-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_2495964-2664029

-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_32466-T1
Valid prediction for Augustus_model.g31494.t1
Valid prediction for snap_scaffold_21-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_47254-T1
Valid prediction for GlimmerHMM_glimmerT_47264-T1
Valid prediction for GlimmerHMM_glimmerT_47270-T1
Valid prediction for pasa_asmbl_28418.p1
Valid prediction for snap_scaffold_21-snap.436-T1
Valid prediction for snap_scaffold_21-snap.449-T1
Valid prediction for snap_scaffold_21-snap.440-T1
Valid prediction for CodingQuarry_transcript_32461-T1
Valid prediction for pasa_asmbl_28400.p1
Valid prediction for GlimmerHMM_glimmerT_47273-T1
Valid prediction for snap_scaffold_21-snap.465-T1
Valid prediction for Augustus_model.g31490.t1
Valid prediction for HiQ_model.g31488.t1
Valid prediction for GlimmerHMM_glimmerT_47260-T1
Valid prediction for snap_scaffold_21-snap.464-T1
Valid prediction for snap_scaffold_21-snap.439-T1
Valid prediction for snap_scaffold_21-snap.438-T1
Valid prediction for GlimmerHMM_glimmerT_47275-T1
Valid prediction for pasa_asmbl_28402.p1
Couldn't classify 123362, 123646
Sorry, prediction pasa_asmbl_28412.p1 fails validation.
(GTC)	 AG	123362-123646	GT	AGG
(GGA)	 AG	123730-123825	GT	AGG
(GTT)	 AG	123990-123995	CC	GAC
-recovered pasa_asmbl_28412.p1, terminal, 123990, 123995
-recovered pasa_asmbl_28412.p1, internal, 123362, 123646
-recovered pasa_asmbl_28412.p1, internal, 123730, 123825
Valid prediction for GlimmerHMM_glimmerT_47267-T1
Valid prediction for Augustus_model.g31478.t1
Couldn't classify 118290, 118427
Sorry, prediction pasa_asmbl_28411.p1 fails validation.
(TTT)	 TT	118290-118427	GT	AGG
(TAT)	 AG	118841-118908	GT	CGG
(GTG)	 AG	119009-119072	GT	ATG
(ATC)	 AG	119196-119272	GT	AGG
(GGG)	 AG	119357-119447	GT	GGG
(CTG)	 AG	119685-119765	GA	GAG
-recovered pasa_asmbl_28411.p1, terminal, 119685, 119765
-recovered pasa_asmbl_28411.p1, internal, 118841, 118908
-recovered pasa_asmbl_28411.p1, internal, 119009, 119072
-recovered pasa_asmbl_28411.p1, internal, 119196, 119272
-recovered pasa_asmbl_28411.p1, internal, 119357, 119447
Valid prediction for GlimmerHMM_glimmerT_47252-T1
Valid prediction for snap_scaffold_21-snap.456-T1
Valid prediction for HiQ_model.g31470.t1
Valid prediction for GlimmerHMM_glimmerT_47272-T1
Couldn't classify 129464, 129645
Sorry, prediction pasa_asmbl_28413.p1 fails validation.
(ATG)	 AA	124519-124647	GT	AGG
(AAT)	 AG	127075-127154	GT	AGG
(GGA)	 AG	127870-128066	GT	AGG
(AAG)	 AG	129464-129645	GA	GGG
-recovered pasa_asmbl_28413.p1, initial, 124519, 124647
add_exon() Sorry, pasa_asmbl_28413.p1 127870-128066-terminal-2 is invalid.
-recovered pasa_asmbl_28413.p1, terminal, 127870, 128066
-recovered pasa_asmbl_28413.p1, internal, 127075, 127154
-recovered pasa_asmbl_28413.p1, internal, 127870, 128066
Valid prediction for CodingQuarry_transcript_32467-T1
Valid prediction for Augustus_model.g31476.t1
Valid prediction for snap_scaffold_21-snap.462-T1
Valid prediction for Augustus_model.g31491.t1
Valid prediction for Augustus_model.g31485.t1
Valid prediction for snap_scaffold_21-snap.446-T1
Valid prediction for HiQ_model.g31471.t1
Valid prediction for Augustus_model.g31475.t1
Couldn't classify 105264, 105494
Couldn't classify 108130, 108261
Sorry, prediction pasa_asmbl_28409.p1 fails validation.
(GAC)	 AG	105264-105494	GT	AGG
(GTT)	 AG	105655-105870	GT	AGG
(GCT)	 AG	106193-106309	GT	AGG
(AAC)	 AG	106477-106623	GT	AGG
(GCC)	 AG	107295-107369	GT	AGG
(TTG)	 AG	107488-107561	GT	AGG
(TTC)	 AG	107661-107775	GT	AGG
(GAG)	 AG	108130-108261	GG	AGG
-recovered pasa_asmbl_28409.p1, internal, 105264, 105494
-recovered pasa_asmbl_28409.p1, internal, 105655, 105870
-recovered pasa_asmbl_28409.p1, internal, 106193, 106309
-recovered pasa_asmbl_28409.p1, internal, 106477, 106623
-recovered pasa_asmbl_28409.p1, internal, 107295, 107369
-recovered pasa_asmbl_28409.p1, internal, 107488, 107561
-recovered pasa_asmbl_28409.p1, internal, 107661, 107775
Valid prediction for GlimmerHMM_glimmerT_47259-T1
Valid prediction for snap_scaffold_21-snap.469-T1
Couldn't classify 130000, 130150
Sorry, prediction pasa_asmbl_28416.p1 fails validation.
(CTG)	 AC	130000-130150	GT	TGG
(GGA)	 AG	131518-131655	GT	GGG
(ATC)	 AG	132564-132731	GT	AGG
(GCA)	 AG	132891-133285	CC	GAC
-recovered pasa_asmbl_28416.p1, terminal, 132891, 133285
-recovered pasa_asmbl_28416.p1, internal, 131518, 131655
-recovered pasa_asmbl_28416.p1, internal, 132564, 132731
Valid prediction for GlimmerHMM_glimmerT_47279-T1
Valid prediction for snap_scaffold_21-snap.444-T1
Valid prediction for snap_scaffold_21-snap.470-T1
Valid prediction for CodingQuarry_transcript_32463-T1
Valid prediction for snap_scaffold_21-snap.458-T1
Valid prediction for snap_scaffold_21-snap.442-T1
Valid prediction for Augustus_model.g31493.t1
Valid prediction for snap_scaffold_21-snap.450-T1
Valid prediction for GlimmerHMM_glimmerT_47258-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g31469.t1
Valid prediction for GlimmerHMM_glimmerT_47253-T1
Valid prediction for snap_scaffold_21-snap.452-T1
Valid prediction for snap_scaffold_21-snap.472-T1
Valid prediction for snap_scaffold_21-snap.460-T1
Valid prediction for Augustus_model.g31489.t1
Valid prediction for HiQ_model.g31483.t1
Valid prediction for snap_scaffold_21-snap.467-T1
Valid prediction for pasa_asmbl_28403.p1
Valid prediction for HiQ_model.g31472.t1
Valid prediction for CodingQuarry_transcript_32462-T1
Valid prediction for snap_scaffold_21-snap.435-T1
Valid prediction for snap_scaffold_21-snap.437-T1
Valid prediction for snap_scaffold_21-snap.463-T1
Couldn't classify 97246, 97584
Sorry, prediction pasa_asmbl_28404.p1 fails validation.
(TCG)	 AC	97246-97584	GT	AGG
(ATG)	 AG	97909-98031	GT	AGG
(GAT)	 AG	98176-98367	AG	AGA
-recovered pasa_asmbl_28404.p1, initial, 97909, 98031
-recovered pasa_asmbl_28404.p1, terminal, 98176, 98367
-recovered pasa_asmbl_28404.p1, internal, 97909, 98031
Valid prediction for Augustus_model.g31473.t1
Valid prediction for GlimmerHMM_glimmerT_47261-T1
Valid prediction for GlimmerHMM_glimmerT_47277-T1
Valid prediction for GlimmerHMM_glimmerT_47256-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_21-snap.447-T1
Couldn't classify 7093, 7221
Sorry, prediction pasa_asmbl_27483.p1 fails validation.
(TCC)	 GC	7093-7221	GT	TGG
(GCA)	 AG	7924-8013	GT	AGG
(GCC)	 AG	8333-8408	GT	GGG
(GTC)	 AG	8494-8598	GT	AGG
(GTA)	 AG	8900-8978	GT	GAG
(GAT)	 AG	9126-9174	GT	AGG
(GTC)	 AG	9685-9789	AG	AAA
-recovered pasa_asmbl_27483.p1, terminal, 9685, 9789
-recovered pasa_asmbl_27483.p1, internal, 7924, 8013
-recovered pasa_asmbl_27483.p1, internal, 8333, 8408
-recovered pasa_asmbl_27483.p1, internal, 8494, 8598
-recovered pasa_asmbl_27483.p1, internal, 8900, 8978
-recovered pasa_asmbl_27483.p1, internal, 9126, 9174
Valid prediction for GlimmerHMM_glimmerT_47274-T1
Valid prediction for HiQ_model.g31480.t1
Valid prediction for snap_scaffold_21-snap.475-T1
Valid prediction for Augustus_model.g31479.t1
Valid prediction for snap_scaffold_21-snap.459-T1
Valid prediction for snap_scaffold_21-snap.434-T1
Valid prediction for snap_scaffold_21-snap.471-T1
Valid prediction for GlimmerHMM_glimmerT_47278-T1
Valid prediction for pasa_asmbl_27477.p1
Valid prediction for GlimmerHMM_glimmerT_47268-T1
Valid prediction for GlimmerHMM_glimmerT_47257-T1
Valid prediction for snap_scaffold_21-snap.461-T1
Couldn't classify 163687, 163936
Sorry, prediction pasa_asmbl_27471.p1 fails validation.
(TCC)	 CC	163687-163936	GT	GGG
(ACT)	 AG	164151-164310	GT	ATG
(TGT)	 AG	164411-164467	GT	AGG
(GGA)	 AG	164844-164923	GT	CGG
(TCT)	 AG	165402-165490	CA	AAC
-recovered pasa_asmbl_27471.p1, terminal, 165402, 165490
-recovered pasa_asmbl_27471.p1, internal, 164151, 164310
-recovered pasa_asmbl_27471.p1, internal, 164411, 164467
-recovered pasa_asmbl_27471.p1, internal, 164844, 164923
Valid prediction for snap_scaffold_21-snap.451-T1
Valid prediction for snap_scaffold_21-snap.441-T1
Valid prediction for GlimmerHMM_glimmerT_47250-T1
Valid prediction for snap_scaffold_21-snap.448-T1
Valid prediction for GlimmerHMM_glimmerT_47281-T1
Valid prediction for GlimmerHMM_glimmerT_47251-T1
Valid prediction for GlimmerHMM_glimmerT_47266-T1
Valid prediction for Augustus_model.g31474.t1
Valid prediction for snap_scaffold_21-snap.473-T1
Valid prediction for snap_scaffold_21-snap.443-T1
Valid prediction for snap_scaffold_21-snap.457-T1
Valid prediction for Augustus_model.g31486.t1
Valid prediction for CodingQuarry_transcript_32464-T1
Valid prediction for GlimmerHMM_glimmerT_47265-T1
Couldn't classify 136333, 136475
Sorry, prediction pasa_asmbl_27472.p1 fails validation.
(TTC)	 TA	136333-136475	GT	GGG
(AAT)	 AG	136798-136891	GT	TGG
(GTT)	 AG	137020-137104	GT	AGG
(TTG)	 AG	137195-137386	GT	AGG
(ACT)	 AG	137688-137944	GT	AGG
(ACT)	 AG	138079-138187	GT	AGG
(ATC)	 AG	138381-138519	GT	GGG
(GCT)	 AG	138628-138818	GT	AGG
(AGA)	 AG	138910-138991	GT	AGG
(GTC)	 AG	139151-139244	AA	AGA
add_exon() Sorry, pasa_asmbl_27472.p1 138910-138991-terminal-3 is invalid.
-recovered pasa_asmbl_27472.p1, terminal, 138910, 138991
-recovered pasa_asmbl_27472.p1, terminal, 139151, 139244
-recovered pasa_asmbl_27472.p1, internal, 136798, 136891
-recovered pasa_asmbl_27472.p1, internal, 137020, 137104
-recovered pasa_asmbl_27472.p1, internal, 137195, 137386
-recovered pasa_asmbl_27472.p1, internal, 137688, 137944
-recovered pasa_asmbl_27472.p1, internal, 138079, 138187
-recovered pasa_asmbl_27472.p1, internal, 138381, 138519
-recovered pasa_asmbl_27472.p1, internal, 138628, 138818
-recovered pasa_asmbl_27472.p1, internal, 138910, 138991
Valid prediction for snap_scaffold_21-snap.454-T1
Valid prediction for snap_scaffold_21-snap.474-T1
Valid prediction for Augustus_model.g31495.t1
Valid prediction for GlimmerHMM_glimmerT_47271-T1
Valid prediction for snap_scaffold_21-snap.468-T1
Valid prediction for GlimmerHMM_glimmerT_47269-T1
Valid prediction for GlimmerHMM_glimmerT_47276-T1
Valid prediction for GlimmerHMM_glimmerT_47280-T1
Valid prediction for Augustus_model.g31487.t1
Valid prediction for GlimmerHMM_glimmerT_47255-T1
Valid prediction for snap_scaffold_21-snap.445-T1
Valid prediction for Augustus_model.g31492.t1
Valid prediction for GlimmerHMM_glimmerT_47262-T1
Valid prediction for Augustus_model.g31468.t1
Valid prediction for Augustus_model.g31482.t1
Valid prediction for GlimmerHMM_glimmerT_47263-T1
Valid prediction for GlimmerHMM_glimmerT_47282-T1
Couldn't classify 135135, 135327
Sorry, prediction pasa_asmbl_27476.p2 fails validation.
(AAA)	 CC	135135-135327	GT	AGG
(AAA)	 AG	135442-135554	CA	GAC
-recovered pasa_asmbl_27476.p2, terminal, 135442, 135554
Valid prediction for CodingQuarry_transcript_32468-T1
Valid prediction for Augustus_model.g31484.t1
Valid prediction for CodingQuarry_transcript_32460-T1
Couldn't classify 85595, 85642
Sorry, prediction pasa_asmbl_27479.p1 fails validation.
(ATG)	 AG	83536-83571	GT	AGG
(GCC)	 AG	83772-83855	GT	TGG
(GTT)	 AG	84397-84450	GT	AGG
(AGA)	 AG	84707-84757	GT	AGG
(GAG)	 AG	84957-85061	GT	ATG
(ACG)	 AG	85193-85246	GT	AGG
(AGG)	 AG	85343-85414	GT	AGG
(ACC)	 AG	85595-85642	TT	AGT
-recovered pasa_asmbl_27479.p1, initial, 83536, 83571
-recovered pasa_asmbl_27479.p1, internal, 83536, 83571
-recovered pasa_asmbl_27479.p1, internal, 83772, 83855
-recovered pasa_asmbl_27479.p1, internal, 84397, 84450
-recovered pasa_asmbl_27479.p1, internal, 84707, 84757
-recovered pasa_asmbl_27479.p1, internal, 84957, 85061
-recovered pasa_asmbl_27479.p1, internal, 85193, 85246
-recovered pasa_asmbl_27479.p1, internal, 85343, 85414
Valid prediction for Augustus_model.g31481.t1
Valid prediction for snap_scaffold_21-snap.455-T1
Valid prediction for Augustus_model.g31477.t1
Valid prediction for snap_scaffold_21-snap.453-T1
Sorry, intron length (4) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14446, rend_intergenic: 4141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44541, rend_intergenic: 37083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55556, rend_intergenic: 49821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66685, rend_intergenic: 58805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71424, rend_intergenic: 67413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89336, rend_intergenic: 80323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97357, rend_intergenic: 96564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108539, rend_intergenic: 102939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114707, rend_intergenic: 109376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168066
-exon list size: 501


building trellis

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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    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
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 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 14446, rend_intergenic: 4141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44541, rend_intergenic: 37083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55556, rend_intergenic: 49821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66685, rend_intergenic: 58805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71424, rend_intergenic: 67413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89336, rend_intergenic: 80323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97357, rend_intergenic: 96564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108539, rend_intergenic: 102939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114707, rend_intergenic: 109376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support