-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_1340606-1521959

-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 GeneMark_model.10127_t
Valid prediction for GeneMark_model.10096_t
Valid prediction for CodingQuarry_transcript_45962-T1
Valid prediction for pasa_asmbl_39809.p2
Valid prediction for GlimmerHMM_glimmerT_6164-T1
Valid prediction for GeneMark_model.10131_t
Couldn't classify 130324, 130665
Sorry, prediction pasa_asmbl_39806.p1 fails validation.
(CCT)	 TC	130324-130665	AA	GAA
Couldn't classify 138628, 138822
Sorry, prediction pasa_asmbl_40758.p1 fails validation.
(GGT)	 GT	138628-138822	GT	AGG
(GAT)	 AG	139226-139321	GT	GAG
(GAG)	 AG	139562-139757	GT	AGG
(GTG)	 AG	140119-140197	GT	GTG
(GGA)	 AG	140445-140559	GT	AGG
(CTG)	 AG	140966-141099	GT	AGG
(ATA)	 AG	141185-141305	GT	AGG
(GAT)	 AG	141671-141795	GT	AAG
(GTA)	 AG	142155-142287	GG	AGG
-recovered pasa_asmbl_40758.p1, terminal, 142155, 142287
-recovered pasa_asmbl_40758.p1, internal, 139226, 139321
-recovered pasa_asmbl_40758.p1, internal, 139562, 139757
-recovered pasa_asmbl_40758.p1, internal, 140119, 140197
-recovered pasa_asmbl_40758.p1, internal, 140445, 140559
-recovered pasa_asmbl_40758.p1, internal, 140966, 141099
-recovered pasa_asmbl_40758.p1, internal, 141185, 141305
-recovered pasa_asmbl_40758.p1, internal, 141671, 141795
Valid prediction for GeneMark_model.10134_t
Valid prediction for GeneMark_model.10090_t
Couldn't classify 106618, 106749
Sorry, prediction pasa_asmbl_39802.p1 fails validation.
(GAC)	 AG	106618-106749	GT	AGG
(AAG)	 AG	107131-107331	GT	GGG
(AAG)	 AG	107778-107888	GT	AGG
(GCG)	 AG	108483-108633	GT	GGG
(GCA)	 AG	109296-109384	TC	GAT
-recovered pasa_asmbl_39802.p1, terminal, 109296, 109384
-recovered pasa_asmbl_39802.p1, internal, 106618, 106749
-recovered pasa_asmbl_39802.p1, internal, 107131, 107331
-recovered pasa_asmbl_39802.p1, internal, 107778, 107888
-recovered pasa_asmbl_39802.p1, internal, 108483, 108633
Valid prediction for GlimmerHMM_glimmerT_6144-T1
Valid prediction for GeneMark_model.10129_t
Valid prediction for GeneMark_model.10105_t
Valid prediction for HiQ_model.g4048.t1
Valid prediction for GeneMark_model.10106_t
Valid prediction for snap_scaffold_3-snap.333-T1
Valid prediction for GeneMark_model.10124_t
Valid prediction for snap_scaffold_3-snap.348-T1
Valid prediction for GlimmerHMM_glimmerT_6142-T1
Valid prediction for GeneMark_model.10135_t
Valid prediction for GlimmerHMM_glimmerT_6157-T1
Valid prediction for HiQ_model.g4046.t1
Valid prediction for snap_scaffold_3-snap.345-T1
Valid prediction for GeneMark_model.10102_t
Valid prediction for snap_scaffold_3-snap.369-T1
Valid prediction for GeneMark_model.10119_t
Valid prediction for Augustus_model.g4041.t1
Valid prediction for snap_scaffold_3-snap.338-T1
Valid prediction for pasa_asmbl_39810.p1
Valid prediction for GeneMark_model.10117_t
Valid prediction for snap_scaffold_3-snap.346-T1
Valid prediction for snap_scaffold_3-snap.341-T1
Valid prediction for snap_scaffold_3-snap.339-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g4044.t1
Valid prediction for snap_scaffold_3-snap.344-T1
Valid prediction for snap_scaffold_3-snap.357-T1
Valid prediction for GeneMark_model.10133_t
Valid prediction for GeneMark_model.10112_t
Valid prediction for GeneMark_model.10094_t
Valid prediction for GlimmerHMM_glimmerT_6143-T1
Valid prediction for GlimmerHMM_glimmerT_6140-T1
Valid prediction for GeneMark_model.10121_t
Valid prediction for snap_scaffold_3-snap.362-T1
Valid prediction for snap_scaffold_3-snap.355-T1
Valid prediction for GeneMark_model.10114_t
Valid prediction for snap_scaffold_3-snap.352-T1
Valid prediction for GlimmerHMM_glimmerT_6155-T1
Valid prediction for GeneMark_model.10125_t
Valid prediction for snap_scaffold_3-snap.335-T1
Valid prediction for GeneMark_model.10092_t
Valid prediction for snap_scaffold_3-snap.343-T1
Valid prediction for Augustus_model.g4040.t1
Valid prediction for CodingQuarry_transcript_45961-T1
Valid prediction for GeneMark_model.10115_t
Valid prediction for GlimmerHMM_glimmerT_6158-T1
Valid prediction for Augustus_model.g4033.t1
Couldn't classify 138184, 138265
Sorry, prediction pasa_asmbl_39807.p1 fails validation.
(ATG)	 AG	136258-136324	GT	TGG
(ATG)	 AG	136610-136770	GT	ACG
(GTT)	 AG	137274-137397	GT	TGG
(AGG)	 AG	137843-137975	GT	TGG
(TAA)	 AG	138184-138265	GT	AGG
-recovered pasa_asmbl_39807.p1, initial, 136258, 136324
add_exon() Sorry, pasa_asmbl_39807.p1 136610-136770-initial-1 is invalid.
-recovered pasa_asmbl_39807.p1, initial, 136610, 136770
-recovered pasa_asmbl_39807.p1, internal, 136258, 136324
-recovered pasa_asmbl_39807.p1, internal, 136610, 136770
-recovered pasa_asmbl_39807.p1, internal, 137274, 137397
-recovered pasa_asmbl_39807.p1, internal, 137843, 137975
-recovered pasa_asmbl_39807.p1, internal, 138184, 138265
Valid prediction for GeneMark_model.10104_t
Couldn't classify 124248, 124294
Couldn't classify 124476, 124788
Sorry, prediction pasa_asmbl_40787.p1 fails validation.
(GAG)	 TG	124248-124294	GT	ACG
(GAA)	 AG	124476-124788	GA	AGG
Valid prediction for snap_scaffold_3-snap.367-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.10109_t
Valid prediction for GlimmerHMM_glimmerT_6162-T1
Valid prediction for snap_scaffold_3-snap.363-T1
Valid prediction for GeneMark_model.10100_t
Valid prediction for GlimmerHMM_glimmerT_6153-T1
Valid prediction for snap_scaffold_3-snap.366-T1
Valid prediction for GlimmerHMM_glimmerT_6149-T1
Valid prediction for GlimmerHMM_glimmerT_6166-T1
Valid prediction for GlimmerHMM_glimmerT_6146-T1
Valid prediction for snap_scaffold_3-snap.350-T1
Valid prediction for GlimmerHMM_glimmerT_6168-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_3-snap.353-T1
Valid prediction for GeneMark_model.10111_t
Valid prediction for snap_scaffold_3-snap.332-T1
Valid prediction for GlimmerHMM_glimmerT_6163-T1
Valid prediction for HiQ_model.g4049.t1
Valid prediction for GeneMark_model.10123_t
Valid prediction for snap_scaffold_3-snap.358-T1
Valid prediction for Augustus_model.g4034.t1
Valid prediction for GlimmerHMM_glimmerT_6141-T1
Valid prediction for GeneMark_model.10101_t
Valid prediction for snap_scaffold_3-snap.359-T1
Valid prediction for Augustus_model.g4031.t1
Valid prediction for GeneMark_model.10110_t
Valid prediction for GeneMark_model.10108_t
Valid prediction for GeneMark_model.10128_t
Valid prediction for HiQ_model.g4042.t1
Valid prediction for HiQ_model.g4045.t1
Valid prediction for snap_scaffold_3-snap.347-T1
Valid prediction for GlimmerHMM_glimmerT_6148-T1
Valid prediction for Augustus_model.g4035.t1
Valid prediction for GlimmerHMM_glimmerT_6138-T1
Valid prediction for GlimmerHMM_glimmerT_6152-T1
Valid prediction for GlimmerHMM_glimmerT_6151-T1
Valid prediction for GeneMark_model.10103_t
Valid prediction for GeneMark_model.10091_t
Valid prediction for GlimmerHMM_glimmerT_6147-T1
Valid prediction for Augustus_model.g4039.t1
Valid prediction for snap_scaffold_3-snap.337-T1
Valid prediction for snap_scaffold_3-snap.368-T1
Valid prediction for snap_scaffold_3-snap.342-T1
Valid prediction for GlimmerHMM_glimmerT_6156-T1
Valid prediction for GeneMark_model.10120_t
Valid prediction for snap_scaffold_3-snap.370-T1
Valid prediction for GeneMark_model.10116_t
Valid prediction for GeneMark_model.10118_t
Valid prediction for GlimmerHMM_glimmerT_6139-T1
Valid prediction for GlimmerHMM_glimmerT_6145-T1
Valid prediction for GeneMark_model.10099_t
Valid prediction for GeneMark_model.10097_t
Valid prediction for snap_scaffold_3-snap.351-T1
Valid prediction for GeneMark_model.10126_t
Valid prediction for Augustus_model.g4043.t1
Valid prediction for GlimmerHMM_glimmerT_6167-T1
Couldn't classify 83865, 83873
Sorry, prediction pasa_asmbl_38664.p1 fails validation.
(CAC)	 AG	83865-83873	GT	TGG
(GCT)	 AG	84036-84093	GT	AGG
(GGA)	 AG	84439-84525	GT	AGG
(GCG)	 AG	84787-84918	GT	TGG
(ACG)	 AG	85512-85684	GT	GAG
-recovered pasa_asmbl_38664.p1, terminal, 85512, 85684
-recovered pasa_asmbl_38664.p1, internal, 83865, 83873
-recovered pasa_asmbl_38664.p1, internal, 84036, 84093
-recovered pasa_asmbl_38664.p1, internal, 84439, 84525
-recovered pasa_asmbl_38664.p1, internal, 84787, 84918
-recovered pasa_asmbl_38664.p1, internal, 85512, 85684
Valid prediction for Augustus_model.g4036.t1
Valid prediction for snap_scaffold_3-snap.371-T1
Couldn't classify 26152, 26330
Sorry, prediction pasa_asmbl_38668.p1 fails validation.
(TGG)	 CC	26152-26330	GT	GGG
(CTT)	 AG	26550-26676	GT	AGG
(AAG)	 AG	27056-27154	GT	CAG
(CTG)	 AG	27574-27642	GT	AGG
(ACC)	 AG	28194-28440	GT	CAG
(ATA)	 AG	29006-29071	GT	AGG
(CTC)	 AG	29186-29272	GT	TGG
(AGG)	 AG	29833-29933	GT	AGG
(AGA)	 AG	30140-30589	CA	GAC
-recovered pasa_asmbl_38668.p1, terminal, 30140, 30589
-recovered pasa_asmbl_38668.p1, internal, 26550, 26676
-recovered pasa_asmbl_38668.p1, internal, 27056, 27154
-recovered pasa_asmbl_38668.p1, internal, 27574, 27642
-recovered pasa_asmbl_38668.p1, internal, 28194, 28440
-recovered pasa_asmbl_38668.p1, internal, 29006, 29071
-recovered pasa_asmbl_38668.p1, internal, 29186, 29272
-recovered pasa_asmbl_38668.p1, internal, 29833, 29933
Valid prediction for GeneMark_model.10089_t
Valid prediction for snap_scaffold_3-snap.365-T1
Valid prediction for GeneMark_model.10107_t
Valid prediction for CodingQuarry_transcript_45963-T1
Valid prediction for GeneMark_model.10113_t
Valid prediction for GeneMark_model.10093_t
Valid prediction for GlimmerHMM_glimmerT_6161-T1
Valid prediction for GeneMark_model.10130_t
Valid prediction for Augustus_model.g4032.t1
Valid prediction for GeneMark_model.10122_t
Valid prediction for snap_scaffold_3-snap.340-T1
Valid prediction for snap_scaffold_3-snap.354-T1
Valid prediction for Augustus_model.g4038.t1
Valid prediction for GeneMark_model.10095_t
Valid prediction for GlimmerHMM_glimmerT_6154-T1
Valid prediction for snap_scaffold_3-snap.364-T1
Valid prediction for snap_scaffold_3-snap.336-T1
Valid prediction for Augustus_model.g4037.t1
Valid prediction for snap_scaffold_3-snap.360-T1
Couldn't classify 21185, 21352
Couldn't classify 22595, 22654
Sorry, prediction pasa_asmbl_38669.p1 fails validation.
(CTG)	 CT	21185-21352	GT	AGG
(GTG)	 AG	22076-22273	GT	TGG
(AGC)	 AG	22595-22654	AT	AGA
-recovered pasa_asmbl_38669.p1, internal, 22076, 22273
Valid prediction for GlimmerHMM_glimmerT_6150-T1
Valid prediction for Augustus_model.g4030.t1
Valid prediction for GlimmerHMM_glimmerT_6165-T1
Valid prediction for snap_scaffold_3-snap.334-T1
Valid prediction for GeneMark_model.10132_t
Valid prediction for GlimmerHMM_glimmerT_6160-T1
Valid prediction for CodingQuarry_transcript_45960-T1
Valid prediction for snap_scaffold_3-snap.361-T1
Valid prediction for Augustus_model.g4047.t1
Valid prediction for GlimmerHMM_glimmerT_6159-T1
Valid prediction for snap_scaffold_3-snap.349-T1
Couldn't classify 53740, 53756
Sorry, prediction pasa_asmbl_38666.p1 fails validation.
(CGG)	 TG	53740-53756	GT	AGG
(GTT)	 AG	54051-54667	GT	AGG
(GTG)	 AG	54962-55245	GG	GAG
add_exon() Sorry, pasa_asmbl_38666.p1 54051-54667-terminal-2 is invalid.
-recovered pasa_asmbl_38666.p1, terminal, 54051, 54667
-recovered pasa_asmbl_38666.p1, terminal, 54962, 55245
-recovered pasa_asmbl_38666.p1, internal, 54051, 54667
Valid prediction for snap_scaffold_3-snap.356-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20593, rend_intergenic: 14930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28757, rend_intergenic: 26567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30345, rend_intergenic: 28817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41667, rend_intergenic: 37653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48218, rend_intergenic: 44717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85711, rend_intergenic: 82105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90175, rend_intergenic: 86810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94649, rend_intergenic: 90468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105031, rend_intergenic: 103552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109384, rend_intergenic: 105506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124797, rend_intergenic: 112908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145521, rend_intergenic: 138066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156762, rend_intergenic: 150766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181354
-exon list size: 666


building trellis

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65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 20593, rend_intergenic: 14930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28757, rend_intergenic: 26567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30345, rend_intergenic: 28817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41667, rend_intergenic: 37653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48218, rend_intergenic: 44717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85711, rend_intergenic: 82105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90175, rend_intergenic: 86810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94649, rend_intergenic: 90468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105031, rend_intergenic: 103552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109384, rend_intergenic: 105506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124797, rend_intergenic: 112908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145521, rend_intergenic: 138066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156762, rend_intergenic: 150766  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