-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_4361203-4638403

-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_3658-T1
Valid prediction for Augustus_model.g2468.t1
Valid prediction for Augustus_model.g2470.t1
Valid prediction for snap_scaffold_2-snap.1008-T1
Valid prediction for Augustus_model.g2464.t1
Valid prediction for HiQ_model.g2456.t1
Valid prediction for GlimmerHMM_glimmerT_3671-T1
Valid prediction for snap_scaffold_2-snap.1006-T1
Valid prediction for snap_scaffold_2-snap.1018-T1
Valid prediction for Augustus_model.g2455.t1
Valid prediction for HiQ_model.g2467.t1
Couldn't classify 117078, 117247
Couldn't classify 119471, 119793
Sorry, prediction pasa_asmbl_24350.p1 fails validation.
(ATC)	 AG	117078-117247	GC	AGG
(AGG)	 AG	118272-118498	GT	TGG
(GTG)	 AG	119471-119793	AC	ACA
-recovered pasa_asmbl_24350.p1, internal, 117078, 117247
-recovered pasa_asmbl_24350.p1, internal, 118272, 118498
Valid prediction for GlimmerHMM_glimmerT_3685-T1
Valid prediction for snap_scaffold_2-snap.1048-T1
Couldn't classify 228241, 228259
Sorry, prediction pasa_asmbl_24367.p1 fails validation.
(TCC)	 TG	228241-228259	GT	AGG
(CCT)	 AG	228452-228522	GT	CGG
(GAC)	 AG	228744-228833	GT	AGG
(GTG)	 AG	228956-229052	GT	TGG
(ACG)	 AG	230352-230451	GT	TTG
(CGC)	 AG	230648-230721	GT	AGG
(ACA)	 AG	230922-231112	GG	GAG
-recovered pasa_asmbl_24367.p1, terminal, 230922, 231112
-recovered pasa_asmbl_24367.p1, internal, 228452, 228522
-recovered pasa_asmbl_24367.p1, internal, 228744, 228833
-recovered pasa_asmbl_24367.p1, internal, 228956, 229052
-recovered pasa_asmbl_24367.p1, internal, 230352, 230451
-recovered pasa_asmbl_24367.p1, internal, 230648, 230721
Valid prediction for Augustus_model.g2459.t1
Valid prediction for snap_scaffold_2-snap.1040-T1
Valid prediction for snap_scaffold_2-snap.1010-T1
Valid prediction for snap_scaffold_2-snap.1014-T1
Valid prediction for GlimmerHMM_glimmerT_3670-T1
Valid prediction for snap_scaffold_2-snap.1028-T1
Couldn't classify 262881, 262943
Couldn't classify 267192, 267262
Sorry, prediction pasa_asmbl_24373.p1 fails validation.
(CGC)	 GT	262881-262943	GT	AGG
(GTC)	 AG	263460-263522	GT	AGG
(GTC)	 AG	263957-263968	GT	TGG
(GAC)	 AG	264864-264998	GT	GGG
(TTC)	 AG	265932-265978	GT	GAG
(CGT)	 AG	266357-266418	GT	AGG
(CGT)	 AG	267192-267262	CT	AGC
-recovered pasa_asmbl_24373.p1, internal, 263460, 263522
-recovered pasa_asmbl_24373.p1, internal, 263957, 263968
-recovered pasa_asmbl_24373.p1, internal, 264864, 264998
-recovered pasa_asmbl_24373.p1, internal, 265932, 265978
-recovered pasa_asmbl_24373.p1, internal, 266357, 266418
Valid prediction for HiQ_model.g2465.t1
Valid prediction for snap_scaffold_2-snap.1026-T1
Couldn't classify 212162, 212197
Sorry, prediction pasa_asmbl_24358.p2 fails validation.
(CCC)	 AC	212162-212197	GT	AGG
(GTG)	 AG	212441-212531	GT	AGG
(ACG)	 AG	213932-214079	GT	ATG
(TGA)	 AG	215175-215374	GT	CGG
(GTG)	 AG	215884-215987	GT	AGG
(GAA)	 AG	216399-216470	GT	AGG
(CTG)	 AG	216723-217007	AT	AGA
-recovered pasa_asmbl_24358.p2, terminal, 216723, 217007
-recovered pasa_asmbl_24358.p2, internal, 212441, 212531
-recovered pasa_asmbl_24358.p2, internal, 213932, 214079
-recovered pasa_asmbl_24358.p2, internal, 215175, 215374
-recovered pasa_asmbl_24358.p2, internal, 215884, 215987
-recovered pasa_asmbl_24358.p2, internal, 216399, 216470
Valid prediction for snap_scaffold_2-snap.1033-T1
Valid prediction for Augustus_model.g2451.t1
Valid prediction for GlimmerHMM_glimmerT_3688-T1
Valid prediction for snap_scaffold_2-snap.1035-T1
Valid prediction for snap_scaffold_2-snap.1015-T1
Valid prediction for snap_scaffold_2-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_3683-T1
Valid prediction for CodingQuarry_transcript_28537-T1
Valid prediction for GlimmerHMM_glimmerT_3677-T1
Valid prediction for snap_scaffold_2-snap.1011-T1
Valid prediction for GlimmerHMM_glimmerT_3669-T1
Valid prediction for snap_scaffold_2-snap.1051-T1
Couldn't classify 235478, 235568
Sorry, prediction pasa_asmbl_24370.p2 fails validation.
(GTA)	 CA	235478-235568	GT	GGG
(AGG)	 AG	235803-235873	GT	AGG
(GTC)	 AG	236042-236144	GT	TGG
(AGA)	 AG	236391-236617	CC	GAC
-recovered pasa_asmbl_24370.p2, terminal, 236391, 236617
-recovered pasa_asmbl_24370.p2, internal, 235803, 235873
-recovered pasa_asmbl_24370.p2, internal, 236042, 236144
Valid prediction for GlimmerHMM_glimmerT_3656-T1
Valid prediction for GlimmerHMM_glimmerT_3686-T1
Valid prediction for snap_scaffold_2-snap.1041-T1
Valid prediction for snap_scaffold_2-snap.1019-T1
Valid prediction for snap_scaffold_2-snap.1050-T1
Valid prediction for Augustus_model.g2466.t1
Valid prediction for snap_scaffold_2-snap.1044-T1
Valid prediction for snap_scaffold_2-snap.1012-T1
Valid prediction for GlimmerHMM_glimmerT_3661-T1
Couldn't classify 212071, 212164
Sorry, prediction pasa_asmbl_24355.p1 fails validation.
(ATG)	 AG	204816-205079	GT	AGG
(TGC)	 AG	207385-207592	GT	CAG
(GTA)	 AG	207897-208013	GT	AGG
(GAC)	 AG	208558-208659	GT	TGG
(GCT)	 AG	209402-209557	GT	AGG
(GCA)	 AG	209913-210013	GT	ATG
(GAC)	 AG	211097-211354	GT	AGG
(CCG)	 AG	211656-211771	GT	AGG
(GGA)	 AG	212071-212164	AA	CCA
-recovered pasa_asmbl_24355.p1, initial, 204816, 205079
-recovered pasa_asmbl_24355.p1, internal, 204816, 205079
-recovered pasa_asmbl_24355.p1, internal, 207385, 207592
-recovered pasa_asmbl_24355.p1, internal, 207897, 208013
-recovered pasa_asmbl_24355.p1, internal, 208558, 208659
-recovered pasa_asmbl_24355.p1, internal, 209402, 209557
-recovered pasa_asmbl_24355.p1, internal, 209913, 210013
-recovered pasa_asmbl_24355.p1, internal, 211097, 211354
-recovered pasa_asmbl_24355.p1, internal, 211656, 211771
Valid prediction for GlimmerHMM_glimmerT_3687-T1
Valid prediction for snap_scaffold_2-snap.1024-T1
Couldn't classify 4532, 4693
Sorry, prediction pasa_asmbl_24346.p1 fails validation.
(AGC)	 AC	4532-4693	GT	TGG
(CAC)	 AG	5402-5486	GT	CTG
(ATC)	 AG	5677-5864	AG	AAA
-recovered pasa_asmbl_24346.p1, terminal, 5677, 5864
-recovered pasa_asmbl_24346.p1, internal, 5402, 5486
Valid prediction for snap_scaffold_2-snap.1027-T1
Couldn't classify 268474, 268638
Sorry, prediction pasa_asmbl_24375.p1 fails validation.
(CAT)	 AG	268474-268638	GT	GGG
(GCG)	 AG	270036-270176	GT	AGG
(ACG)	 AG	270380-270532	GT	TGG
(GTG)	 AG	270921-271034	CA	AAC
-recovered pasa_asmbl_24375.p1, terminal, 270921, 271034
-recovered pasa_asmbl_24375.p1, internal, 268474, 268638
-recovered pasa_asmbl_24375.p1, internal, 270036, 270176
-recovered pasa_asmbl_24375.p1, internal, 270380, 270532
Valid prediction for snap_scaffold_2-snap.1046-T1
Valid prediction for Augustus_model.g2454.t1
Valid prediction for GlimmerHMM_glimmerT_3657-T1
Couldn't classify 113740, 113888
Couldn't classify 116056, 116159
Sorry, prediction pasa_asmbl_24349.p1 fails validation.
(GCT)	 AG	113740-113888	GT	GGG
(TTA)	 AG	114134-114254	GT	GAG
(GTC)	 AG	114497-114608	GT	AGG
(ATG)	 AG	116056-116159	GT	AAG
add_exon() Sorry, pasa_asmbl_24349.p1 116056-116159-initial-1 is invalid.
-recovered pasa_asmbl_24349.p1, initial, 116056, 116159
-recovered pasa_asmbl_24349.p1, internal, 113740, 113888
-recovered pasa_asmbl_24349.p1, internal, 114134, 114254
-recovered pasa_asmbl_24349.p1, internal, 114497, 114608
-recovered pasa_asmbl_24349.p1, internal, 116056, 116159
Valid prediction for GlimmerHMM_glimmerT_3660-T1
Valid prediction for GlimmerHMM_glimmerT_3663-T1
Valid prediction for GlimmerHMM_glimmerT_3680-T1
Valid prediction for pasa_asmbl_24347.p1
Valid prediction for snap_scaffold_2-snap.1025-T1
Valid prediction for GlimmerHMM_glimmerT_3681-T1
Couldn't classify 220768, 220975
Sorry, prediction pasa_asmbl_24363.p1 fails validation.
(CTG)	 GC	220768-220975	GT	GGG
(GGA)	 AG	221227-221300	GT	TGG
(GAT)	 AG	221469-221786	CC	AGC
-recovered pasa_asmbl_24363.p1, terminal, 221469, 221786
-recovered pasa_asmbl_24363.p1, internal, 221227, 221300
Valid prediction for snap_scaffold_2-snap.1007-T1
Valid prediction for GlimmerHMM_glimmerT_3678-T1
Valid prediction for snap_scaffold_2-snap.1016-T1
Valid prediction for CodingQuarry_transcript_28531-T1
Valid prediction for CodingQuarry_transcript_28530-T1
Valid prediction for Augustus_model.g2452.t1
Valid prediction for Augustus_model.g2469.t1
Valid prediction for CodingQuarry_transcript_28536-T1
Valid prediction for pasa_asmbl_24369.p1

-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 GlimmerHMM_glimmerT_3667-T1
Valid prediction for GlimmerHMM_glimmerT_3673-T1
Valid prediction for snap_scaffold_2-snap.1009-T1
Valid prediction for snap_scaffold_2-snap.1047-T1
Valid prediction for snap_scaffold_2-snap.1032-T1
Valid prediction for snap_scaffold_2-snap.1042-T1
Valid prediction for snap_scaffold_2-snap.1049-T1
Couldn't classify 90158, 90263
Sorry, prediction pasa_asmbl_23081.p1 fails validation.
(AGC)	 TC	90158-90263	GT	CGG
(GGA)	 AG	90670-90839	GT	AGG
(CTT)	 AG	91050-91238	AT	AAA
-recovered pasa_asmbl_23081.p1, terminal, 91050, 91238
-recovered pasa_asmbl_23081.p1, internal, 90670, 90839
Valid prediction for GlimmerHMM_glimmerT_3664-T1
Valid prediction for GlimmerHMM_glimmerT_3682-T1
Valid prediction for CodingQuarry_transcript_28535-T1
Valid prediction for GlimmerHMM_glimmerT_3676-T1
Valid prediction for CodingQuarry_transcript_28533-T1
Valid prediction for snap_scaffold_2-snap.1038-T1
Valid prediction for Augustus_model.g2458.t1
Valid prediction for snap_scaffold_2-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_3668-T1
Valid prediction for snap_scaffold_2-snap.1020-T1
Valid prediction for snap_scaffold_2-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_3674-T1
Valid prediction for snap_scaffold_2-snap.1043-T1
Valid prediction for GlimmerHMM_glimmerT_3665-T1
Valid prediction for snap_scaffold_2-snap.1036-T1
Valid prediction for HiQ_model.g2463.t1
Valid prediction for Augustus_model.g2457.t1
Valid prediction for CodingQuarry_transcript_28532-T1
Valid prediction for Augustus_model.g2453.t1
Valid prediction for snap_scaffold_2-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_3659-T1
Valid prediction for GlimmerHMM_glimmerT_3666-T1
Valid prediction for pasa_asmbl_23074.p1
Valid prediction for snap_scaffold_2-snap.1039-T1
Valid prediction for snap_scaffold_2-snap.1021-T1
Valid prediction for snap_scaffold_2-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_3679-T1
Valid prediction for GlimmerHMM_glimmerT_3672-T1
Valid prediction for snap_scaffold_2-snap.1017-T1
Valid prediction for snap_scaffold_2-snap.1037-T1
Valid prediction for Augustus_model.g2461.t1
Valid prediction for Augustus_model.g2460.t1
Couldn't classify 21831, 22133
Sorry, prediction pasa_asmbl_24372.p1 fails validation.
(GTA)	 CC	21831-22133	GC	AGG
Valid prediction for snap_scaffold_2-snap.1022-T1
Valid prediction for snap_scaffold_2-snap.1013-T1
Valid prediction for GlimmerHMM_glimmerT_3684-T1
Couldn't classify 132108, 132215
Sorry, prediction pasa_asmbl_23077.p1 fails validation.
(ATT)	 AG	132108-132215	GT	TAG
(AAA)	 AG	133832-133888	GT	AGG
(AGT)	 AG	134007-134159	GT	TGG
(GAG)	 AG	134284-134488	GT	AGG
(TCA)	 AG	135115-135171	GT	ATG
(GGA)	 AG	135691-135794	GT	AGG
(GTC)	 AG	136031-136140	GT	AGG
(AAA)	 AG	136417-136447	CT	AAC
-recovered pasa_asmbl_23077.p1, terminal, 136417, 136447
-recovered pasa_asmbl_23077.p1, internal, 132108, 132215
-recovered pasa_asmbl_23077.p1, internal, 133832, 133888
-recovered pasa_asmbl_23077.p1, internal, 134007, 134159
-recovered pasa_asmbl_23077.p1, internal, 134284, 134488
-recovered pasa_asmbl_23077.p1, internal, 135115, 135171
-recovered pasa_asmbl_23077.p1, internal, 135691, 135794
-recovered pasa_asmbl_23077.p1, internal, 136031, 136140
Valid prediction for snap_scaffold_2-snap.1031-T1
Valid prediction for pasa_asmbl_23082.p1
Valid prediction for GlimmerHMM_glimmerT_3662-T1
Valid prediction for HiQ_model.g2462.t1
Valid prediction for CodingQuarry_transcript_28534-T1
Valid prediction for GlimmerHMM_glimmerT_3675-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25555, rend_intergenic: 22122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202781, rend_intergenic: 200802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206824, rend_intergenic: 203873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221786, rend_intergenic: 207319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229389, rend_intergenic: 224850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240682, rend_intergenic: 237137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254920, rend_intergenic: 250561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256610, rend_intergenic: 256443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268180, rend_intergenic: 257006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 277201
-exon list size: 526


building trellis

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72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 25555, rend_intergenic: 22122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202781, rend_intergenic: 200802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206824, rend_intergenic: 203873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221786, rend_intergenic: 207319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229389, rend_intergenic: 224850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240682, rend_intergenic: 237137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254920, rend_intergenic: 250561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256610, rend_intergenic: 256443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268180, rend_intergenic: 257006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support