-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_9455016-9637478

-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 snap_scaffold_28-snap.2114-T1
Valid prediction for snap_scaffold_28-snap.2118-T1
Valid prediction for snap_scaffold_28-snap.2124-T1
Couldn't classify 109131, 109224
Sorry, prediction pasa_asmbl_37790.p1 fails validation.
(CAG)	 AC	109131-109224	GT	TGG
(CAG)	 AG	110700-110864	GT	AGG
(GTT)	 AG	111102-111178	GT	AGG
(GCT)	 AG	111630-111804	GT	GGG
(GCC)	 AG	112036-112141	GT	AAG
(CTT)	 AG	112274-112320	GT	GGG
(ACA)	 AG	112523-113675	GT	AGG
(GCT)	 AG	113946-114113	GT	TGG
(TGA)	 AG	114260-114467	GG	GAG
-recovered pasa_asmbl_37790.p1, terminal, 114260, 114467
-recovered pasa_asmbl_37790.p1, internal, 110700, 110864
-recovered pasa_asmbl_37790.p1, internal, 111102, 111178
-recovered pasa_asmbl_37790.p1, internal, 111630, 111804
-recovered pasa_asmbl_37790.p1, internal, 112036, 112141
-recovered pasa_asmbl_37790.p1, internal, 112274, 112320
-recovered pasa_asmbl_37790.p1, internal, 112523, 113675
-recovered pasa_asmbl_37790.p1, internal, 113946, 114113
Couldn't classify 180025, 180184
Sorry, prediction pasa_asmbl_37875.p1 fails validation.
(TAC)	 CG	180025-180184	GT	AGG
(GTA)	 AG	180434-180621	GT	AGG
(GTG)	 AG	180823-181101	AG	AGA
-recovered pasa_asmbl_37875.p1, terminal, 180823, 181101
-recovered pasa_asmbl_37875.p1, internal, 180434, 180621
Couldn't classify 46549, 46570
Couldn't classify 48344, 48389
Sorry, prediction pasa_asmbl_37788.p1 fails validation.
(CAG)	 AA	46549-46570	GT	AGG
(TTC)	 AG	47405-47527	GT	TGG
(GGA)	 AG	47725-47842	GT	ATG
(GTG)	 AG	47938-48096	GT	CGG
(GTG)	 AG	48344-48389	GC	ATG
-recovered pasa_asmbl_37788.p1, internal, 47405, 47527
-recovered pasa_asmbl_37788.p1, internal, 47725, 47842
-recovered pasa_asmbl_37788.p1, internal, 47938, 48096
-recovered pasa_asmbl_37788.p1, internal, 48344, 48389
Valid prediction for snap_scaffold_28-snap.2116-T1
Valid prediction for GlimmerHMM_glimmerT_59386-T1
Valid prediction for CodingQuarry_transcript_43767-T1
Valid prediction for CodingQuarry_transcript_43766-T1
Valid prediction for snap_scaffold_28-snap.2143-T1
Valid prediction for GlimmerHMM_glimmerT_59379-T1
Valid prediction for Augustus_model.g39353.t1
Valid prediction for snap_scaffold_28-snap.2115-T1
Valid prediction for HiQ_model.g39349.t1
Valid prediction for snap_scaffold_28-snap.2152-T1
Valid prediction for GlimmerHMM_glimmerT_59378-T1
Valid prediction for Augustus_model.g39346.t1
Valid prediction for HiQ_model.g39341.t1
Valid prediction for GlimmerHMM_glimmerT_59376-T1
Valid prediction for GlimmerHMM_glimmerT_59388-T1
Valid prediction for Augustus_model.g39340.t1
Valid prediction for snap_scaffold_28-snap.2139-T1
Valid prediction for Augustus_model.g39351.t1
Valid prediction for snap_scaffold_28-snap.2120-T1
Valid prediction for snap_scaffold_28-snap.2140-T1
Valid prediction for snap_scaffold_28-snap.2132-T1
Valid prediction for snap_scaffold_28-snap.2145-T1
Valid prediction for pasa_asmbl_37794.p1
Valid prediction for snap_scaffold_28-snap.2128-T1
Couldn't classify 179803, 179903
Sorry, prediction pasa_asmbl_37824.p1 fails validation.
(ATG)	 AC	173588-173657	GT	AGG
(GAA)	 AG	174337-174468	GT	AGG
(GGA)	 AG	175170-175276	GT	AGG
(GTG)	 AG	175441-175515	GT	AGG
(GTT)	 AG	175890-176086	GT	CGG
(GTT)	 AG	176375-176531	GT	GAG
(GTG)	 AG	176646-176759	GT	AGG
(GTG)	 AG	176987-177077	GT	AGG
(GGA)	 AG	177918-178072	GT	AGG
(GTG)	 AG	178178-178283	GT	GGG
(GAA)	 AG	178390-178536	GT	TGG
(GGT)	 AG	178718-178891	GT	CGG
(GCA)	 AG	179350-179478	GT	AGG
(ATG)	 AG	179566-179715	GT	CAG
(GTA)	 AG	179803-179903	GT	AGG
-recovered pasa_asmbl_37824.p1, initial, 173588, 173657
add_exon() Sorry, pasa_asmbl_37824.p1 179566-179715-initial-1 is invalid.
-recovered pasa_asmbl_37824.p1, initial, 179566, 179715
add_exon() Sorry, pasa_asmbl_37824.p1 174337-174468-terminal-1 is invalid.
-recovered pasa_asmbl_37824.p1, terminal, 174337, 174468
add_exon() Sorry, pasa_asmbl_37824.p1 176987-177077-terminal-3 is invalid.
-recovered pasa_asmbl_37824.p1, terminal, 176987, 177077
-recovered pasa_asmbl_37824.p1, internal, 174337, 174468
-recovered pasa_asmbl_37824.p1, internal, 175170, 175276
-recovered pasa_asmbl_37824.p1, internal, 175441, 175515
-recovered pasa_asmbl_37824.p1, internal, 175890, 176086
-recovered pasa_asmbl_37824.p1, internal, 176375, 176531
-recovered pasa_asmbl_37824.p1, internal, 176646, 176759
-recovered pasa_asmbl_37824.p1, internal, 176987, 177077
-recovered pasa_asmbl_37824.p1, internal, 177918, 178072
-recovered pasa_asmbl_37824.p1, internal, 178178, 178283
-recovered pasa_asmbl_37824.p1, internal, 178390, 178536
-recovered pasa_asmbl_37824.p1, internal, 178718, 178891
-recovered pasa_asmbl_37824.p1, internal, 179350, 179478
-recovered pasa_asmbl_37824.p1, internal, 179566, 179715
-recovered pasa_asmbl_37824.p1, internal, 179803, 179903
Valid prediction for snap_scaffold_28-snap.2134-T1
Valid prediction for snap_scaffold_28-snap.2146-T1
Valid prediction for snap_scaffold_28-snap.2148-T1
Valid prediction for snap_scaffold_28-snap.2150-T1
Couldn't classify 42803, 42875
Couldn't classify 44941, 45032
Sorry, prediction pasa_asmbl_37787.p1 fails validation.
(GGT)	 CC	42803-42875	GT	AGG
(GTG)	 AG	44528-44620	GT	AGG
(GAG)	 AG	44703-44828	GT	GGG
(GTG)	 AG	44941-45032	GC	CGG
-recovered pasa_asmbl_37787.p1, internal, 44528, 44620
-recovered pasa_asmbl_37787.p1, internal, 44703, 44828
-recovered pasa_asmbl_37787.p1, internal, 44941, 45032
Valid prediction for snap_scaffold_28-snap.2126-T1
Valid prediction for HiQ_model.g39355.t1
Valid prediction for GlimmerHMM_glimmerT_59380-T1
Valid prediction for GlimmerHMM_glimmerT_59391-T1
Valid prediction for snap_scaffold_28-snap.2137-T1
Valid prediction for snap_scaffold_28-snap.2130-T1
Valid prediction for snap_scaffold_28-snap.2141-T1
Couldn't classify 141789, 142020
Sorry, prediction pasa_asmbl_37795.p1 fails validation.
(GAT)	 TG	141789-142020	GT	AGG
(GCA)	 AG	142722-142918	GT	AGG
(GAG)	 AG	143053-143331	TG	GAT
-recovered pasa_asmbl_37795.p1, terminal, 143053, 143331
-recovered pasa_asmbl_37795.p1, internal, 142722, 142918
Valid prediction for snap_scaffold_28-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_59384-T1
Valid prediction for HiQ_model.g39352.t1
Valid prediction for GlimmerHMM_glimmerT_59390-T1
Valid prediction for GlimmerHMM_glimmerT_59393-T1
Valid prediction for snap_scaffold_28-snap.2122-T1
Valid prediction for Augustus_model.g39342.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 pasa_asmbl_38522.p1
Couldn't classify 43314, 43489
Couldn't classify 43758, 43920
Sorry, prediction pasa_asmbl_38599.p1 fails validation.
(CTT)	 AG	43314-43489	GT	AGG
(ACA)	 AG	43758-43920	GT	AGG
-recovered pasa_asmbl_38599.p1, internal, 43314, 43489
-recovered pasa_asmbl_38599.p1, internal, 43758, 43920
Valid prediction for GlimmerHMM_glimmerT_59382-T1
Valid prediction for Augustus_model.g39339.t1
Valid prediction for Augustus_model.g39348.t1
Couldn't classify 175454, 175768
Sorry, prediction pasa_asmbl_38518.p2 fails validation.
(TTG)	 GT	175454-175768	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_59381-T1
Valid prediction for snap_scaffold_28-snap.2123-T1
Valid prediction for CodingQuarry_transcript_43764-T1
Valid prediction for GlimmerHMM_glimmerT_59377-T1
Couldn't classify 172177, 172261
Sorry, prediction pasa_asmbl_38519.p1 fails validation.
(ATG)	 AG	164403-164691	GT	GGG
(GTT)	 AG	164873-165013	GT	TGG
(TTG)	 AG	165459-165544	GT	AGG
(GAG)	 AG	165828-165924	GT	ATG
(TGC)	 AG	166836-166955	GT	AAG
(GTC)	 AG	167465-167686	GT	TGG
(GTC)	 AG	168192-168825	GT	AGG
(TAA)	 AG	169454-169639	GT	AGG
(TGG)	 AG	172177-172261	GT	AGG
-recovered pasa_asmbl_38519.p1, initial, 164403, 164691
-recovered pasa_asmbl_38519.p1, internal, 164403, 164691
-recovered pasa_asmbl_38519.p1, internal, 164873, 165013
-recovered pasa_asmbl_38519.p1, internal, 165459, 165544
-recovered pasa_asmbl_38519.p1, internal, 165828, 165924
-recovered pasa_asmbl_38519.p1, internal, 166836, 166955
-recovered pasa_asmbl_38519.p1, internal, 167465, 167686
-recovered pasa_asmbl_38519.p1, internal, 168192, 168825
-recovered pasa_asmbl_38519.p1, internal, 169454, 169639
-recovered pasa_asmbl_38519.p1, internal, 172177, 172261
Valid prediction for GlimmerHMM_glimmerT_59389-T1
Valid prediction for GlimmerHMM_glimmerT_59383-T1
Valid prediction for snap_scaffold_28-snap.2153-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g39347.t1
Valid prediction for GlimmerHMM_glimmerT_59392-T1
Valid prediction for snap_scaffold_28-snap.2135-T1
Valid prediction for GlimmerHMM_glimmerT_59387-T1
Valid prediction for snap_scaffold_28-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_59385-T1
Valid prediction for Augustus_model.g39343.t1
Valid prediction for snap_scaffold_28-snap.2113-T1
Valid prediction for snap_scaffold_28-snap.2131-T1
Valid prediction for snap_scaffold_28-snap.2127-T1
Valid prediction for CodingQuarry_transcript_43765-T1
Valid prediction for snap_scaffold_28-snap.2119-T1
Valid prediction for Augustus_model.g39345.t1
Valid prediction for snap_scaffold_28-snap.2151-T1
Valid prediction for snap_scaffold_28-snap.2129-T1
Valid prediction for Augustus_model.g39354.t1
Valid prediction for snap_scaffold_28-snap.2125-T1
Valid prediction for Augustus_model.g39350.t1
Valid prediction for Augustus_model.g39344.t1
Valid prediction for snap_scaffold_28-snap.2147-T1
Valid prediction for snap_scaffold_28-snap.2149-T1
Valid prediction for snap_scaffold_28-snap.2142-T1
Valid prediction for snap_scaffold_28-snap.2138-T1
Valid prediction for pasa_asmbl_38523.p1
Valid prediction for snap_scaffold_28-snap.2117-T1
Valid prediction for snap_scaffold_28-snap.2112-T1
Valid prediction for snap_scaffold_28-snap.2133-T1
Valid prediction for snap_scaffold_28-snap.2136-T1
Sorry, intron length (3) 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: 27255, rend_intergenic: 9808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32407, rend_intergenic: 32297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46602, rend_intergenic: 39890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56208, rend_intergenic: 48922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61022, rend_intergenic: 59193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69974, rend_intergenic: 66948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71783, rend_intergenic: 69991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72901, rend_intergenic: 72323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75055, rend_intergenic: 72930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78997, rend_intergenic: 75135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88861, rend_intergenic: 86827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95682, rend_intergenic: 88877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108479, rend_intergenic: 100231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114467, rend_intergenic: 108528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120898, rend_intergenic: 118213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139138, rend_intergenic: 135479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162477, rend_intergenic: 157191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169985, rend_intergenic: 167276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181101, rend_intergenic: 175375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182463
-exon list size: 390


building trellis

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20.9    
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23.7    
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24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
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26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
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50.0    
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50.5    
50.8    
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51.3    
51.5    
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52.0    
52.3    
52.6    
52.8    
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53.3    
53.6    
53.8    
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54.6    
54.8    
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55.6    
55.9    
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56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
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59.4    
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59.9    
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60.5    
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90.6    
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91.6    
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92.1    
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92.6    
92.9    
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93.4    
93.6    
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96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 27255, rend_intergenic: 9808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32407, rend_intergenic: 32297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46602, rend_intergenic: 39890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56208, rend_intergenic: 48922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61022, rend_intergenic: 59193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69974, rend_intergenic: 66948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71783, rend_intergenic: 69991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72901, rend_intergenic: 72323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75055, rend_intergenic: 72930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78997, rend_intergenic: 75135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88861, rend_intergenic: 86827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95682, rend_intergenic: 88877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108479, rend_intergenic: 100231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114467, rend_intergenic: 108528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120898, rend_intergenic: 118213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139138, rend_intergenic: 135479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162477, rend_intergenic: 157191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169985, rend_intergenic: 167276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181101, rend_intergenic: 175375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support