-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_3632608-3786194

-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_3551-T1
Valid prediction for snap_scaffold_2-snap.873-T1
Valid prediction for snap_scaffold_2-snap.847-T1
Valid prediction for Augustus_model.g2388.t1
Valid prediction for snap_scaffold_2-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_3556-T1
Valid prediction for snap_scaffold_2-snap.852-T1
Couldn't classify 45618, 46148
Sorry, prediction pasa_asmbl_24299.p1 fails validation.
(GTC)	 CT	45618-46148	AA	AGA
Valid prediction for Augustus_model.g2377.t1
Valid prediction for pasa_asmbl_24308.p1
Valid prediction for snap_scaffold_2-snap.862-T1
Valid prediction for snap_scaffold_2-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_3574-T1
Valid prediction for Augustus_model.g2380.t1
Valid prediction for snap_scaffold_2-snap.869-T1
Valid prediction for GlimmerHMM_glimmerT_3562-T1
Valid prediction for pasa_asmbl_24297.p1
Couldn't classify 83060, 83143
Couldn't classify 83707, 83836
Sorry, prediction pasa_asmbl_25365.p2 fails validation.
(GGG)	 GG	83060-83143	GT	AAG
(GGT)	 AG	83314-83471	GT	AGG
(GTT)	 AG	83707-83836	GC	GGG
-recovered pasa_asmbl_25365.p2, internal, 83314, 83471
-recovered pasa_asmbl_25365.p2, internal, 83707, 83836
Valid prediction for GlimmerHMM_glimmerT_3557-T1
Valid prediction for snap_scaffold_2-snap.874-T1
Valid prediction for snap_scaffold_2-snap.878-T1
Valid prediction for GlimmerHMM_glimmerT_3553-T1
Couldn't classify 135169, 135415
Couldn't classify 138051, 138219
Sorry, prediction pasa_asmbl_24311.p1 fails validation.
(GCC)	 AG	135169-135415	GT	TGG
(ACT)	 AG	135595-135676	GT	AGG
(AGA)	 AG	135793-135873	GT	AGG
(GGT)	 AG	135985-136098	GT	AGG
(AGA)	 AG	136582-136657	GT	AGG
(AAG)	 AG	137005-137122	GT	AGG
(AGG)	 AG	137563-137662	GT	CAG
(GTG)	 AG	138051-138219	GG	AGG
-recovered pasa_asmbl_24311.p1, internal, 135169, 135415
-recovered pasa_asmbl_24311.p1, internal, 135595, 135676
-recovered pasa_asmbl_24311.p1, internal, 135793, 135873
-recovered pasa_asmbl_24311.p1, internal, 135985, 136098
-recovered pasa_asmbl_24311.p1, internal, 136582, 136657
-recovered pasa_asmbl_24311.p1, internal, 137005, 137122
-recovered pasa_asmbl_24311.p1, internal, 137563, 137662
Valid prediction for Augustus_model.g2390.t1
Valid prediction for HiQ_model.g2375.t1
Valid prediction for snap_scaffold_2-snap.884-T1
Valid prediction for snap_scaffold_2-snap.850-T1
Valid prediction for pasa_asmbl_24296.p1
Valid prediction for snap_scaffold_2-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_3555-T1
Valid prediction for snap_scaffold_2-snap.864-T1
Valid prediction for CodingQuarry_transcript_28503-T1
Valid prediction for snap_scaffold_2-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_3575-T1
Valid prediction for GlimmerHMM_glimmerT_3568-T1
Valid prediction for snap_scaffold_2-snap.865-T1
Valid prediction for snap_scaffold_2-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_3570-T1
Valid prediction for Augustus_model.g2376.t1
Valid prediction for GlimmerHMM_glimmerT_3564-T1
Valid prediction for snap_scaffold_2-snap.856-T1
Valid prediction for HiQ_model.g2373.t1
Valid prediction for HiQ_model.g2385.t1
Valid prediction for GlimmerHMM_glimmerT_3550-T1
Valid prediction for snap_scaffold_2-snap.853-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_2-snap.848-T1
Couldn't classify 41049, 41264
Sorry, prediction pasa_asmbl_22993.p1 fails validation.
(ATG)	 CG	40518-40862	GT	AGG
(ATG)	 AG	41049-41264	GC	GCG
-recovered pasa_asmbl_22993.p1, initial, 40518, 40862
-recovered pasa_asmbl_22993.p1, initial, 41049, 41264
-recovered pasa_asmbl_22993.p1, internal, 41049, 41264
Valid prediction for HiQ_model.g2387.t1
Valid prediction for snap_scaffold_2-snap.875-T1
Couldn't classify 77483, 77590
Sorry, prediction pasa_asmbl_22990.p1 fails validation.
(ATG)	 AA	74139-74215	GT	TGG
(GGC)	 AG	74717-74799	GT	AGG
(ACG)	 AG	77200-77357	GT	AGG
(AAC)	 AG	77483-77590	TA	AGT
-recovered pasa_asmbl_22990.p1, initial, 74139, 74215
-recovered pasa_asmbl_22990.p1, internal, 74717, 74799
-recovered pasa_asmbl_22990.p1, internal, 77200, 77357
Valid prediction for snap_scaffold_2-snap.863-T1
Valid prediction for snap_scaffold_2-snap.860-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.876-T1
Valid prediction for snap_scaffold_2-snap.858-T1
Couldn't classify 42208, 42804
Sorry, prediction pasa_asmbl_22992.p1 fails validation.
(TCG)	 CC	42208-42804	TT	AGT
Valid prediction for Augustus_model.g2391.t1
Valid prediction for GlimmerHMM_glimmerT_3552-T1
Valid prediction for GlimmerHMM_glimmerT_3561-T1
Couldn't classify 95993, 96075
Couldn't classify 97990, 98018
Sorry, prediction pasa_asmbl_22988.p1 fails validation.
(GAC)	 AT	95993-96075	GT	TGG
(GTG)	 AG	96249-96345	GT	AGG
(GAC)	 AG	96430-96496	GT	TAG
(TTC)	 AG	96651-96823	GC	AGG
(ATC)	 AG	97331-97433	GT	TGG
(GAA)	 AG	97676-97879	GT	CGG
(ACA)	 AG	97990-98018	TT	TCT
-recovered pasa_asmbl_22988.p1, internal, 96249, 96345
-recovered pasa_asmbl_22988.p1, internal, 96430, 96496
-recovered pasa_asmbl_22988.p1, internal, 96651, 96823
-recovered pasa_asmbl_22988.p1, internal, 97331, 97433
-recovered pasa_asmbl_22988.p1, internal, 97676, 97879
Valid prediction for Augustus_model.g2384.t1
Couldn't classify 12907, 12948
Sorry, prediction pasa_asmbl_22999.p1 fails validation.
(CTG)	 AC	12907-12948	GT	AGG
(GAG)	 AG	13150-13252	GT	AGG
(ACC)	 AG	13398-13473	GT	AGG
(TCT)	 AG	13624-13774	GT	AGG
(ATG)	 AG	13987-14085	GT	AGG
(CTG)	 AG	14202-14300	AC	AGA
-recovered pasa_asmbl_22999.p1, initial, 13987, 14085
-recovered pasa_asmbl_22999.p1, terminal, 14202, 14300
-recovered pasa_asmbl_22999.p1, internal, 13150, 13252
-recovered pasa_asmbl_22999.p1, internal, 13398, 13473
-recovered pasa_asmbl_22999.p1, internal, 13624, 13774
-recovered pasa_asmbl_22999.p1, internal, 13987, 14085
Valid prediction for Augustus_model.g2374.t1
Valid prediction for GlimmerHMM_glimmerT_3567-T1
Valid prediction for GlimmerHMM_glimmerT_3565-T1
Valid prediction for Augustus_model.g2383.t1
Couldn't classify 102620, 102685
Sorry, prediction pasa_asmbl_22986.p1 fails validation.
(TGC)	 CC	102620-102685	GT	TGG
(GGT)	 AG	102776-102961	GT	AGG
(AAG)	 AG	103057-103164	AC	AGA
-recovered pasa_asmbl_22986.p1, terminal, 103057, 103164
-recovered pasa_asmbl_22986.p1, internal, 102776, 102961
Valid prediction for snap_scaffold_2-snap.857-T1
Valid prediction for Augustus_model.g2382.t1
Valid prediction for GlimmerHMM_glimmerT_3573-T1
Valid prediction for snap_scaffold_2-snap.854-T1
Valid prediction for snap_scaffold_2-snap.879-T1
Couldn't classify 58906, 58959
Couldn't classify 61965, 62072
Sorry, prediction pasa_asmbl_24014.p1 fails validation.
(GTG)	 TA	58906-58959	GT	TGG
(GTG)	 AG	61538-61690	GT	AGG
(ATC)	 AG	61965-62072	AG	ACA
-recovered pasa_asmbl_24014.p1, internal, 61538, 61690
Valid prediction for GlimmerHMM_glimmerT_3566-T1
Valid prediction for GlimmerHMM_glimmerT_3554-T1
Valid prediction for GlimmerHMM_glimmerT_3576-T1
Valid prediction for Augustus_model.g2381.t1
Valid prediction for snap_scaffold_2-snap.870-T1
Valid prediction for snap_scaffold_2-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_3559-T1
Valid prediction for snap_scaffold_2-snap.867-T1
Valid prediction for snap_scaffold_2-snap.883-T1
Valid prediction for GlimmerHMM_glimmerT_3558-T1
Valid prediction for GlimmerHMM_glimmerT_3572-T1
Valid prediction for snap_scaffold_2-snap.855-T1
Valid prediction for snap_scaffold_2-snap.859-T1
Valid prediction for snap_scaffold_2-snap.849-T1
Valid prediction for snap_scaffold_2-snap.866-T1
Valid prediction for GlimmerHMM_glimmerT_3571-T1
Valid prediction for pasa_asmbl_22987.p1
Valid prediction for HiQ_model.g2389.t1
Valid prediction for HiQ_model.g2379.t1
Valid prediction for CodingQuarry_transcript_28502-T1
Couldn't classify 101801, 101842
Sorry, prediction pasa_asmbl_23965.p1 fails validation.
(ATG)	 GC	101088-101246	GT	AGG
(CGT)	 AG	101400-101654	GT	AGG
(TTC)	 AG	101801-101842	CA	CCC
-recovered pasa_asmbl_23965.p1, initial, 101088, 101246
-recovered pasa_asmbl_23965.p1, internal, 101400, 101654
Valid prediction for snap_scaffold_2-snap.872-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.885-T1
Couldn't classify 20665, 20778
Sorry, prediction pasa_asmbl_22995.p1 fails validation.
(TCC)	 CA	20665-20778	GT	AGG
(GAA)	 AG	21062-21134	GT	AAG
(CGG)	 AG	21922-22263	GT	TGG
(CCA)	 AG	22370-22526	GT	AAG
(GGA)	 AG	23011-23122	GT	TGG
(AAG)	 AG	24304-24366	GT	CTG
(CTT)	 AG	25184-25236	GT	AGG
(GAG)	 AG	25984-26071	GT	ACG
(AAC)	 AG	26178-26263	GT	AGG
(CCG)	 AG	26372-26853	GT	AGG
(ACC)	 AG	27029-27158	GT	AGG
(GAA)	 AG	27680-27885	GT	GGG
(TGA)	 AG	28194-28278	GT	ATG
(TGG)	 AG	30626-30730	GT	GGG
(GTA)	 AG	31769-31871	GA	GAG
add_exon() Sorry, pasa_asmbl_22995.p1 26372-26853-terminal-2 is invalid.
-recovered pasa_asmbl_22995.p1, terminal, 26372, 26853
-recovered pasa_asmbl_22995.p1, terminal, 31769, 31871
-recovered pasa_asmbl_22995.p1, internal, 21062, 21134
-recovered pasa_asmbl_22995.p1, internal, 21922, 22263
-recovered pasa_asmbl_22995.p1, internal, 22370, 22526
-recovered pasa_asmbl_22995.p1, internal, 23011, 23122
-recovered pasa_asmbl_22995.p1, internal, 24304, 24366
-recovered pasa_asmbl_22995.p1, internal, 25184, 25236
-recovered pasa_asmbl_22995.p1, internal, 25984, 26071
-recovered pasa_asmbl_22995.p1, internal, 26178, 26263
-recovered pasa_asmbl_22995.p1, internal, 26372, 26853
-recovered pasa_asmbl_22995.p1, internal, 27029, 27158
-recovered pasa_asmbl_22995.p1, internal, 27680, 27885
-recovered pasa_asmbl_22995.p1, internal, 28194, 28278
-recovered pasa_asmbl_22995.p1, internal, 30626, 30730
Valid prediction for Augustus_model.g2386.t1
Valid prediction for Augustus_model.g2378.t1
Valid prediction for GlimmerHMM_glimmerT_3569-T1
Couldn't classify 26502, 26853
Sorry, prediction pasa_asmbl_22997.p1 fails validation.
(CAG)	 CT	26502-26853	GT	AGG
(ACC)	 AG	27029-27158	GT	AGG
(TGA)	 AG	28194-28227	AG	GAA
-recovered pasa_asmbl_22997.p1, terminal, 28194, 28227
-recovered pasa_asmbl_22997.p1, internal, 27029, 27158
Valid prediction for GlimmerHMM_glimmerT_3560-T1
Valid prediction for snap_scaffold_2-snap.871-T1
Valid prediction for GlimmerHMM_glimmerT_3563-T1
Valid prediction for snap_scaffold_2-snap.851-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13797, rend_intergenic: 10710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24445, rend_intergenic: 21748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36675, rend_intergenic: 33255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45016, rend_intergenic: 36736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48045, rend_intergenic: 45283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64983, rend_intergenic: 59177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74523, rend_intergenic: 68238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78484, rend_intergenic: 75039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91283, rend_intergenic: 85621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108231, rend_intergenic: 103439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115384, rend_intergenic: 114105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128392, rend_intergenic: 121240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139577, rend_intergenic: 138521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141570, rend_intergenic: 140163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150954, rend_intergenic: 141570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153587
-exon list size: 476


building trellis

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92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 13797, rend_intergenic: 10710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24445, rend_intergenic: 21748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36675, rend_intergenic: 33255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45016, rend_intergenic: 36736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48045, rend_intergenic: 45283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64983, rend_intergenic: 59177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74523, rend_intergenic: 68238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78484, rend_intergenic: 75039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91283, rend_intergenic: 85621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108231, rend_intergenic: 103439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115384, rend_intergenic: 114105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128392, rend_intergenic: 121240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139577, rend_intergenic: 138521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141570, rend_intergenic: 140163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150954, rend_intergenic: 141570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support