-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_5722761-5875497

-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 CodingQuarry_transcript_34102-T1
Valid prediction for GeneMark_model.87757_t
Valid prediction for Augustus_model.g33994.t1
Valid prediction for GeneMark_model.87776_t
Valid prediction for GeneMark_model.87779_t
Valid prediction for snap_scaffold_22-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_50712-T1
Valid prediction for GeneMark_model.87748_t
Valid prediction for snap_scaffold_22-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_50724-T1
Valid prediction for GeneMark_model.87786_t
Couldn't classify 83242, 83387
Couldn't classify 91868, 92011
Sorry, prediction pasa_asmbl_29355.p1 fails validation.
(GAC)	 CA	83242-83387	GT	AGG
(TCG)	 AG	83677-83806	GT	TGG
(GAT)	 AG	84206-84311	GT	AGG
(AGC)	 AG	84786-85032	GT	TGG
(TCT)	 AG	86042-86138	GT	AGG
(TCT)	 AG	86319-86427	GT	AGG
(TGA)	 AG	86858-86964	GT	AGG
(GAA)	 AG	87078-87127	GT	AGG
(GAG)	 AG	88260-88424	GT	AGG
(TCT)	 AG	88714-88779	GT	GGG
(TGG)	 AG	88968-89022	GT	CGG
(AGT)	 AG	89121-89184	GT	AGG
(ACA)	 AG	89262-89363	GT	TGG
(GGT)	 AG	89461-89558	GT	AGG
(ACT)	 AG	89975-90112	GT	TGG
(CCC)	 AG	90248-90325	GT	AGG
(ATG)	 AG	91868-92011	TC	CCT
-recovered pasa_asmbl_29355.p1, internal, 83677, 83806
-recovered pasa_asmbl_29355.p1, internal, 84206, 84311
-recovered pasa_asmbl_29355.p1, internal, 84786, 85032
-recovered pasa_asmbl_29355.p1, internal, 86042, 86138
-recovered pasa_asmbl_29355.p1, internal, 86319, 86427
-recovered pasa_asmbl_29355.p1, internal, 86858, 86964
-recovered pasa_asmbl_29355.p1, internal, 87078, 87127
-recovered pasa_asmbl_29355.p1, internal, 88260, 88424
-recovered pasa_asmbl_29355.p1, internal, 88714, 88779
-recovered pasa_asmbl_29355.p1, internal, 88968, 89022
-recovered pasa_asmbl_29355.p1, internal, 89121, 89184
-recovered pasa_asmbl_29355.p1, internal, 89262, 89363
-recovered pasa_asmbl_29355.p1, internal, 89461, 89558
-recovered pasa_asmbl_29355.p1, internal, 89975, 90112
-recovered pasa_asmbl_29355.p1, internal, 90248, 90325
Valid prediction for GeneMark_model.87755_t
Valid prediction for GeneMark_model.87738_t
Valid prediction for snap_scaffold_22-snap.1093-T1
Valid prediction for snap_scaffold_22-snap.1100-T1
Valid prediction for snap_scaffold_22-snap.1112-T1
Valid prediction for GeneMark_model.87763_t
Valid prediction for GeneMark_model.87770_t
Valid prediction for GeneMark_model.87750_t
Valid prediction for Augustus_model.g33986.t1
Valid prediction for GlimmerHMM_glimmerT_50716-T1
Valid prediction for GeneMark_model.87768_t
Valid prediction for GeneMark_model.87745_t
Valid prediction for snap_scaffold_22-snap.1107-T1
Valid prediction for GeneMark_model.87744_t
Valid prediction for snap_scaffold_22-snap.1092-T1
Valid prediction for Augustus_model.g33987.t1
Valid prediction for snap_scaffold_22-snap.1119-T1
Valid prediction for GeneMark_model.87740_t
Valid prediction for snap_scaffold_22-snap.1098-T1
Valid prediction for GeneMark_model.87746_t
Valid prediction for GlimmerHMM_glimmerT_50718-T1
Valid prediction for snap_scaffold_22-snap.1103-T1
Couldn't classify 36957, 37178
Sorry, prediction pasa_asmbl_29353.p1 fails validation.
(CCG)	 CC	36957-37178	GT	CCG
(GGG)	 AG	37317-37494	GT	CAG
(GGA)	 AG	37761-38107	GT	CGG
(GCC)	 AG	38244-38495	GG	GAG
-recovered pasa_asmbl_29353.p1, terminal, 38244, 38495
-recovered pasa_asmbl_29353.p1, internal, 37317, 37494
-recovered pasa_asmbl_29353.p1, internal, 37761, 38107
Valid prediction for HiQ_model.g33990.t1
Valid prediction for snap_scaffold_22-snap.1120-T1
Valid prediction for GeneMark_model.87777_t
Valid prediction for GeneMark_model.87741_t
Valid prediction for snap_scaffold_22-snap.1089-T1
Valid prediction for GeneMark_model.87784_t
Valid prediction for GeneMark_model.87753_t
Valid prediction for GeneMark_model.87765_t
Valid prediction for GeneMark_model.87774_t
Valid prediction for GlimmerHMM_glimmerT_50726-T1
Couldn't classify 32410, 32468
Couldn't classify 33221, 33488
Sorry, prediction pasa_asmbl_29351.p1 fails validation.
(AAG)	 AC	32410-32468	GT	AGG
(GGC)	 AG	32655-32761	GT	GAG
(TCC)	 AG	32870-33023	GT	ACG
(GAG)	 AG	33221-33488	GT	CCG
-recovered pasa_asmbl_29351.p1, internal, 32655, 32761
-recovered pasa_asmbl_29351.p1, internal, 32870, 33023
-recovered pasa_asmbl_29351.p1, internal, 33221, 33488
Valid prediction for snap_scaffold_22-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_50719-T1
Valid prediction for GeneMark_model.87742_t
Valid prediction for GlimmerHMM_glimmerT_50717-T1
Valid prediction for GeneMark_model.87760_t
Valid prediction for GeneMark_model.87787_t
Valid prediction for GeneMark_model.87773_t
Valid prediction for snap_scaffold_22-snap.1111-T1
Valid prediction for GeneMark_model.87736_t
Valid prediction for snap_scaffold_22-snap.1115-T1
Couldn't classify 44871, 44922
Sorry, prediction pasa_asmbl_29354.p1 fails validation.
(GGG)	 CC	44871-44922	GT	AGG
(AGG)	 AG	45026-45150	GT	ACG
(GTG)	 AG	45848-45984	GT	GGG
(ATC)	 AG	46241-46716	GT	ATG
(TAA)	 AG	46863-46934	GT	TGG
(TCA)	 AG	47320-47490	GC	AGG
(GAG)	 AG	47601-47731	CC	GAC
-recovered pasa_asmbl_29354.p1, terminal, 47601, 47731
-recovered pasa_asmbl_29354.p1, internal, 45026, 45150
-recovered pasa_asmbl_29354.p1, internal, 45848, 45984
-recovered pasa_asmbl_29354.p1, internal, 46241, 46716
-recovered pasa_asmbl_29354.p1, internal, 46863, 46934
-recovered pasa_asmbl_29354.p1, internal, 47320, 47490
Valid prediction for GeneMark_model.87782_t
Valid prediction for GlimmerHMM_glimmerT_50725-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_22-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_50708-T1
Valid prediction for GeneMark_model.87737_t
Valid prediction for snap_scaffold_22-snap.1114-T1
Valid prediction for GeneMark_model.87743_t
Valid prediction for CodingQuarry_transcript_34103-T1
Couldn't classify 29025, 29101
Couldn't classify 43222, 43359
Sorry, prediction pasa_asmbl_30056.p1 fails validation.
(GAT)	 AG	29025-29101	GT	AGG
(GGG)	 AG	31604-31790	GT	GGG
(GTT)	 AG	33861-33926	GT	TGG
(TAT)	 AG	34622-34693	GT	AGG
(TTC)	 AG	35344-35510	GT	ACG
(GGG)	 AG	36228-36312	GT	TGG
(GAC)	 AG	37053-37195	GT	GGG
(GCA)	 AG	37289-37466	GT	AGG
(GAG)	 AG	38635-38724	GT	AAG
(TTG)	 AG	39011-39206	GT	TGG
(GTG)	 AG	40009-40117	GT	AGG
(CGA)	 AG	40797-41001	GC	AGG
(GTG)	 AG	41203-41280	GT	GGG
(GTA)	 AG	43222-43359	CG	CGC
-recovered pasa_asmbl_30056.p1, internal, 29025, 29101
-recovered pasa_asmbl_30056.p1, internal, 31604, 31790
-recovered pasa_asmbl_30056.p1, internal, 33861, 33926
-recovered pasa_asmbl_30056.p1, internal, 34622, 34693
-recovered pasa_asmbl_30056.p1, internal, 35344, 35510
-recovered pasa_asmbl_30056.p1, internal, 36228, 36312
-recovered pasa_asmbl_30056.p1, internal, 37053, 37195
-recovered pasa_asmbl_30056.p1, internal, 37289, 37466
-recovered pasa_asmbl_30056.p1, internal, 38635, 38724
-recovered pasa_asmbl_30056.p1, internal, 39011, 39206
-recovered pasa_asmbl_30056.p1, internal, 40009, 40117
-recovered pasa_asmbl_30056.p1, internal, 40797, 41001
-recovered pasa_asmbl_30056.p1, internal, 41203, 41280
Valid prediction for GeneMark_model.87759_t
Valid prediction for GeneMark_model.87758_t
Valid prediction for snap_scaffold_22-snap.1105-T1
Valid prediction for GeneMark_model.87767_t
Valid prediction for Augustus_model.g33985.t1
Valid prediction for snap_scaffold_22-snap.1117-T1
Valid prediction for GeneMark_model.87785_t
Valid prediction for Augustus_model.g33991.t1
Valid prediction for GeneMark_model.87783_t
Valid prediction for GlimmerHMM_glimmerT_50713-T1
Valid prediction for GeneMark_model.87772_t
Valid prediction for GeneMark_model.87754_t
Valid prediction for GeneMark_model.87771_t
Valid prediction for snap_scaffold_22-snap.1113-T1
Valid prediction for GeneMark_model.87749_t
Valid prediction for Augustus_model.g33992.t1
Valid prediction for GeneMark_model.87747_t
Valid prediction for snap_scaffold_22-snap.1097-T1
Valid prediction for snap_scaffold_22-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_50715-T1
Valid prediction for snap_scaffold_22-snap.1109-T1
Valid prediction for snap_scaffold_22-snap.1110-T1
Valid prediction for GeneMark_model.87769_t
Valid prediction for snap_scaffold_22-snap.1108-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.87778_t
Valid prediction for GlimmerHMM_glimmerT_50723-T1
Valid prediction for snap_scaffold_22-snap.1090-T1
Valid prediction for snap_scaffold_22-snap.1096-T1
Valid prediction for GeneMark_model.87761_t
Valid prediction for GeneMark_model.87764_t
Valid prediction for Augustus_model.g33989.t1
Valid prediction for GlimmerHMM_glimmerT_50722-T1
Valid prediction for snap_scaffold_22-snap.1086-T1
Valid prediction for snap_scaffold_22-snap.1106-T1
Valid prediction for Augustus_model.g33993.t1
Valid prediction for GlimmerHMM_glimmerT_50707-T1
Valid prediction for Augustus_model.g33988.t1
Valid prediction for GeneMark_model.87775_t
Valid prediction for GlimmerHMM_glimmerT_50710-T1
Valid prediction for GlimmerHMM_glimmerT_50721-T1
Valid prediction for GlimmerHMM_glimmerT_50727-T1
Valid prediction for snap_scaffold_22-snap.1118-T1
Valid prediction for snap_scaffold_22-snap.1121-T1
Valid prediction for GeneMark_model.87766_t
Valid prediction for snap_scaffold_22-snap.1091-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50714-T1
Couldn't classify 45422, 45661
Sorry, prediction pasa_asmbl_30054.p1 fails validation.
(AGT)	 CC	45422-45661	GT	TGG
(CTG)	 AG	46198-46406	GT	AGG
(ACC)	 AG	47566-47617	CC	GAC
-recovered pasa_asmbl_30054.p1, terminal, 47566, 47617
-recovered pasa_asmbl_30054.p1, internal, 46198, 46406
Valid prediction for snap_scaffold_22-snap.1102-T1
Valid prediction for snap_scaffold_22-snap.1101-T1
Valid prediction for snap_scaffold_22-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_50720-T1
Valid prediction for GeneMark_model.87752_t
Valid prediction for GeneMark_model.87756_t
Valid prediction for GeneMark_model.87762_t
Valid prediction for snap_scaffold_22-snap.1095-T1
Valid prediction for GeneMark_model.87781_t
Valid prediction for GeneMark_model.87739_t
Valid prediction for GlimmerHMM_glimmerT_50711-T1
Valid prediction for GlimmerHMM_glimmerT_50709-T1
Valid prediction for GeneMark_model.87780_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11254, rend_intergenic: 7572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20221, rend_intergenic: 11375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47731, rend_intergenic: 41187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60702, rend_intergenic: 55172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79261, rend_intergenic: 69018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86629, rend_intergenic: 79590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92098, rend_intergenic: 88236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121211, rend_intergenic: 119037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137295, rend_intergenic: 133645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145610, rend_intergenic: 141254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152737
-exon list size: 638


building trellis

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82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 11254, rend_intergenic: 7572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20221, rend_intergenic: 11375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47731, rend_intergenic: 41187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60702, rend_intergenic: 55172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79261, rend_intergenic: 69018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86629, rend_intergenic: 79590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92098, rend_intergenic: 88236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121211, rend_intergenic: 119037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137295, rend_intergenic: 133645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145610, rend_intergenic: 141254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support