	GT	AGG
(GTA)	 AG	166387-166471	GT	AGG
-recovered pasa_asmbl_20292.p1, initial, 164123, 164206
add_exon() Sorry, pasa_asmbl_20292.p1 165381-165539-terminal-1 is invalid.
-recovered pasa_asmbl_20292.p1, terminal, 165381, 165539
-recovered pasa_asmbl_20292.p1, internal, 164706, 164787
-recovered pasa_asmbl_20292.p1, internal, 164963, 165119
-recovered pasa_asmbl_20292.p1, internal, 165381, 165539
-recovered pasa_asmbl_20292.p1, internal, 165708, 165864
-recovered pasa_asmbl_20292.p1, internal, 166002, 166091
-recovered pasa_asmbl_20292.p1, internal, 166188, 166282
-recovered pasa_asmbl_20292.p1, internal, 166387, 166471
Valid prediction for snap_scaffold_18-snap.39-T1
Valid prediction for snap_scaffold_18-snap.19-T1
Valid prediction for GeneMark_model.73559_t
Valid prediction for GlimmerHMM_glimmerT_42555-T1
Couldn't classify 77796, 77947
Couldn't classify 80064, 80204
Sorry, prediction pasa_asmbl_20282.p1 fails validation.
(GTG)	 AG	77796-77947	GT	AGG
(ACC)	 AG	79256-79334	GT	AGG
(GTA)	 AG	79493-79561	GT	AGG
(AGA)	 AG	80064-80204	GA	GTG
-recovered pasa_asmbl_20282.p1, internal, 77796, 77947
-recovered pasa_asmbl_20282.p1, internal, 79256, 79334
-recovered pasa_asmbl_20282.p1, internal, 79493, 79561
Valid prediction for snap_scaffold_18-snap.37-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g28446.t1
Couldn't classify 70295, 70491
Couldn't classify 70705, 70816
Sorry, prediction pasa_asmbl_21077.p1 fails validation.
(AGG)	 AC	70295-70491	GT	AGG
(GGG)	 AG	70705-70816	GT	AGG
-recovered pasa_asmbl_21077.p1, internal, 70705, 70816
Valid prediction for GeneMark_model.73561_t
Couldn't classify 63302, 63409
Couldn't classify 66435, 66528
Sorry, prediction pasa_asmbl_20280.p1 fails validation.
(TCT)	 CA	63302-63409	GT	GGG
(TCA)	 AG	63761-63920	GT	AGG
(ATG)	 AG	65928-66061	GT	AGG
(ACT)	 AG	66259-66335	GT	AAG
(GGT)	 AG	66435-66528	TT	GGT
add_exon() Sorry, pasa_asmbl_20280.p1 65928-66061-initial-1 is invalid.
-recovered pasa_asmbl_20280.p1, initial, 65928, 66061
add_exon() Sorry, pasa_asmbl_20280.p1 66259-66335-terminal-2 is invalid.
-recovered pasa_asmbl_20280.p1, terminal, 66259, 66335
-recovered pasa_asmbl_20280.p1, internal, 63761, 63920
-recovered pasa_asmbl_20280.p1, internal, 65928, 66061
-recovered pasa_asmbl_20280.p1, internal, 66259, 66335
Valid prediction for GlimmerHMM_glimmerT_42544-T1
Valid prediction for GlimmerHMM_glimmerT_42569-T1
Valid prediction for Augustus_model.g28443.t1
Valid prediction for Augustus_model.g28465.t1
Valid prediction for snap_scaffold_18-snap.11-T1
Valid prediction for snap_scaffold_18-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_42561-T1
Valid prediction for snap_scaffold_18-snap.22-T1
Valid prediction for Augustus_model.g28441.t1
Valid prediction for GeneMark_model.73568_t
Valid prediction for GeneMark_model.73580_t
Valid prediction for GlimmerHMM_glimmerT_42547-T1
Valid prediction for Augustus_model.g28464.t1
Valid prediction for GlimmerHMM_glimmerT_42566-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_42536-T1
Valid prediction for Augustus_model.g28444.t1
Valid prediction for snap_scaffold_18-snap.7-T1
Valid prediction for Augustus_model.g28449.t1
Valid prediction for snap_scaffold_18-snap.35-T1
Valid prediction for snap_scaffold_18-snap.30-T1
Valid prediction for Augustus_model.g28461.t1
Valid prediction for GeneMark_model.73582_t
Valid prediction for GeneMark_model.73581_t
Valid prediction for snap_scaffold_18-snap.14-T1
Valid prediction for snap_scaffold_18-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_42550-T1
Couldn't classify 151261, 151295
Couldn't classify 152254, 152313
Sorry, prediction pasa_asmbl_21104.p1 fails validation.
(AAT)	 AA	151261-151295	GT	GGG
(GAA)	 AG	151736-151982	GT	AGG
(ATT)	 AG	152114-152176	GT	TTG
(GAA)	 AG	152254-152313	AA	ATA
-recovered pasa_asmbl_21104.p1, internal, 151736, 151982
-recovered pasa_asmbl_21104.p1, internal, 152114, 152176
Valid prediction for Augustus_model.g28440.t1
Valid prediction for snap_scaffold_18-snap.40-T1
Valid prediction for snap_scaffold_18-snap.9-T1
Couldn't classify 154610, 154630
Couldn't classify 155449, 155511
Sorry, prediction pasa_asmbl_20288.p1 fails validation.
(GTC)	 AG	154610-154630	GT	ACG
(TGT)	 AG	154739-154843	GT	ATG
(GAA)	 AG	154958-155056	GT	CGG
(ACA)	 AG	155142-155273	GT	CTG
(ATA)	 AG	155449-155511	GT	GTG
-recovered pasa_asmbl_20288.p1, internal, 154610, 154630
-recovered pasa_asmbl_20288.p1, internal, 154739, 154843
-recovered pasa_asmbl_20288.p1, internal, 154958, 155056
-recovered pasa_asmbl_20288.p1, internal, 155142, 155273
-recovered pasa_asmbl_20288.p1, internal, 155449, 155511
Valid prediction for snap_scaffold_18-snap.32-T1
Couldn't classify 148111, 148259
Couldn't classify 148455, 148650
Sorry, prediction pasa_asmbl_21125.p1 fails validation.
(TCC)	 AC	148111-148259	GT	AGG
(ACG)	 AG	148455-148650	AA	GGA
Valid prediction for snap_scaffold_18-snap.6-T1
Valid prediction for pasa_asmbl_20301.p2

-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 GeneMark_model.73560_t
Valid prediction for GeneMark_model.73563_t
Valid prediction for GlimmerHMM_glimmerT_42535-T1
Valid prediction for Augustus_model.g28438.t1
Valid prediction for snap_scaffold_18-snap.4-T1
Valid prediction for snap_scaffold_18-snap.17-T1
Valid prediction for GlimmerHMM_glimmerT_42558-T1
Valid prediction for GeneMark_model.73579_t
Valid prediction for GlimmerHMM_glimmerT_42567-T1
Valid prediction for snap_scaffold_18-snap.38-T1
Valid prediction for GeneMark_model.73583_t
Valid prediction for GeneMark_model.73564_t
Valid prediction for GlimmerHMM_glimmerT_42556-T1
Valid prediction for GeneMark_model.73562_t
Valid prediction for GeneMark_model.73558_t
Valid prediction for Augustus_model.g28463.t1
Valid prediction for GlimmerHMM_glimmerT_42551-T1
Valid prediction for snap_scaffold_18-snap.12-T1
Valid prediction for GeneMark_model.73571_t
Valid prediction for snap_scaffold_18-snap.21-T1
Valid prediction for GlimmerHMM_glimmerT_42554-T1
Valid prediction for Augustus_model.g28459.t1
Valid prediction for GeneMark_model.73569_t
Valid prediction for GeneMark_model.73552_t
Valid prediction for GeneMark_model.73566_t
Valid prediction for Augustus_model.g28455.t1
Valid prediction for Augustus_model.g28450.t1
Valid prediction for GeneMark_model.73567_t
Valid prediction for GeneMark_model.73570_t
Valid prediction for GeneMark_model.73565_t
Valid prediction for GlimmerHMM_glimmerT_42560-T1
Valid prediction for GlimmerHMM_glimmerT_42562-T1
Valid prediction for GlimmerHMM_glimmerT_42548-T1
Valid prediction for Augustus_model.g28453.t1
Valid prediction for Augustus_model.g28448.t1
Valid prediction for Augustus_model.g28452.t1
Valid prediction for GeneMark_model.73550_t
Valid prediction for snap_scaffold_18-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_42552-T1
Valid prediction for snap_scaffold_18-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_42538-T1
Valid prediction for GeneMark_model.73551_t
Valid prediction for snap_scaffold_18-snap.1-T1
Valid prediction for Augustus_model.g28451.t1
Valid prediction for GlimmerHMM_glimmerT_42537-T1
Valid prediction for GlimmerHMM_glimmerT_42568-T1
Valid prediction for snap_scaffold_18-snap.20-T1
Valid prediction for GeneMark_model.73584_t
Valid prediction for Augustus_model.g28436.t1
Valid prediction for GeneMark_model.73576_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30735, rend_intergenic: 29092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84456, rend_intergenic: 82483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215286
-exon list size: 533


building trellis

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69.0    
69.2    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.6    
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    
77.8    
77.9    
78.1    
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    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 30735, rend_intergenic: 29092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84456, rend_intergenic: 82483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support