-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_14627139-14846967

-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 snap_scaffold_9-snap.2972-T1
Valid prediction for GlimmerHMM_glimmerT_23379-T1
Valid prediction for Augustus_model.g15559.t1
Valid prediction for GlimmerHMM_glimmerT_23363-T1
Couldn't classify 193946, 194097
Sorry, prediction pasa_asmbl_54539.p1 fails validation.
(GAG)	 AG	193946-194097	GT	AGG
(GTT)	 AG	194266-195592	GT	AGG
(GAG)	 AG	195823-195990	GG	GAG
-recovered pasa_asmbl_54539.p1, terminal, 195823, 195990
-recovered pasa_asmbl_54539.p1, internal, 193946, 194097
-recovered pasa_asmbl_54539.p1, internal, 194266, 195592
Valid prediction for HiQ_model.g15574.t1
Valid prediction for GlimmerHMM_glimmerT_23367-T1
Valid prediction for snap_scaffold_9-snap.3000-T1
Valid prediction for Augustus_model.g15557.t1
Valid prediction for GlimmerHMM_glimmerT_23360-T1
Valid prediction for GlimmerHMM_glimmerT_23380-T1
Valid prediction for snap_scaffold_9-snap.2965-T1
Valid prediction for snap_scaffold_9-snap.2968-T1
Valid prediction for snap_scaffold_9-snap.2975-T1
Valid prediction for GlimmerHMM_glimmerT_23378-T1
Valid prediction for Augustus_model.g15568.t1
Valid prediction for Augustus_model.g15560.t1
Couldn't classify 51038, 51235
Couldn't classify 55056, 55117
Sorry, prediction pasa_asmbl_54777.p1 fails validation.
(TGG)	 CC	51038-51235	GT	AGG
(TGC)	 AG	51398-51500	GT	AGG
(GAA)	 AG	52690-52752	GT	TGG
(CCC)	 AG	55056-55117	CC	GCC
-recovered pasa_asmbl_54777.p1, internal, 51398, 51500
-recovered pasa_asmbl_54777.p1, internal, 52690, 52752
Valid prediction for Augustus_model.g15567.t1
Valid prediction for snap_scaffold_9-snap.2997-T1
Couldn't classify 59646, 59760
Sorry, prediction pasa_asmbl_54691.p1 fails validation.
(GAT)	 CA	59646-59760	GT	AGG
(ATG)	 AG	60151-60270	GT	AGG
(ACG)	 AG	60542-60661	GT	GGG
(ATG)	 AG	60805-60924	GT	GGG
(ATG)	 AG	61116-61229	GT	AGG
(ACA)	 AG	61347-61466	GT	AGG
(ATG)	 AG	62688-62813	GT	AGG
(ACA)	 AG	63073-63198	GT	GGG
(ATG)	 AG	63795-63917	GT	GGG
(ACG)	 AG	64114-64245	GT	CGG
(ACA)	 AG	64826-64951	GT	GGG
(ATG)	 AG	65115-65255	GT	AGG
(GAC)	 AG	65525-65782	GT	TGG
(CTG)	 AG	65976-66047	GT	AGG
(ATG)	 AG	66133-66261	GT	AGG
(ATA)	 AG	66644-66787	GT	GGG
(ATG)	 AG	67004-67156	GT	AGG
(AGG)	 AG	67415-67730	GT	CTG
(ACC)	 AG	68044-68309	GT	GAG
(GGC)	 AG	68651-68800	GT	AGG
(ACA)	 AG	69138-69277	CC	AGC
-recovered pasa_asmbl_54691.p1, initial, 60151, 60270
-recovered pasa_asmbl_54691.p1, initial, 60805, 60924
-recovered pasa_asmbl_54691.p1, initial, 61116, 61229
add_exon() Sorry, pasa_asmbl_54691.p1 62688-62813-initial-1 is invalid.
-recovered pasa_asmbl_54691.p1, initial, 62688, 62813
-recovered pasa_asmbl_54691.p1, initial, 63795, 63917
-recovered pasa_asmbl_54691.p1, initial, 65115, 65255
add_exon() Sorry, pasa_asmbl_54691.p1 66133-66261-initial-1 is invalid.
-recovered pasa_asmbl_54691.p1, initial, 66133, 66261
add_exon() Sorry, pasa_asmbl_54691.p1 67004-67156-initial-1 is invalid.
-recovered pasa_asmbl_54691.p1, initial, 67004, 67156
add_exon() Sorry, pasa_asmbl_54691.p1 66133-66261-terminal-1 is invalid.
-recovered pasa_asmbl_54691.p1, terminal, 66133, 66261
-recovered pasa_asmbl_54691.p1, terminal, 69138, 69277
-recovered pasa_asmbl_54691.p1, internal, 60151, 60270
-recovered pasa_asmbl_54691.p1, internal, 60542, 60661
-recovered pasa_asmbl_54691.p1, internal, 60805, 60924
-recovered pasa_asmbl_54691.p1, internal, 61116, 61229
-recovered pasa_asmbl_54691.p1, internal, 61347, 61466
-recovered pasa_asmbl_54691.p1, internal, 62688, 62813
-recovered pasa_asmbl_54691.p1, internal, 63073, 63198
-recovered pasa_asmbl_54691.p1, internal, 63795, 63917
-recovered pasa_asmbl_54691.p1, internal, 64114, 64245
-recovered pasa_asmbl_54691.p1, internal, 64826, 64951
-recovered pasa_asmbl_54691.p1, internal, 65115, 65255
-recovered pasa_asmbl_54691.p1, internal, 65525, 65782
-recovered pasa_asmbl_54691.p1, internal, 65976, 66047
-recovered pasa_asmbl_54691.p1, internal, 66133, 66261
-recovered pasa_asmbl_54691.p1, internal, 66644, 66787
-recovered pasa_asmbl_54691.p1, internal, 67004, 67156
-recovered pasa_asmbl_54691.p1, internal, 67415, 67730
-recovered pasa_asmbl_54691.p1, internal, 68044, 68309
-recovered pasa_asmbl_54691.p1, internal, 68651, 68800
Valid prediction for snap_scaffold_9-snap.2995-T1
Valid prediction for snap_scaffold_9-snap.2958-T1
Valid prediction for GlimmerHMM_glimmerT_23364-T1
Valid prediction for snap_scaffold_9-snap.2990-T1
Valid prediction for snap_scaffold_9-snap.3001-T1
Valid prediction for snap_scaffold_9-snap.2956-T1
Valid prediction for pasa_asmbl_54534.p1
Valid prediction for GlimmerHMM_glimmerT_23382-T1
Valid prediction for snap_scaffold_9-snap.2984-T1
Valid prediction for snap_scaffold_9-snap.2976-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2982-T1
Valid prediction for snap_scaffold_9-snap.2979-T1
Valid prediction for Augustus_model.g15561.t1
Valid prediction for snap_scaffold_9-snap.2951-T1
Valid prediction for Augustus_model.g15558.t1
Valid prediction for snap_scaffold_9-snap.2994-T1
Valid prediction for snap_scaffold_9-snap.2962-T1
Valid prediction for snap_scaffold_9-snap.2953-T1
Valid prediction for snap_scaffold_9-snap.2985-T1
Valid prediction for snap_scaffold_9-snap.2974-T1
Valid prediction for GlimmerHMM_glimmerT_23374-T1
Valid prediction for CodingQuarry_transcript_62404-T1
Valid prediction for snap_scaffold_9-snap.2959-T1
Valid prediction for GlimmerHMM_glimmerT_23365-T1
Valid prediction for snap_scaffold_9-snap.2977-T1
Valid prediction for snap_scaffold_9-snap.2992-T1
Valid prediction for GlimmerHMM_glimmerT_23366-T1
Valid prediction for snap_scaffold_9-snap.2948-T1

-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_9-snap.2963-T1
Valid prediction for GlimmerHMM_glimmerT_23373-T1
Valid prediction for snap_scaffold_9-snap.2950-T1
Valid prediction for snap_scaffold_9-snap.2952-T1
Valid prediction for snap_scaffold_9-snap.2996-T1
Valid prediction for Augustus_model.g15571.t1
Valid prediction for pasa_asmbl_55505.p1
Valid prediction for snap_scaffold_9-snap.2981-T1
Valid prediction for Augustus_model.g15573.t1
Valid prediction for snap_scaffold_9-snap.2983-T1
Couldn't classify 59141, 59274
Sorry, prediction pasa_asmbl_55490.p1 fails validation.
(TCG)	 TC	59141-59274	GT	CGG
(GCT)	 AG	59942-60056	GT	GAG
(GAC)	 AG	60420-60548	CT	AGC
-recovered pasa_asmbl_55490.p1, terminal, 60420, 60548
-recovered pasa_asmbl_55490.p1, internal, 59942, 60056
Valid prediction for Augustus_model.g15570.t1
Valid prediction for GlimmerHMM_glimmerT_23376-T1
Valid prediction for snap_scaffold_9-snap.2966-T1
Valid prediction for snap_scaffold_9-snap.2993-T1
Valid prediction for snap_scaffold_9-snap.2967-T1
Valid prediction for snap_scaffold_9-snap.2987-T1
Valid prediction for snap_scaffold_9-snap.2980-T1
Valid prediction for Augustus_model.g15572.t1
Valid prediction for snap_scaffold_9-snap.2986-T1
Valid prediction for snap_scaffold_9-snap.2998-T1
Valid prediction for snap_scaffold_9-snap.2988-T1
Valid prediction for Augustus_model.g15566.t1
Valid prediction for snap_scaffold_9-snap.2955-T1
Valid prediction for snap_scaffold_9-snap.2964-T1
Valid prediction for GlimmerHMM_glimmerT_23372-T1
Valid prediction for snap_scaffold_9-snap.2954-T1
Valid prediction for snap_scaffold_9-snap.2946-T1
Valid prediction for snap_scaffold_9-snap.2991-T1
Valid prediction for Augustus_model.g15555.t1
Valid prediction for snap_scaffold_9-snap.2961-T1
Valid prediction for snap_scaffold_9-snap.2973-T1
Valid prediction for Augustus_model.g15565.t1
Valid prediction for snap_scaffold_9-snap.2971-T1
Valid prediction for GlimmerHMM_glimmerT_23383-T1
Valid prediction for snap_scaffold_9-snap.2957-T1
Valid prediction for GlimmerHMM_glimmerT_23368-T1
Valid prediction for Augustus_model.g15556.t1
Valid prediction for GlimmerHMM_glimmerT_23381-T1
Valid prediction for GlimmerHMM_glimmerT_23361-T1
Valid prediction for Augustus_model.g15562.t1
Valid prediction for Augustus_model.g15576.t1
Valid prediction for CodingQuarry_transcript_62407-T1
Valid prediction for GlimmerHMM_glimmerT_23377-T1
Valid prediction for GlimmerHMM_glimmerT_23384-T1
Valid prediction for GlimmerHMM_glimmerT_23370-T1
Valid prediction for snap_scaffold_9-snap.2947-T1
Valid prediction for HiQ_model.g15575.t1
Valid prediction for snap_scaffold_9-snap.2989-T1
Valid prediction for snap_scaffold_9-snap.2960-T1
Valid prediction for snap_scaffold_9-snap.2969-T1
Valid prediction for CodingQuarry_transcript_62408-T1
Valid prediction for GlimmerHMM_glimmerT_23375-T1
Couldn't classify 135025, 135041
Sorry, prediction pasa_asmbl_55487.p1 fails validation.
(ATG)	 GC	133313-133383	GT	AGG
(AGT)	 AG	133531-133721	GT	TGG
(GGG)	 AG	133924-134039	GT	AGG
(AAC)	 AG	134162-134249	GT	AGG
(ATG)	 AG	134388-134504	GT	AAG
(GCG)	 AG	135025-135041	AT	GGA
-recovered pasa_asmbl_55487.p1, initial, 133313, 133383
add_exon() Sorry, pasa_asmbl_55487.p1 134388-134504-initial-1 is invalid.
-recovered pasa_asmbl_55487.p1, initial, 134388, 134504
-recovered pasa_asmbl_55487.p1, terminal, 134162, 134249
-recovered pasa_asmbl_55487.p1, internal, 133531, 133721
-recovered pasa_asmbl_55487.p1, internal, 133924, 134039
-recovered pasa_asmbl_55487.p1, internal, 134162, 134249
-recovered pasa_asmbl_55487.p1, internal, 134388, 134504
Valid prediction for GlimmerHMM_glimmerT_23371-T1
Couldn't classify 135120, 135195
Couldn't classify 135784, 135881
Sorry, prediction pasa_asmbl_55486.p1 fails validation.
(CAG)	 CG	135120-135195	GT	AGG
(TGT)	 AG	135413-135568	GT	AGG
(GTC)	 AG	135784-135881	TA	GGT
add_exon() Sorry, pasa_asmbl_55486.p1 135413-135568-terminal-1 is invalid.
-recovered pasa_asmbl_55486.p1, terminal, 135413, 135568
-recovered pasa_asmbl_55486.p1, internal, 135413, 135568
Valid prediction for snap_scaffold_9-snap.2970-T1
Couldn't classify 66092, 66332
Sorry, prediction pasa_asmbl_55488.p1 fails validation.
(CGG)	 AG	66092-66332	GT	GGG
(TTT)	 AG	68244-68479	CT	AGC
-recovered pasa_asmbl_55488.p1, terminal, 68244, 68479
-recovered pasa_asmbl_55488.p1, internal, 66092, 66332
Couldn't classify 135864, 135880
Couldn't classify 136983, 137073
Sorry, prediction pasa_asmbl_55485.p2 fails validation.
(TCC)	 TC	135864-135880	GT	AGG
(GGT)	 AG	136180-136364	GT	AGG
(CAC)	 AG	136690-136828	GT	AGG
(CCT)	 AG	136983-137073	TC	GCT
-recovered pasa_asmbl_55485.p2, internal, 136180, 136364
-recovered pasa_asmbl_55485.p2, internal, 136690, 136828
Couldn't classify 58851, 58978
Sorry, prediction pasa_asmbl_55491.p1 fails validation.
(ATG)	 AT	56136-57873	GT	TGG
(CGC)	 AG	58851-58978	GA	GGG
-recovered pasa_asmbl_55491.p1, initial, 56136, 57873
Valid prediction for Augustus_model.g15564.t1
Valid prediction for GlimmerHMM_glimmerT_23362-T1
Valid prediction for GlimmerHMM_glimmerT_23359-T1
Valid prediction for CodingQuarry_transcript_62405-T1
Valid prediction for snap_scaffold_9-snap.2949-T1
Valid prediction for Augustus_model.g15563.t1
Valid prediction for GlimmerHMM_glimmerT_23369-T1
Valid prediction for snap_scaffold_9-snap.2978-T1
Valid prediction for Augustus_model.g15569.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12194, rend_intergenic: 8766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17167, rend_intergenic: 15653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18071, rend_intergenic: 17307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24030, rend_intergenic: 20455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26842, rend_intergenic: 25388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34054, rend_intergenic: 28822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51907, rend_intergenic: 34459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69277, rend_intergenic: 54301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78843, rend_intergenic: 75764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87776, rend_intergenic: 82158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98996, rend_intergenic: 98191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100800, rend_intergenic: 99330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115398, rend_intergenic: 100828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116652, rend_intergenic: 115473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118817, rend_intergenic: 117155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124423, rend_intergenic: 119338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136185, rend_intergenic: 128803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140700, rend_intergenic: 137388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164594, rend_intergenic: 160634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189253, rend_intergenic: 184312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210153, rend_intergenic: 205669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219829
-exon list size: 500


building trellis

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70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 12194, rend_intergenic: 8766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17167, rend_intergenic: 15653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18071, rend_intergenic: 17307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24030, rend_intergenic: 20455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26842, rend_intergenic: 25388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34054, rend_intergenic: 28822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51907, rend_intergenic: 34459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69277, rend_intergenic: 54301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78843, rend_intergenic: 75764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87776, rend_intergenic: 82158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98996, rend_intergenic: 98191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100800, rend_intergenic: 99330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115398, rend_intergenic: 100828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116652, rend_intergenic: 115473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118817, rend_intergenic: 117155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124423, rend_intergenic: 119338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136185, rend_intergenic: 128803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140700, rend_intergenic: 137388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164594, rend_intergenic: 160634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189253, rend_intergenic: 184312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210153, rend_intergenic: 205669  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