-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_9385737-9621456

-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 Augustus_model.g37362.t1
Valid prediction for GlimmerHMM_glimmerT_56363-T1
Valid prediction for CodingQuarry_transcript_40441-T1
Valid prediction for snap_scaffold_26-snap.2134-T1
Couldn't classify 222714, 223022
Sorry, prediction pasa_asmbl_35246.p1 fails validation.
(TAT)	 TC	222714-223022	CA	AAC
Valid prediction for snap_scaffold_26-snap.2135-T1
Valid prediction for snap_scaffold_26-snap.2149-T1
Valid prediction for HiQ_model.g37368.t1
Valid prediction for pasa_asmbl_35238.p1
Valid prediction for Augustus_model.g37349.t1
Valid prediction for snap_scaffold_26-snap.2129-T1
Couldn't classify 150742, 150901
Sorry, prediction pasa_asmbl_35325.p1 fails validation.
(TTC)	 CT	150742-150901	GT	GGG
(GTT)	 AG	152700-152835	GT	AGG
(GTT)	 AG	153468-153651	GT	AGG
(GGT)	 AG	155979-156116	GT	AGG
(GCG)	 AG	156870-156959	AC	GAA
-recovered pasa_asmbl_35325.p1, terminal, 156870, 156959
-recovered pasa_asmbl_35325.p1, internal, 152700, 152835
-recovered pasa_asmbl_35325.p1, internal, 153468, 153651
-recovered pasa_asmbl_35325.p1, internal, 155979, 156116
Valid prediction for snap_scaffold_26-snap.2132-T1
Valid prediction for snap_scaffold_26-snap.2115-T1
Valid prediction for GlimmerHMM_glimmerT_56380-T1
Valid prediction for snap_scaffold_26-snap.2126-T1
Valid prediction for Augustus_model.g37369.t1
Valid prediction for snap_scaffold_26-snap.2140-T1
Couldn't classify 145715, 145840
Sorry, prediction Augustus_model.g37360.t1 fails validation.
(AAC)	 TC	145715-145840	GT	GGG
(GAC)	 AG	147123-147277	GT	AGG
(TGG)	 AG	147874-147953	GT	TGG
(ACT)	 AG	148696-148731	GT	AAG
(GGT)	 AG	149924-150111	GT	AGG
(AAT)	 AG	150598-150647	GT	AGG
(GGT)	 AG	150786-150901	GT	GGG
(GTT)	 AG	152700-152835	GT	AGG
(GTT)	 AG	153468-153651	GT	AGG
(GGT)	 AG	155979-156116	GT	AGG
(GCG)	 AG	156870-156959	AC	GAA
-recovered Augustus_model.g37360.t1, terminal, 156870, 156959
-recovered Augustus_model.g37360.t1, internal, 147123, 147277
-recovered Augustus_model.g37360.t1, internal, 147874, 147953
-recovered Augustus_model.g37360.t1, internal, 148696, 148731
-recovered Augustus_model.g37360.t1, internal, 149924, 150111
-recovered Augustus_model.g37360.t1, internal, 150598, 150647
-recovered Augustus_model.g37360.t1, internal, 150786, 150901
-recovered Augustus_model.g37360.t1, internal, 152700, 152835
-recovered Augustus_model.g37360.t1, internal, 153468, 153651
-recovered Augustus_model.g37360.t1, internal, 155979, 156116
Couldn't classify 128615, 128615
Sorry, prediction CodingQuarry_transcript_40438-T1 fails validation.
(AGT)	 AC	128615-128615	GT	CAG
(TGA)	 AG	128779-128883	GT	CGG
(GAG)	 AG	129190-129276	GT	AGG
(GGA)	 AG	129393-129489	GT	AAG
(GGA)	 AG	129814-129905	GT	AGG
(GTG)	 AG	131651-131710	GT	TGG
(GTA)	 AG	131962-131999	GC	AGG
(TAT)	 AG	133108-133154	GT	AGG
(GCA)	 AG	134072-134158	GT	AGG
(GTC)	 AG	134336-134380	GT	AGG
(GGT)	 AG	135030-135086	GT	AAG
(TCT)	 AG	135641-135692	GT	AGG
(AGT)	 AG	137229-137297	GT	AGG
(GAC)	 AG	137541-137606	GT	AGG
(GGG)	 AG	137752-137878	GT	AGG
(GGA)	 AG	138172-138242	CT	AGC
add_exon() Sorry, CodingQuarry_transcript_40438-T1 133108-133154-terminal-2 is invalid.
-recovered CodingQuarry_transcript_40438-T1, terminal, 133108, 133154
-recovered CodingQuarry_transcript_40438-T1, terminal, 135030, 135086
add_exon() Sorry, CodingQuarry_transcript_40438-T1 137752-137878-terminal-3 is invalid.
-recovered CodingQuarry_transcript_40438-T1, terminal, 137752, 137878
-recovered CodingQuarry_transcript_40438-T1, terminal, 138172, 138242
-recovered CodingQuarry_transcript_40438-T1, internal, 128779, 128883
-recovered CodingQuarry_transcript_40438-T1, internal, 129190, 129276
-recovered CodingQuarry_transcript_40438-T1, internal, 129393, 129489
-recovered CodingQuarry_transcript_40438-T1, internal, 129814, 129905
-recovered CodingQuarry_transcript_40438-T1, internal, 131651, 131710
-recovered CodingQuarry_transcript_40438-T1, internal, 131962, 131999
-recovered CodingQuarry_transcript_40438-T1, internal, 133108, 133154
-recovered CodingQuarry_transcript_40438-T1, internal, 134072, 134158
-recovered CodingQuarry_transcript_40438-T1, internal, 134336, 134380
-recovered CodingQuarry_transcript_40438-T1, internal, 135030, 135086
-recovered CodingQuarry_transcript_40438-T1, internal, 135641, 135692
-recovered CodingQuarry_transcript_40438-T1, internal, 137229, 137297
-recovered CodingQuarry_transcript_40438-T1, internal, 137541, 137606
-recovered CodingQuarry_transcript_40438-T1, internal, 137752, 137878
Couldn't classify 147123, 147278
Sorry, prediction pasa_asmbl_35241.p1 fails validation.
(ATG)	 GG	143231-143488	GT	GGG
(ATT)	 AG	144320-144482	GT	AGG
(GTC)	 AG	145216-145362	GT	AGG
(TGG)	 AG	145446-145571	GT	AGG
(TGA)	 AG	145650-145840	GT	GGG
(GAC)	 AG	147123-147278	TA	GGT
-recovered pasa_asmbl_35241.p1, initial, 143231, 143488
-recovered pasa_asmbl_35241.p1, internal, 144320, 144482
-recovered pasa_asmbl_35241.p1, internal, 145216, 145362
-recovered pasa_asmbl_35241.p1, internal, 145446, 145571
-recovered pasa_asmbl_35241.p1, internal, 145650, 145840
Valid prediction for Augustus_model.g37366.t1
Valid prediction for GlimmerHMM_glimmerT_56383-T1
Valid prediction for snap_scaffold_26-snap.2112-T1
Valid prediction for snap_scaffold_26-snap.2110-T1
Valid prediction for snap_scaffold_26-snap.2150-T1
Valid prediction for snap_scaffold_26-snap.2118-T1
Valid prediction for pasa_asmbl_35244.p1
Valid prediction for snap_scaffold_26-snap.2117-T1
Valid prediction for snap_scaffold_26-snap.2109-T1
Valid prediction for snap_scaffold_26-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_56376-T1
Valid prediction for GlimmerHMM_glimmerT_56377-T1
Valid prediction for snap_scaffold_26-snap.2120-T1
Valid prediction for snap_scaffold_26-snap.2131-T1
Valid prediction for snap_scaffold_26-snap.2137-T1
Valid prediction for snap_scaffold_26-snap.2133-T1
Valid prediction for Augustus_model.g37359.t1
Valid prediction for CodingQuarry_transcript_40440-T1
Valid prediction for HiQ_model.g37358.t1
Valid prediction for snap_scaffold_26-snap.2106-T1
Valid prediction for Augustus_model.g37351.t1
Valid prediction for GlimmerHMM_glimmerT_56385-T1
Couldn't classify 223416, 223610
Sorry, prediction pasa_asmbl_35250.p1 fails validation.
(TGT)	 TG	223416-223610	GT	TGG
(GTG)	 AG	223768-223965	GT	AGG
(GAG)	 AG	224666-224755	GT	AGG
(GGT)	 AG	225220-225282	TG	GAT
-recovered pasa_asmbl_35250.p1, terminal, 225220, 225282
-recovered pasa_asmbl_35250.p1, internal, 223768, 223965
-recovered pasa_asmbl_35250.p1, internal, 224666, 224755
Valid prediction for GlimmerHMM_glimmerT_56381-T1
Valid prediction for GlimmerHMM_glimmerT_56386-T1
Valid prediction for GlimmerHMM_glimmerT_56359-T1
Valid prediction for snap_scaffold_26-snap.2111-T1
Valid prediction for snap_scaffold_26-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_56378-T1
Valid prediction for GlimmerHMM_glimmerT_56369-T1
Valid prediction for GlimmerHMM_glimmerT_56367-T1
Valid prediction for snap_scaffold_26-snap.2139-T1
Valid prediction for GlimmerHMM_glimmerT_56361-T1
Valid prediction for snap_scaffold_26-snap.2128-T1
Valid prediction for CodingQuarry_transcript_40435-T1
Valid prediction for CodingQuarry_transcript_40442-T1
Valid prediction for GlimmerHMM_glimmerT_56387-T1
Valid prediction for snap_scaffold_26-snap.2146-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_26-snap.2138-T1
Valid prediction for snap_scaffold_26-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_56358-T1
Valid prediction for GlimmerHMM_glimmerT_56368-T1
Valid prediction for snap_scaffold_26-snap.2114-T1
Couldn't classify 61460, 61873
Sorry, prediction pasa_asmbl_35783.p1 fails validation.
(CAC)	 GC	61460-61873	CT	GAC
Valid prediction for Augustus_model.g37364.t1
Valid prediction for snap_scaffold_26-snap.2116-T1
Valid prediction for GlimmerHMM_glimmerT_56365-T1
Valid prediction for HiQ_model.g37367.t1
Valid prediction for GlimmerHMM_glimmerT_56364-T1
Valid prediction for Augustus_model.g37363.t1
Valid prediction for snap_scaffold_26-snap.2125-T1
Valid prediction for Augustus_model.g37361.t1
Valid prediction for GlimmerHMM_glimmerT_56360-T1
Valid prediction for Augustus_model.g37354.t1
Valid prediction for snap_scaffold_26-snap.2107-T1
Couldn't classify 50983, 51166
Couldn't classify 52142, 52201
Sorry, prediction pasa_asmbl_35786.p1 fails validation.
(CGG)	 TA	50983-51166	GT	TGG
(GGG)	 AG	51509-51657	GT	AGG
(GTA)	 AG	52142-52201	GA	CAG
-recovered pasa_asmbl_35786.p1, internal, 51509, 51657
Valid prediction for GlimmerHMM_glimmerT_56371-T1
Valid prediction for GlimmerHMM_glimmerT_56384-T1
Valid prediction for Augustus_model.g37353.t1
Valid prediction for snap_scaffold_26-snap.2113-T1
Valid prediction for Augustus_model.g37365.t1
Valid prediction for GlimmerHMM_glimmerT_56372-T1
Couldn't classify 25708, 25801
Sorry, prediction pasa_asmbl_35787.p1 fails validation.
(CTA)	 CT	25708-25801	GT	TGG
(CTT)	 AG	26822-26862	GT	AGG
(GAG)	 AG	27901-28143	AC	AGA
-recovered pasa_asmbl_35787.p1, terminal, 27901, 28143
-recovered pasa_asmbl_35787.p1, internal, 26822, 26862
Valid prediction for GlimmerHMM_glimmerT_56370-T1
Valid prediction for snap_scaffold_26-snap.2143-T1
Valid prediction for snap_scaffold_26-snap.2122-T1
Valid prediction for Augustus_model.g37350.t1
Valid prediction for snap_scaffold_26-snap.2147-T1
Valid prediction for Augustus_model.g37356.t1
Valid prediction for snap_scaffold_26-snap.2119-T1
Valid prediction for Augustus_model.g37357.t1
Valid prediction for snap_scaffold_26-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_56373-T1
Couldn't classify 142031, 142078
Sorry, prediction pasa_asmbl_35782.p1 fails validation.
(AAG)	 AC	142031-142078	GT	AGG
(AAT)	 AG	142288-142374	GT	AGG
(GCC)	 AG	142542-142778	GT	AGG
(TTT)	 AG	143274-143417	GT	AGG
(GGG)	 AG	144737-144843	GT	AGG
(GTG)	 AG	146373-146543	GT	AGG
(GGA)	 AG	147026-147077	GA	GAG
-recovered pasa_asmbl_35782.p1, terminal, 147026, 147077
-recovered pasa_asmbl_35782.p1, internal, 142288, 142374
-recovered pasa_asmbl_35782.p1, internal, 142542, 142778
-recovered pasa_asmbl_35782.p1, internal, 143274, 143417
-recovered pasa_asmbl_35782.p1, internal, 144737, 144843
-recovered pasa_asmbl_35782.p1, internal, 146373, 146543
Valid prediction for GlimmerHMM_glimmerT_56379-T1
Valid prediction for snap_scaffold_26-snap.2141-T1
Valid prediction for CodingQuarry_transcript_40437-T1
Valid prediction for GlimmerHMM_glimmerT_56375-T1
Valid prediction for GlimmerHMM_glimmerT_56366-T1
Valid prediction for GlimmerHMM_glimmerT_56374-T1
Valid prediction for snap_scaffold_26-snap.2108-T1
Valid prediction for GlimmerHMM_glimmerT_56362-T1
Valid prediction for snap_scaffold_26-snap.2124-T1
Valid prediction for snap_scaffold_26-snap.2148-T1
Couldn't classify 59854, 59971
Couldn't classify 61008, 61105
Sorry, prediction pasa_asmbl_35784.p1 fails validation.
(TCG)	 TG	59854-59971	GT	AGG
(GTG)	 AG	60204-60367	GT	AGG
(GTG)	 AG	60776-60857	GT	AGG
(GTG)	 AG	61008-61105	AC	GCA
add_exon() Sorry, pasa_asmbl_35784.p1 60776-60857-terminal-3 is invalid.
-recovered pasa_asmbl_35784.p1, terminal, 60776, 60857
-recovered pasa_asmbl_35784.p1, internal, 60204, 60367
-recovered pasa_asmbl_35784.p1, internal, 60776, 60857
Valid prediction for snap_scaffold_26-snap.2142-T1
Valid prediction for Augustus_model.g37352.t1
Valid prediction for snap_scaffold_26-snap.2127-T1
Valid prediction for Augustus_model.g37355.t1
Valid prediction for snap_scaffold_26-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_56382-T1
Couldn't classify 170057, 170149
Sorry, prediction pasa_asmbl_35832.p1 fails validation.
(GAC)	 AG	170057-170149	GT	AGG
(GGT)	 AG	170361-170468	GT	AGG
(GAT)	 AG	171283-171420	TT	AAT
-recovered pasa_asmbl_35832.p1, terminal, 171283, 171420
-recovered pasa_asmbl_35832.p1, internal, 170057, 170149
-recovered pasa_asmbl_35832.p1, internal, 170361, 170468
Valid prediction for snap_scaffold_26-snap.2123-T1
Couldn't classify 54320, 54371
Couldn't classify 56555, 56591
Sorry, prediction pasa_asmbl_35785.p1 fails validation.
(CTA)	 CG	54320-54371	GT	AGG
(AGC)	 AG	54472-54618	GT	AGG
(ACT)	 AG	54934-55194	GT	GGG
(GTG)	 AG	56180-56315	GT	CGG
(CTG)	 AG	56555-56591	GG	GAG
-recovered pasa_asmbl_35785.p1, internal, 54472, 54618
-recovered pasa_asmbl_35785.p1, internal, 54934, 55194
-recovered pasa_asmbl_35785.p1, internal, 56180, 56315

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15340, rend_intergenic: 5268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24828, rend_intergenic: 18639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44405, rend_intergenic: 37952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57423, rend_intergenic: 51632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63756, rend_intergenic: 57502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66852, rend_intergenic: 66517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69783, rend_intergenic: 67077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98694, rend_intergenic: 96227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101833, rend_intergenic: 99138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123189, rend_intergenic: 103187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156101, rend_intergenic: 147132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167511, rend_intergenic: 164363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194931, rend_intergenic: 188027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235720
-exon list size: 435


building trellis

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26.3    
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28.4    
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28.8    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
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43.9    
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44.6    
44.9    
45.1    
45.3    
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45.8    
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48.5    
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49.9    
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50.6    
50.8    
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51.9    
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52.9    
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55.8    
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63.8    
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73.0    
73.2    
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73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 15340, rend_intergenic: 5268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24828, rend_intergenic: 18639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44405, rend_intergenic: 37952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57423, rend_intergenic: 51632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63756, rend_intergenic: 57502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66852, rend_intergenic: 66517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69783, rend_intergenic: 67077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98694, rend_intergenic: 96227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101833, rend_intergenic: 99138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123189, rend_intergenic: 103187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156101, rend_intergenic: 147132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167511, rend_intergenic: 164363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194931, rend_intergenic: 188027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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