-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_18012241-18265865

-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.g14213.t1
Valid prediction for snap_scaffold_8-snap.3329-T1
Valid prediction for Augustus_model.g14202.t1
Valid prediction for Augustus_model.g14203.t1
Valid prediction for snap_scaffold_8-snap.3313-T1
Valid prediction for CodingQuarry_transcript_59958-T1
Valid prediction for GlimmerHMM_glimmerT_21328-T1
Valid prediction for GlimmerHMM_glimmerT_21319-T1
Valid prediction for GlimmerHMM_glimmerT_21335-T1
Valid prediction for snap_scaffold_8-snap.3320-T1
Valid prediction for GlimmerHMM_glimmerT_21345-T1
Valid prediction for GlimmerHMM_glimmerT_21326-T1
Valid prediction for Augustus_model.g14218.t1
Valid prediction for GlimmerHMM_glimmerT_21325-T1
Valid prediction for pasa_asmbl_53521.p1
Valid prediction for snap_scaffold_8-snap.3337-T1
Valid prediction for GlimmerHMM_glimmerT_21333-T1
Couldn't classify 133813, 133964
Couldn't classify 134275, 134327
Sorry, prediction pasa_asmbl_53628.p1 fails validation.
(GAC)	 CT	133813-133964	GC	AGG
(AAA)	 AG	134065-134156	GT	AGG
(ACA)	 AG	134275-134327	AG	CCA
-recovered pasa_asmbl_53628.p1, internal, 134065, 134156
Valid prediction for GlimmerHMM_glimmerT_21349-T1
Valid prediction for snap_scaffold_8-snap.3323-T1
Valid prediction for Augustus_model.g14215.t1
Valid prediction for snap_scaffold_8-snap.3330-T1
Valid prediction for snap_scaffold_8-snap.3351-T1
Valid prediction for Augustus_model.g14223.t1
Valid prediction for GlimmerHMM_glimmerT_21344-T1
Valid prediction for snap_scaffold_8-snap.3335-T1
Couldn't classify 205328, 205726
Sorry, prediction pasa_asmbl_53657.p1 fails validation.
(GAT)	 AG	205328-205726	GC	ACG
-recovered pasa_asmbl_53657.p1, internal, 205328, 205726
Valid prediction for pasa_asmbl_53537.p1
Valid prediction for GlimmerHMM_glimmerT_21348-T1
Valid prediction for GlimmerHMM_glimmerT_21323-T1
Valid prediction for Augustus_model.g14216.t1
Valid prediction for snap_scaffold_8-snap.3340-T1
Valid prediction for pasa_asmbl_53529.p1
Couldn't classify 94099, 94135
Sorry, prediction pasa_asmbl_53532.p1 fails validation.
(TGC)	 GT	94099-94135	GC	GGG
(GTC)	 AG	95369-95502	GT	AGG
(GCA)	 AG	95908-95986	GT	AGG
(GGA)	 AG	96190-96329	GG	GAG
-recovered pasa_asmbl_53532.p1, terminal, 96190, 96329
-recovered pasa_asmbl_53532.p1, internal, 95369, 95502
-recovered pasa_asmbl_53532.p1, internal, 95908, 95986
Valid prediction for GlimmerHMM_glimmerT_21321-T1
Valid prediction for Augustus_model.g14221.t1
Couldn't classify 143527, 143703
Sorry, prediction pasa_asmbl_53535.p1 fails validation.
(ATG)	 AC	138001-138231	GT	CTG
(ATT)	 AG	138342-138438	GT	TCG
(CTA)	 AG	138572-138737	GT	CGG
(GGG)	 AG	138828-138917	GT	TCG
(AAT)	 AG	139088-139239	GT	AGG
(TGT)	 AG	139345-139445	GT	AGG
(CTG)	 AG	139540-139666	GT	AGG
(GTG)	 AG	139809-139886	GT	CGG
(GCA)	 AG	140075-140247	GT	AGG
(TGT)	 AG	140349-140464	GT	TGG
(TGG)	 AG	141261-141428	GT	AGG
(GGC)	 AG	141625-141883	GT	AGG
(GTG)	 AG	142125-142313	GT	AGG
(CGC)	 AG	142432-142744	GT	AGG
(ATT)	 AG	142836-142947	GT	GGG
(AGC)	 AG	143068-143215	GT	GGG
(AAA)	 AG	143527-143703	CT	ACC
-recovered pasa_asmbl_53535.p1, initial, 138001, 138231
add_exon() Sorry, pasa_asmbl_53535.p1 139540-139666-terminal-3 is invalid.
-recovered pasa_asmbl_53535.p1, terminal, 139540, 139666
-recovered pasa_asmbl_53535.p1, internal, 138342, 138438
-recovered pasa_asmbl_53535.p1, internal, 138572, 138737
-recovered pasa_asmbl_53535.p1, internal, 138828, 138917
-recovered pasa_asmbl_53535.p1, internal, 139088, 139239
-recovered pasa_asmbl_53535.p1, internal, 139345, 139445
-recovered pasa_asmbl_53535.p1, internal, 139540, 139666
-recovered pasa_asmbl_53535.p1, internal, 139809, 139886
-recovered pasa_asmbl_53535.p1, internal, 140075, 140247
-recovered pasa_asmbl_53535.p1, internal, 140349, 140464
-recovered pasa_asmbl_53535.p1, internal, 141261, 141428
-recovered pasa_asmbl_53535.p1, internal, 141625, 141883
-recovered pasa_asmbl_53535.p1, internal, 142125, 142313
-recovered pasa_asmbl_53535.p1, internal, 142432, 142744
-recovered pasa_asmbl_53535.p1, internal, 142836, 142947
-recovered pasa_asmbl_53535.p1, internal, 143068, 143215
Valid prediction for snap_scaffold_8-snap.3317-T1
Couldn't classify 85580, 85699
Sorry, prediction pasa_asmbl_53527.p1 fails validation.
(ATG)	 AT	83154-83383	GT	AGG
(GCC)	 AG	83551-83653	GT	AAG
(GGG)	 AG	85580-85699	AG	TAA
-recovered pasa_asmbl_53527.p1, initial, 83154, 83383
-recovered pasa_asmbl_53527.p1, internal, 83551, 83653
Valid prediction for snap_scaffold_8-snap.3347-T1
Valid prediction for snap_scaffold_8-snap.3356-T1
Valid prediction for HiQ_model.g14228.t1
Valid prediction for GlimmerHMM_glimmerT_21341-T1
Valid prediction for snap_scaffold_8-snap.3352-T1
Valid prediction for GlimmerHMM_glimmerT_21336-T1
Valid prediction for snap_scaffold_8-snap.3357-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.3336-T1
Valid prediction for snap_scaffold_8-snap.3339-T1
Valid prediction for HiQ_model.g14204.t1
Valid prediction for snap_scaffold_8-snap.3353-T1
Valid prediction for pasa_asmbl_53542.p1
Valid prediction for snap_scaffold_8-snap.3341-T1
Valid prediction for CodingQuarry_transcript_59951-T1
Valid prediction for GlimmerHMM_glimmerT_21329-T1
Valid prediction for HiQ_model.g14226.t1
Valid prediction for snap_scaffold_8-snap.3328-T1
Valid prediction for snap_scaffold_8-snap.3326-T1
Valid prediction for Augustus_model.g14207.t1
Valid prediction for CodingQuarry_transcript_59961-T1
Valid prediction for Augustus_model.g14201.t1
Valid prediction for GlimmerHMM_glimmerT_21338-T1
Valid prediction for snap_scaffold_8-snap.3350-T1
Valid prediction for snap_scaffold_8-snap.3321-T1
Valid prediction for CodingQuarry_transcript_59954-T1
Valid prediction for Augustus_model.g14209.t1
Valid prediction for Augustus_model.g14229.t1
Valid prediction for GlimmerHMM_glimmerT_21322-T1
Valid prediction for snap_scaffold_8-snap.3315-T1
Valid prediction for CodingQuarry_transcript_59952-T1
Valid prediction for Augustus_model.g14205.t1
Valid prediction for snap_scaffold_8-snap.3319-T1
Valid prediction for snap_scaffold_8-snap.3334-T1
Valid prediction for GlimmerHMM_glimmerT_21330-T1
Valid prediction for Augustus_model.g14224.t1
Valid prediction for snap_scaffold_8-snap.3344-T1
Couldn't classify 73601, 73744
Sorry, prediction pasa_asmbl_53525.p1 fails validation.
(TAC)	 GA	73601-73744	GT	ACG
(ATG)	 AG	73941-74064	GT	TTG
(CCA)	 AG	74819-74893	GT	CGG
(CCT)	 AG	74990-75092	GT	TGG
(GCA)	 AG	75254-75397	GT	AGG
(GTA)	 AG	76537-76603	GT	AGG
(GAG)	 AG	76769-76896	GT	CGG
(GTA)	 AG	77295-77535	GT	GAG
-recovered pasa_asmbl_53525.p1, initial, 73941, 74064
-recovered pasa_asmbl_53525.p1, terminal, 77295, 77535
-recovered pasa_asmbl_53525.p1, internal, 73941, 74064
-recovered pasa_asmbl_53525.p1, internal, 74819, 74893
-recovered pasa_asmbl_53525.p1, internal, 74990, 75092
-recovered pasa_asmbl_53525.p1, internal, 75254, 75397
-recovered pasa_asmbl_53525.p1, internal, 76537, 76603
-recovered pasa_asmbl_53525.p1, internal, 76769, 76896
-recovered pasa_asmbl_53525.p1, internal, 77295, 77535
Valid prediction for Augustus_model.g14208.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_8-snap.3316-T1
Valid prediction for pasa_asmbl_52509.p1
Valid prediction for CodingQuarry_transcript_59953-T1
Valid prediction for CodingQuarry_transcript_59960-T1
Valid prediction for CodingQuarry_transcript_59955-T1
Valid prediction for pasa_asmbl_52513.p1
Valid prediction for snap_scaffold_8-snap.3342-T1
Valid prediction for snap_scaffold_8-snap.3343-T1
Valid prediction for snap_scaffold_8-snap.3332-T1
Valid prediction for pasa_asmbl_52524.p1
Valid prediction for GlimmerHMM_glimmerT_21343-T1
Valid prediction for GlimmerHMM_glimmerT_21332-T1
Valid prediction for snap_scaffold_8-snap.3314-T1
Couldn't classify 74633, 74941
Sorry, prediction pasa_asmbl_52519.p1 fails validation.
(CAG)	 TC	74633-74941	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_21327-T1
Valid prediction for snap_scaffold_8-snap.3338-T1
Valid prediction for GlimmerHMM_glimmerT_21334-T1
Couldn't classify 74150, 74527
Sorry, prediction pasa_asmbl_52520.p1 fails validation.
(GGC)	 AT	74150-74527	CC	CCC
Valid prediction for snap_scaffold_8-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_21331-T1
Valid prediction for Augustus_model.g14222.t1
Valid prediction for GlimmerHMM_glimmerT_21339-T1
Valid prediction for GlimmerHMM_glimmerT_21340-T1
Valid prediction for GlimmerHMM_glimmerT_21347-T1
Valid prediction for GlimmerHMM_glimmerT_21346-T1
Valid prediction for snap_scaffold_8-snap.3325-T1
Valid prediction for Augustus_model.g14219.t1
Valid prediction for Augustus_model.g14225.t1
Valid prediction for snap_scaffold_8-snap.3318-T1
Couldn't classify 66971, 67012
Sorry, prediction pasa_asmbl_52523.p1 fails validation.
(ATG)	 CA	64404-64516	GT	CCG
(ATG)	 AG	64857-65007	GT	CGG
(GTT)	 AG	65935-66018	GT	AGG
(GAT)	 AG	66501-66578	GT	AGG
(GGG)	 AG	66971-67012	CA	AAC
-recovered pasa_asmbl_52523.p1, initial, 64404, 64516
-recovered pasa_asmbl_52523.p1, initial, 64857, 65007
-recovered pasa_asmbl_52523.p1, internal, 64857, 65007
-recovered pasa_asmbl_52523.p1, internal, 65935, 66018
-recovered pasa_asmbl_52523.p1, internal, 66501, 66578
Valid prediction for snap_scaffold_8-snap.3322-T1
Valid prediction for snap_scaffold_8-snap.3346-T1
Valid prediction for Augustus_model.g14212.t1
Valid prediction for HiQ_model.g14206.t1
Valid prediction for Augustus_model.g14227.t1
Couldn't classify 68411, 68481
Couldn't classify 69262, 69379
Sorry, prediction pasa_asmbl_52522.p1 fails validation.
(AGT)	 TT	68411-68481	GT	AGG
(GAT)	 AG	68729-68801	GT	AGG
(TGG)	 AG	68916-69121	GT	TGG
(CTG)	 AG	69262-69379	CT	GAC
-recovered pasa_asmbl_52522.p1, internal, 68729, 68801
-recovered pasa_asmbl_52522.p1, internal, 68916, 69121
Valid prediction for GlimmerHMM_glimmerT_21320-T1
Valid prediction for Augustus_model.g14211.t1
Valid prediction for snap_scaffold_8-snap.3354-T1
Couldn't classify 63985, 64024
Couldn't classify 64932, 65007
Sorry, prediction CodingQuarry_transcript_59956-T1 fails validation.
(ATG)	 TG	62592-62686	GT	TGG
(GTT)	 AG	62805-63016	GT	AGG
(CAA)	 AG	63205-63306	GT	TGG
(GTA)	 AG	63440-63578	GT	AGG
(ACA)	 AG	63735-63822	GT	CTG
(GAC)	 AG	63985-64024	TC	CTT
(CCA)	 GT	64932-65007	GT	CGG
(GTT)	 AG	65935-65959	CA	AGC
-recovered CodingQuarry_transcript_59956-T1, initial, 62592, 62686
add_exon() Sorry, CodingQuarry_transcript_59956-T1 62805-63016-terminal-2 is invalid.
-recovered CodingQuarry_transcript_59956-T1, terminal, 62805, 63016
-recovered CodingQuarry_transcript_59956-T1, terminal, 65935, 65959
-recovered CodingQuarry_transcript_59956-T1, internal, 62805, 63016
-recovered CodingQuarry_transcript_59956-T1, internal, 63205, 63306
-recovered CodingQuarry_transcript_59956-T1, internal, 63440, 63578
-recovered CodingQuarry_transcript_59956-T1, internal, 63735, 63822
Valid prediction for snap_scaffold_8-snap.3349-T1
Valid prediction for snap_scaffold_8-snap.3348-T1
Valid prediction for CodingQuarry_transcript_59959-T1
Valid prediction for pasa_asmbl_52502.p1
Valid prediction for snap_scaffold_8-snap.3331-T1
Valid prediction for GlimmerHMM_glimmerT_21337-T1
Valid prediction for Augustus_model.g14220.t1
Valid prediction for Augustus_model.g14210.t1
Valid prediction for snap_scaffold_8-snap.3355-T1
Valid prediction for snap_scaffold_8-snap.3327-T1
Valid prediction for GlimmerHMM_glimmerT_21342-T1
Valid prediction for snap_scaffold_8-snap.3345-T1
Valid prediction for GlimmerHMM_glimmerT_21324-T1
Valid prediction for Augustus_model.g14214.t1
Valid prediction for snap_scaffold_8-snap.3324-T1
Valid prediction for HiQ_model.g14217.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7929, rend_intergenic: 1796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17513, rend_intergenic: 11745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21450, rend_intergenic: 20508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25101, rend_intergenic: 21832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52515, rend_intergenic: 45537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60268, rend_intergenic: 52870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138741, rend_intergenic: 128815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253625
-exon list size: 467


building trellis

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91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 7929, rend_intergenic: 1796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17513, rend_intergenic: 11745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21450, rend_intergenic: 20508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25101, rend_intergenic: 21832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52515, rend_intergenic: 45537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60268, rend_intergenic: 52870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138741, rend_intergenic: 128815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17456
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-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 - 16089
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 2 predictions from path traversal
GOT 5prime partial gene.
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 - 10182
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

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