-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_3228675-3444361

-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_3513-T1
Valid prediction for snap_scaffold_2-snap.764-T1
Valid prediction for snap_scaffold_2-snap.800-T1
Valid prediction for snap_scaffold_2-snap.752-T1
Valid prediction for GlimmerHMM_glimmerT_3520-T1
Valid prediction for Augustus_model.g2341.t1
Valid prediction for snap_scaffold_2-snap.775-T1
Valid prediction for snap_scaffold_2-snap.790-T1
Valid prediction for GlimmerHMM_glimmerT_3492-T1
Valid prediction for Augustus_model.g2357.t1
Valid prediction for snap_scaffold_2-snap.751-T1
Valid prediction for snap_scaffold_2-snap.761-T1
Valid prediction for snap_scaffold_2-snap.777-T1
Valid prediction for GlimmerHMM_glimmerT_3517-T1
Valid prediction for GlimmerHMM_glimmerT_3498-T1
Valid prediction for snap_scaffold_2-snap.755-T1
Valid prediction for GlimmerHMM_glimmerT_3489-T1
Valid prediction for snap_scaffold_2-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_3521-T1
Valid prediction for GlimmerHMM_glimmerT_3500-T1
Valid prediction for snap_scaffold_2-snap.762-T1
Valid prediction for snap_scaffold_2-snap.782-T1
Valid prediction for snap_scaffold_2-snap.779-T1
Valid prediction for snap_scaffold_2-snap.796-T1
Valid prediction for GlimmerHMM_glimmerT_3518-T1
Valid prediction for Augustus_model.g2352.t1
Valid prediction for snap_scaffold_2-snap.765-T1
Valid prediction for HiQ_model.g2346.t1
Valid prediction for Augustus_model.g2348.t1
Valid prediction for GlimmerHMM_glimmerT_3508-T1
Couldn't classify 109826, 109899
Sorry, prediction pasa_asmbl_24276.p1 fails validation.
(GGA)	 CA	109826-109899	GT	GGG
(GAA)	 AG	110264-110428	GT	ATG
(GTC)	 AG	110517-110717	GT	ATG
(GTG)	 AG	110852-110993	GT	CGG
(GTG)	 AG	111077-111210	GT	AGG
(CAC)	 AG	111696-111849	GT	TGG
(CTT)	 AG	111938-112042	GT	AGG
(ATG)	 AG	112232-112330	GT	AGG
(GAC)	 AG	112460-112603	GT	GCG
(TTC)	 AG	112813-112890	GT	ATG
(CCT)	 AG	112974-113121	GT	AGG
(ATG)	 AG	113419-113568	GT	CAG
(ACC)	 AG	113687-113759	GT	GGG
(GAA)	 AG	113892-114075	GC	GAG
-recovered pasa_asmbl_24276.p1, initial, 112232, 112330
add_exon() Sorry, pasa_asmbl_24276.p1 113419-113568-initial-1 is invalid.
-recovered pasa_asmbl_24276.p1, initial, 113419, 113568
-recovered pasa_asmbl_24276.p1, terminal, 113892, 114075
-recovered pasa_asmbl_24276.p1, internal, 110264, 110428
-recovered pasa_asmbl_24276.p1, internal, 110517, 110717
-recovered pasa_asmbl_24276.p1, internal, 110852, 110993
-recovered pasa_asmbl_24276.p1, internal, 111077, 111210
-recovered pasa_asmbl_24276.p1, internal, 111696, 111849
-recovered pasa_asmbl_24276.p1, internal, 111938, 112042
-recovered pasa_asmbl_24276.p1, internal, 112232, 112330
-recovered pasa_asmbl_24276.p1, internal, 112460, 112603
-recovered pasa_asmbl_24276.p1, internal, 112813, 112890
-recovered pasa_asmbl_24276.p1, internal, 112974, 113121
-recovered pasa_asmbl_24276.p1, internal, 113419, 113568
-recovered pasa_asmbl_24276.p1, internal, 113687, 113759
-recovered pasa_asmbl_24276.p1, internal, 113892, 114075
Valid prediction for snap_scaffold_2-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_3524-T1
Valid prediction for GlimmerHMM_glimmerT_3502-T1
Couldn't classify 132593, 132760
Sorry, prediction pasa_asmbl_24277.p1 fails validation.
(GCA)	 CA	132593-132760	GT	ACG
(TAT)	 AG	132873-132989	GT	AGG
(AGC)	 AG	133128-133202	GT	CTG
(GCG)	 AG	133324-133419	GT	AGG
(GTG)	 AG	133790-133891	GT	AGG
(TCC)	 AG	134153-134215	TG	GAT
-recovered pasa_asmbl_24277.p1, terminal, 134153, 134215
-recovered pasa_asmbl_24277.p1, internal, 132873, 132989
-recovered pasa_asmbl_24277.p1, internal, 133128, 133202
-recovered pasa_asmbl_24277.p1, internal, 133324, 133419
-recovered pasa_asmbl_24277.p1, internal, 133790, 133891
Valid prediction for GlimmerHMM_glimmerT_3493-T1
Valid prediction for Augustus_model.g2351.t1
Valid prediction for snap_scaffold_2-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_3505-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3495-T1
Valid prediction for snap_scaffold_2-snap.776-T1
Valid prediction for GlimmerHMM_glimmerT_3523-T1
Valid prediction for GlimmerHMM_glimmerT_3507-T1
Valid prediction for GlimmerHMM_glimmerT_3494-T1
Valid prediction for snap_scaffold_2-snap.760-T1
Valid prediction for Augustus_model.g2335.t1
Couldn't classify 146537, 146669
Sorry, prediction pasa_asmbl_24279.p1 fails validation.
(ATG)	 CG	146169-146377	GT	TGG
(GAT)	 AG	146537-146669	GG	CAG
-recovered pasa_asmbl_24279.p1, initial, 146169, 146377
Valid prediction for Augustus_model.g2350.t1
Valid prediction for snap_scaffold_2-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_3516-T1
Valid prediction for HiQ_model.g2345.t1
Couldn't classify 109617, 109714
Sorry, prediction pasa_asmbl_24275.p1 fails validation.
(ATG)	 TT	106028-106106	GT	TGG
(GCC)	 AG	106839-107028	GT	ATG
(GTG)	 AG	107200-107338	GT	CGG
(GTC)	 AG	107792-108079	GT	TGG
(CTT)	 AG	108168-108272	GT	AGG
(TTG)	 AG	108683-108781	GT	AGG
(GAC)	 AG	108977-109120	GT	GCG
(TTC)	 AG	109212-109289	GT	ATG
(CCT)	 AG	109373-109520	GT	AGG
(ATG)	 AG	109617-109714	CT	ACC
-recovered pasa_asmbl_24275.p1, initial, 106028, 106106
-recovered pasa_asmbl_24275.p1, internal, 106839, 107028
-recovered pasa_asmbl_24275.p1, internal, 107200, 107338
-recovered pasa_asmbl_24275.p1, internal, 107792, 108079
-recovered pasa_asmbl_24275.p1, internal, 108168, 108272
-recovered pasa_asmbl_24275.p1, internal, 108683, 108781
-recovered pasa_asmbl_24275.p1, internal, 108977, 109120
-recovered pasa_asmbl_24275.p1, internal, 109212, 109289
-recovered pasa_asmbl_24275.p1, internal, 109373, 109520
Valid prediction for GlimmerHMM_glimmerT_3490-T1
Valid prediction for GlimmerHMM_glimmerT_3514-T1
Valid prediction for Augustus_model.g2356.t1
Valid prediction for snap_scaffold_2-snap.780-T1
Valid prediction for snap_scaffold_2-snap.758-T1
Valid prediction for Augustus_model.g2354.t1
Valid prediction for GlimmerHMM_glimmerT_3486-T1
Valid prediction for GlimmerHMM_glimmerT_3510-T1
Valid prediction for Augustus_model.g2353.t1
Valid prediction for GlimmerHMM_glimmerT_3488-T1
Valid prediction for Augustus_model.g2337.t1
Valid prediction for snap_scaffold_2-snap.798-T1
Valid prediction for snap_scaffold_2-snap.771-T1
Valid prediction for Augustus_model.g2339.t1
Valid prediction for GlimmerHMM_glimmerT_3525-T1
Valid prediction for GlimmerHMM_glimmerT_3522-T1
Valid prediction for snap_scaffold_2-snap.770-T1
Valid prediction for snap_scaffold_2-snap.794-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 Augustus_model.g2343.t1
Valid prediction for snap_scaffold_2-snap.754-T1
Valid prediction for Augustus_model.g2347.t1
Valid prediction for snap_scaffold_2-snap.763-T1
Valid prediction for GlimmerHMM_glimmerT_3487-T1
Valid prediction for snap_scaffold_2-snap.789-T1
Valid prediction for snap_scaffold_2-snap.791-T1
Valid prediction for GlimmerHMM_glimmerT_3511-T1
Valid prediction for Augustus_model.g2336.t1
Valid prediction for Augustus_model.g2344.t1
Couldn't classify 76783, 76824
Couldn't classify 78375, 78429
Sorry, prediction pasa_asmbl_23991.p1 fails validation.
(TTA)	 CC	76783-76824	GT	CGG
(GTG)	 AG	77063-77140	GT	AGG
(GGA)	 AG	77414-77533	GT	AGG
(GAC)	 AG	77630-77790	GT	AGG
(TTC)	 AG	78375-78429	TC	GGT
-recovered pasa_asmbl_23991.p1, internal, 77063, 77140
-recovered pasa_asmbl_23991.p1, internal, 77414, 77533
-recovered pasa_asmbl_23991.p1, internal, 77630, 77790
Valid prediction for GlimmerHMM_glimmerT_3499-T1
Valid prediction for Augustus_model.g2355.t1
Valid prediction for snap_scaffold_2-snap.795-T1
Valid prediction for CodingQuarry_transcript_28494-T1
Valid prediction for GlimmerHMM_glimmerT_3496-T1
Valid prediction for snap_scaffold_2-snap.766-T1
Valid prediction for snap_scaffold_2-snap.759-T1
Valid prediction for snap_scaffold_2-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_3504-T1
Valid prediction for snap_scaffold_2-snap.787-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.792-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_28496-T1
Valid prediction for GlimmerHMM_glimmerT_3501-T1
Valid prediction for snap_scaffold_2-snap.784-T1
Valid prediction for snap_scaffold_2-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_3519-T1
Valid prediction for GlimmerHMM_glimmerT_3515-T1
Valid prediction for GlimmerHMM_glimmerT_3503-T1
Valid prediction for snap_scaffold_2-snap.778-T1
Valid prediction for GlimmerHMM_glimmerT_3491-T1
Valid prediction for snap_scaffold_2-snap.774-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g2340.t1
Valid prediction for snap_scaffold_2-snap.797-T1
Valid prediction for snap_scaffold_2-snap.793-T1
Valid prediction for Augustus_model.g2342.t1
Valid prediction for snap_scaffold_2-snap.773-T1
Valid prediction for GlimmerHMM_glimmerT_3509-T1
Valid prediction for pasa_asmbl_22974.p1
Valid prediction for snap_scaffold_2-snap.781-T1
Valid prediction for snap_scaffold_2-snap.767-T1
Valid prediction for GlimmerHMM_glimmerT_3497-T1
Valid prediction for GlimmerHMM_glimmerT_3506-T1
Valid prediction for Augustus_model.g2334.t1
Valid prediction for snap_scaffold_2-snap.768-T1
Valid prediction for Augustus_model.g2338.t1
Valid prediction for snap_scaffold_2-snap.772-T1
Couldn't classify 120090, 120134
Sorry, prediction pasa_asmbl_22971.p1 fails validation.
(ATG)	 GA	112824-112896	GT	TGG
(ACA)	 AG	113028-113128	GT	AGG
(GCC)	 AG	113392-113594	GT	TGG
(TGT)	 AG	113932-114033	GT	AAG
(CGC)	 AG	114161-114333	GT	GGG
(ATG)	 AG	115233-115472	GT	CTG
(GTC)	 AG	116380-116538	GT	AGG
(AGG)	 AG	118687-118817	GT	TGG
(ATT)	 AG	120090-120134	GA	AGG
-recovered pasa_asmbl_22971.p1, initial, 112824, 112896
add_exon() Sorry, pasa_asmbl_22971.p1 115233-115472-initial-1 is invalid.
-recovered pasa_asmbl_22971.p1, initial, 115233, 115472
-recovered pasa_asmbl_22971.p1, internal, 113028, 113128
-recovered pasa_asmbl_22971.p1, internal, 113392, 113594
-recovered pasa_asmbl_22971.p1, internal, 113932, 114033
-recovered pasa_asmbl_22971.p1, internal, 114161, 114333
-recovered pasa_asmbl_22971.p1, internal, 115233, 115472
-recovered pasa_asmbl_22971.p1, internal, 116380, 116538
-recovered pasa_asmbl_22971.p1, internal, 118687, 118817
Valid prediction for Augustus_model.g2349.t1
Valid prediction for snap_scaffold_2-snap.757-T1
Valid prediction for snap_scaffold_2-snap.753-T1
Valid prediction for CodingQuarry_transcript_28493-T1
Valid prediction for CodingQuarry_transcript_28495-T1
Valid prediction for snap_scaffold_2-snap.769-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3512-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6515, rend_intergenic: 4277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12858, rend_intergenic: 11006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18755, rend_intergenic: 12863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23373, rend_intergenic: 21746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32879, rend_intergenic: 24368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36924, rend_intergenic: 33868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39140, rend_intergenic: 37426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66600, rend_intergenic: 41688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74912, rend_intergenic: 70912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84548, rend_intergenic: 77924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89543, rend_intergenic: 84981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94608, rend_intergenic: 89678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102300, rend_intergenic: 94973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135889, rend_intergenic: 123222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137334, rend_intergenic: 137333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142129, rend_intergenic: 137852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175947, rend_intergenic: 143548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191123, rend_intergenic: 178264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199008, rend_intergenic: 194375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205142, rend_intergenic: 200305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206643, rend_intergenic: 205340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215687
-exon list size: 545


building trellis

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69.1    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 6515, rend_intergenic: 4277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12858, rend_intergenic: 11006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18755, rend_intergenic: 12863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23373, rend_intergenic: 21746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32879, rend_intergenic: 24368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36924, rend_intergenic: 33868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39140, rend_intergenic: 37426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66600, rend_intergenic: 41688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74912, rend_intergenic: 70912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84548, rend_intergenic: 77924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89543, rend_intergenic: 84981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94608, rend_intergenic: 89678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102300, rend_intergenic: 94973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135889, rend_intergenic: 123222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137334, rend_intergenic: 137333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142129, rend_intergenic: 137852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175947, rend_intergenic: 143548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191123, rend_intergenic: 178264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199008, rend_intergenic: 194375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205142, rend_intergenic: 200305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206643, rend_intergenic: 205340  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