-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_11883750-12098088

-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_12-snap.2210-T1
Valid prediction for Augustus_model.g20528.t1
Couldn't classify 133209, 133391
Sorry, prediction pasa_asmbl_8935.p1 fails validation.
(TCC)	 CT	133209-133391	GT	AGG
(GTG)	 AG	134160-134264	GT	CGG
(GTA)	 AG	134376-134436	GT	CCG
(CTC)	 AG	134637-134737	GT	AGG
(GAG)	 AG	135101-135223	GT	CGG
(ATC)	 AG	135562-135669	GG	GAG
-recovered pasa_asmbl_8935.p1, terminal, 135562, 135669
-recovered pasa_asmbl_8935.p1, internal, 134160, 134264
-recovered pasa_asmbl_8935.p1, internal, 134376, 134436
-recovered pasa_asmbl_8935.p1, internal, 134637, 134737
-recovered pasa_asmbl_8935.p1, internal, 135101, 135223
Valid prediction for snap_scaffold_12-snap.2231-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g20536.t1
Couldn't classify 181467, 181691
Couldn't classify 181923, 181926
Sorry, prediction CodingQuarry_transcript_10376-T1 fails validation.
(ATG)	 AA	181107-181198	GT	AGG
(TAA)	 AG	181467-181691	GG	ATG
(GTA)	 TG	181923-181926	TC	AGT
-recovered CodingQuarry_transcript_10376-T1, initial, 181107, 181198
Valid prediction for HiQ_model.g20530.t1
Valid prediction for HiQ_model.g20533.t1
Valid prediction for GeneMark_model.53124_t
Valid prediction for GeneMark_model.53107_t
Valid prediction for snap_scaffold_12-snap.2204-T1
Valid prediction for GeneMark_model.53129_t
Couldn't classify 192971, 193541
Sorry, prediction pasa_asmbl_8945.p1 fails validation.
(CGC)	 TC	192971-193541	GT	TGG
(ATG)	 AG	193637-193712	GT	AGG
(GTT)	 AG	193844-193940	CT	AAC
-recovered pasa_asmbl_8945.p1, initial, 193637, 193712
-recovered pasa_asmbl_8945.p1, terminal, 193844, 193940
-recovered pasa_asmbl_8945.p1, internal, 193637, 193712
Valid prediction for CodingQuarry_transcript_10375-T1
Valid prediction for GeneMark_model.53103_t
Valid prediction for CodingQuarry_transcript_10377-T1
Valid prediction for Augustus_model.g20538.t1
Valid prediction for GeneMark_model.53130_t
Valid prediction for GlimmerHMM_glimmerT_30779-T1
Valid prediction for snap_scaffold_12-snap.2206-T1
Valid prediction for snap_scaffold_12-snap.2224-T1
Valid prediction for GlimmerHMM_glimmerT_30790-T1
Valid prediction for pasa_asmbl_8946.p1
Valid prediction for GeneMark_model.53110_t
Valid prediction for GeneMark_model.53116_t
Valid prediction for CodingQuarry_transcript_10372-T1
Valid prediction for HiQ_model.g20539.t1
Valid prediction for snap_scaffold_12-snap.2216-T1
Valid prediction for snap_scaffold_12-snap.2226-T1
Valid prediction for snap_scaffold_12-snap.2227-T1
Valid prediction for snap_scaffold_12-snap.2232-T1
Valid prediction for GeneMark_model.53101_t
Valid prediction for Augustus_model.g20540.t1
Valid prediction for snap_scaffold_12-snap.2234-T1
Valid prediction for snap_scaffold_12-snap.2208-T1
Valid prediction for pasa_asmbl_8939.p1
Valid prediction for snap_scaffold_12-snap.2235-T1
Valid prediction for GeneMark_model.53122_t
Valid prediction for snap_scaffold_12-snap.2229-T1
Valid prediction for GeneMark_model.53108_t
Valid prediction for GlimmerHMM_glimmerT_30772-T1
Valid prediction for GlimmerHMM_glimmerT_30776-T1
Valid prediction for GlimmerHMM_glimmerT_30773-T1
Valid prediction for GeneMark_model.53098_t
Valid prediction for GeneMark_model.53128_t
Valid prediction for GlimmerHMM_glimmerT_30785-T1
Valid prediction for GlimmerHMM_glimmerT_30783-T1
Valid prediction for GlimmerHMM_glimmerT_30791-T1
Valid prediction for GeneMark_model.53131_t
Valid prediction for GeneMark_model.53115_t
Couldn't classify 203257, 204084
Sorry, prediction pasa_asmbl_8948.p1 fails validation.
(CAG)	 AT	203257-204084	TT	AAT
Valid prediction for snap_scaffold_12-snap.2223-T1
Valid prediction for GeneMark_model.53126_t
Valid prediction for GeneMark_model.53120_t
Valid prediction for GeneMark_model.53118_t
Valid prediction for GlimmerHMM_glimmerT_30793-T1
Valid prediction for snap_scaffold_12-snap.2236-T1
Valid prediction for GlimmerHMM_glimmerT_30794-T1
Valid prediction for GeneMark_model.53112_t
Couldn't classify 192274, 192306
Couldn't classify 192470, 192892
Sorry, prediction pasa_asmbl_8944.p1 fails validation.
(GCC)	 CA	192274-192306	GT	AGG
(GAG)	 AG	192470-192892	AC	CAA

-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.g20524.t1
Valid prediction for HiQ_model.g20532.t1
Valid prediction for GlimmerHMM_glimmerT_30787-T1
Valid prediction for GeneMark_model.53099_t
Valid prediction for GlimmerHMM_glimmerT_30774-T1
Valid prediction for GeneMark_model.53123_t
Valid prediction for snap_scaffold_12-snap.2225-T1
Valid prediction for snap_scaffold_12-snap.2221-T1
Valid prediction for snap_scaffold_12-snap.2205-T1
Valid prediction for Augustus_model.g20537.t1
Valid prediction for snap_scaffold_12-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_30784-T1
Couldn't classify 142299, 142339
Couldn't classify 142666, 142935
Sorry, prediction pasa_asmbl_7972.p1 fails validation.
(AAG)	 AA	142299-142339	GT	AGG
(GAA)	 AG	142462-142525	GT	AAG
(GAG)	 AG	142666-142935	CG	AGC
-recovered pasa_asmbl_7972.p1, internal, 142462, 142525
Couldn't classify 73535, 73564
Couldn't classify 74597, 74666
Sorry, prediction pasa_asmbl_7980.p1 fails validation.
(CGT)	 CA	73535-73564	GT	AGG
(TGT)	 AG	73762-73884	GT	ATG
(GCT)	 AG	74088-74199	GT	GGG
(GAG)	 AG	74366-74465	GT	ATG
(ATA)	 AG	74597-74666	AT	AGA
-recovered pasa_asmbl_7980.p1, internal, 73762, 73884
-recovered pasa_asmbl_7980.p1, internal, 74088, 74199
-recovered pasa_asmbl_7980.p1, internal, 74366, 74465
Valid prediction for CodingQuarry_transcript_10373-T1
Valid prediction for GlimmerHMM_glimmerT_30788-T1
Valid prediction for snap_scaffold_12-snap.2237-T1
Valid prediction for GlimmerHMM_glimmerT_30782-T1
Valid prediction for Augustus_model.g20535.t1
Valid prediction for GeneMark_model.53117_t
Valid prediction for pasa_asmbl_7976.p1
Valid prediction for CodingQuarry_transcript_10374-T1
Valid prediction for GeneMark_model.53104_t
Valid prediction for GeneMark_model.53111_t
Valid prediction for snap_scaffold_12-snap.2211-T1
Valid prediction for snap_scaffold_12-snap.2215-T1
Valid prediction for Augustus_model.g20534.t1
Valid prediction for GlimmerHMM_glimmerT_30789-T1
Valid prediction for snap_scaffold_12-snap.2214-T1
Valid prediction for Augustus_model.g20527.t1
Valid prediction for GlimmerHMM_glimmerT_30780-T1
Valid prediction for Augustus_model.g20526.t1
Valid prediction for snap_scaffold_12-snap.2213-T1
Valid prediction for Augustus_model.g20525.t1
Couldn't classify 74788, 74909
Sorry, prediction pasa_asmbl_7979.p1 fails validation.
(GGA)	 AT	74788-74909	GT	AGG
(GTA)	 AG	75392-75512	GT	ACG
(GAC)	 AG	75674-75759	GT	AGG
(TCA)	 AG	75992-76214	TC	AGT
-recovered pasa_asmbl_7979.p1, terminal, 75992, 76214
-recovered pasa_asmbl_7979.p1, internal, 75392, 75512
-recovered pasa_asmbl_7979.p1, internal, 75674, 75759
Valid prediction for snap_scaffold_12-snap.2233-T1
Valid prediction for GeneMark_model.53127_t
Valid prediction for snap_scaffold_12-snap.2217-T1
Valid prediction for CodingQuarry_transcript_10371-T1
Valid prediction for Augustus_model.g20531.t1
Valid prediction for snap_scaffold_12-snap.2209-T1
Valid prediction for GlimmerHMM_glimmerT_30781-T1
Valid prediction for snap_scaffold_12-snap.2207-T1
Valid prediction for GlimmerHMM_glimmerT_30792-T1
Valid prediction for snap_scaffold_12-snap.2222-T1
Valid prediction for GlimmerHMM_glimmerT_30795-T1
Valid prediction for GlimmerHMM_glimmerT_30775-T1
Valid prediction for Augustus_model.g20541.t1
Valid prediction for GlimmerHMM_glimmerT_30786-T1
Valid prediction for snap_scaffold_12-snap.2212-T1
Valid prediction for GeneMark_model.53100_t
Couldn't classify 165153, 165249
Couldn't classify 170069, 170197
Sorry, prediction pasa_asmbl_7968.p1 fails validation.
(ACG)	 AG	165153-165249	GT	AGG
(GCA)	 AG	168026-168114	GT	AGG
(GGG)	 AG	170069-170197	AG	AGA
-recovered pasa_asmbl_7968.p1, internal, 165153, 165249
-recovered pasa_asmbl_7968.p1, internal, 168026, 168114
Couldn't classify 143098, 143982
Sorry, prediction pasa_asmbl_7971.p1 fails validation.
(AGG)	 GC	143098-143982	CA	CCC
Couldn't classify 115122, 115373
Couldn't classify 116902, 117650
Sorry, prediction pasa_asmbl_7975.p1 fails validation.
(CCA)	 CC	115122-115373	GT	AGG
(GTG)	 AG	115622-115955	GT	AGG
(AGA)	 AG	116902-117650	GG	TGG
add_exon() Sorry, pasa_asmbl_7975.p1 115622-115955-terminal-3 is invalid.
-recovered pasa_asmbl_7975.p1, terminal, 115622, 115955
-recovered pasa_asmbl_7975.p1, internal, 115622, 115955
Valid prediction for GeneMark_model.53119_t
Valid prediction for snap_scaffold_12-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_30777-T1
Valid prediction for CodingQuarry_transcript_10369-T1
Valid prediction for Augustus_model.g20523.t1
Couldn't classify 42162, 42332
Sorry, prediction pasa_asmbl_7981.p1 fails validation.
(ATG)	 CA	41034-41312	GT	AGG
(AAA)	 AG	41743-41838	GT	AGG
(AGG)	 AG	42162-42332	GA	TGG
-recovered pasa_asmbl_7981.p1, initial, 41034, 41312
-recovered pasa_asmbl_7981.p1, internal, 41743, 41838
Couldn't classify 140373, 140398
Couldn't classify 140852, 141027
Sorry, prediction pasa_asmbl_8381.p1 fails validation.
(AAC)	 GA	140373-140398	GT	CAG
(GTC)	 AG	140532-140722	GT	AGG
(CCT)	 AG	140852-141027	GG	AGG
-recovered pasa_asmbl_8381.p1, internal, 140532, 140722
Valid prediction for GeneMark_model.53105_t
Valid prediction for snap_scaffold_12-snap.2230-T1
Valid prediction for CodingQuarry_transcript_10370-T1
Valid prediction for pasa_asmbl_7970.p1
Valid prediction for Augustus_model.g20529.t1
Valid prediction for GeneMark_model.53113_t
Valid prediction for snap_scaffold_12-snap.2238-T1
Valid prediction for GeneMark_model.53109_t
Couldn't classify 118695, 118779
Sorry, prediction pasa_asmbl_7974.p3 fails validation.
(TCC)	 GC	118695-118779	GT	GGG
(TGA)	 AG	119064-119311	TT	GAT
-recovered pasa_asmbl_7974.p3, terminal, 119064, 119311
Valid prediction for GeneMark_model.53121_t
Valid prediction for GeneMark_model.53106_t
Couldn't classify 42776, 42893
Sorry, prediction pasa_asmbl_8337.p1 fails validation.
(AGA)	 GC	42776-42893	GT	AGG
(GCC)	 AG	43101-43660	CT	AGC
-recovered pasa_asmbl_8337.p1, terminal, 43101, 43660
Valid prediction for GlimmerHMM_glimmerT_30778-T1
Valid prediction for snap_scaffold_12-snap.2228-T1
Valid prediction for snap_scaffold_12-snap.2218-T1
Valid prediction for GeneMark_model.53102_t
Valid prediction for GlimmerHMM_glimmerT_30771-T1
Valid prediction for GeneMark_model.53114_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35362, rend_intergenic: 32754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130740, rend_intergenic: 127289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150423, rend_intergenic: 139335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153472, rend_intergenic: 150621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214339
-exon list size: 471


building trellis

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14.8    
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20.9    
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21.6    
21.8    
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22.8    
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23.3    
23.5    
23.7    
23.9    
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24.9    
25.2    
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25.6    
25.8    
26.0    
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26.4    
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26.8    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
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56.4    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
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62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.2    
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70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 35362, rend_intergenic: 32754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130740, rend_intergenic: 127289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150423, rend_intergenic: 139335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153472, rend_intergenic: 150621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21705
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15073
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support