-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_12210186-12382168

-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.g19971.t1
Valid prediction for snap_scaffold_12-snap.2260-T1
Valid prediction for snap_scaffold_12-snap.2251-T1
Valid prediction for GlimmerHMM_glimmerT_30174-T1
Valid prediction for snap_scaffold_12-snap.2265-T1
Valid prediction for snap_scaffold_12-snap.2242-T1
Valid prediction for Augustus_model.g19964.t1
Valid prediction for GlimmerHMM_glimmerT_30155-T1
Valid prediction for pasa_asmbl_7985.p1
Valid prediction for snap_scaffold_12-snap.2250-T1
Valid prediction for CodingQuarry_transcript_10414-T1
Valid prediction for GlimmerHMM_glimmerT_30175-T1
Valid prediction for snap_scaffold_12-snap.2255-T1
Valid prediction for snap_scaffold_12-snap.2256-T1
Valid prediction for CodingQuarry_transcript_10419-T1
Valid prediction for snap_scaffold_12-snap.2235-T1
Valid prediction for snap_scaffold_12-snap.2237-T1
Valid prediction for snap_scaffold_12-snap.2268-T1
Valid prediction for Augustus_model.g19957.t1
Valid prediction for HiQ_model.g19972.t1
Valid prediction for Augustus_model.g19962.t1
Valid prediction for Augustus_model.g19956.t1
Valid prediction for snap_scaffold_12-snap.2238-T1
Valid prediction for snap_scaffold_12-snap.2249-T1
Valid prediction for snap_scaffold_12-snap.2229-T1
Valid prediction for snap_scaffold_12-snap.2257-T1
Valid prediction for snap_scaffold_12-snap.2252-T1
Valid prediction for Augustus_model.g19969.t1
Valid prediction for snap_scaffold_12-snap.2232-T1
Valid prediction for snap_scaffold_12-snap.2266-T1
Valid prediction for CodingQuarry_transcript_10420-T1
Valid prediction for Augustus_model.g19959.t1
Valid prediction for GlimmerHMM_glimmerT_30163-T1
Valid prediction for snap_scaffold_12-snap.2236-T1
Valid prediction for snap_scaffold_12-snap.2267-T1
Valid prediction for snap_scaffold_12-snap.2258-T1
Valid prediction for GlimmerHMM_glimmerT_30157-T1
Valid prediction for HiQ_model.g19965.t1
Valid prediction for CodingQuarry_transcript_10413-T1
Valid prediction for snap_scaffold_12-snap.2263-T1
Valid prediction for snap_scaffold_12-snap.2262-T1
Valid prediction for Augustus_model.g19960.t1
Valid prediction for CodingQuarry_transcript_10418-T1
Valid prediction for snap_scaffold_12-snap.2245-T1
Valid prediction for snap_scaffold_12-snap.2246-T1
Valid prediction for snap_scaffold_12-snap.2231-T1
Valid prediction for snap_scaffold_12-snap.2239-T1
Valid prediction for pasa_asmbl_7989.p1
Valid prediction for pasa_asmbl_7991.p1
Valid prediction for GlimmerHMM_glimmerT_30166-T1
Valid prediction for GlimmerHMM_glimmerT_30160-T1
Valid prediction for GlimmerHMM_glimmerT_30169-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_12-snap.2244-T1
Valid prediction for GlimmerHMM_glimmerT_30164-T1
Valid prediction for snap_scaffold_12-snap.2230-T1
Valid prediction for GlimmerHMM_glimmerT_30176-T1
Valid prediction for snap_scaffold_12-snap.2269-T1
Valid prediction for Augustus_model.g19963.t1
Couldn't classify 58427, 58478
Couldn't classify 59637, 59801
Sorry, prediction pasa_asmbl_8872.p1 fails validation.
(CCT)	 AG	58427-58478	GT	AGG
(CCG)	 AG	58760-59022	GT	AGG
(GTG)	 AG	59205-59528	GT	AGG
(GAT)	 AG	59637-59801	CC	CCC
-recovered pasa_asmbl_8872.p1, internal, 58427, 58478
-recovered pasa_asmbl_8872.p1, internal, 58760, 59022
-recovered pasa_asmbl_8872.p1, internal, 59205, 59528
Valid prediction for snap_scaffold_12-snap.2233-T1
Valid prediction for GlimmerHMM_glimmerT_30167-T1
Valid prediction for CodingQuarry_transcript_10416-T1
Valid prediction for Augustus_model.g19973.t1
Valid prediction for snap_scaffold_12-snap.2261-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_30177-T1
Valid prediction for GlimmerHMM_glimmerT_30170-T1
Valid prediction for HiQ_model.g19970.t1
Valid prediction for Augustus_model.g19974.t1
Valid prediction for snap_scaffold_12-snap.2234-T1
Valid prediction for Augustus_model.g19968.t1
Couldn't classify 66102, 66455
Couldn't classify 67280, 67530
Sorry, prediction pasa_asmbl_8870.p1 fails validation.
(TCT)	 TC	66102-66455	GT	AGG
(GGA)	 AG	66563-66740	GT	AGG
(CTC)	 AG	67001-67126	GT	CGG
(GTG)	 AG	67280-67530	GG	CTG
add_exon() Sorry, pasa_asmbl_8870.p1 66563-66740-terminal-3 is invalid.
-recovered pasa_asmbl_8870.p1, terminal, 66563, 66740
-recovered pasa_asmbl_8870.p1, internal, 66563, 66740
-recovered pasa_asmbl_8870.p1, internal, 67001, 67126
Valid prediction for CodingQuarry_transcript_10417-T1
Valid prediction for GlimmerHMM_glimmerT_30165-T1
Valid prediction for GlimmerHMM_glimmerT_30158-T1
Valid prediction for GlimmerHMM_glimmerT_30171-T1
Valid prediction for Augustus_model.g19955.t1
Valid prediction for GlimmerHMM_glimmerT_30173-T1
Couldn't classify 96493, 96544
Sorry, prediction pasa_asmbl_8851.p1 fails validation.
(CAC)	 GT	96493-96544	GT	CGG
(CCT)	 AG	96702-96948	GT	AGG
(GGG)	 AG	97346-97526	GT	GAG
(GAG)	 AG	97622-97742	GT	AGG
(ACT)	 AG	98885-99000	GT	CTG
(CTC)	 AG	99357-99443	AA	GAA
-recovered pasa_asmbl_8851.p1, terminal, 96702, 96948
-recovered pasa_asmbl_8851.p1, terminal, 99357, 99443
-recovered pasa_asmbl_8851.p1, internal, 96702, 96948
-recovered pasa_asmbl_8851.p1, internal, 97346, 97526
-recovered pasa_asmbl_8851.p1, internal, 97622, 97742
-recovered pasa_asmbl_8851.p1, internal, 98885, 99000
Valid prediction for snap_scaffold_12-snap.2241-T1
Couldn't classify 54766, 54863
Couldn't classify 57356, 57459
Sorry, prediction pasa_asmbl_9212.p1 fails validation.
(AGG)	 GG	54766-54863	GT	AAG
(TCT)	 AG	55374-55536	GT	AGG
(GTG)	 AG	55663-55810	GT	GGG
(GAA)	 AG	55921-56154	GT	AGG
(GTC)	 AG	56256-56350	GT	TGG
(GAC)	 AG	56623-56778	GT	AGG
(GTG)	 AG	56879-56960	GT	GGG
(GAG)	 AG	57052-57243	GT	AGG
(GGG)	 AG	57356-57459	AA	CCA
-recovered pasa_asmbl_9212.p1, internal, 55374, 55536
-recovered pasa_asmbl_9212.p1, internal, 55663, 55810
-recovered pasa_asmbl_9212.p1, internal, 55921, 56154
-recovered pasa_asmbl_9212.p1, internal, 56256, 56350
-recovered pasa_asmbl_9212.p1, internal, 56623, 56778
-recovered pasa_asmbl_9212.p1, internal, 56879, 56960
-recovered pasa_asmbl_9212.p1, internal, 57052, 57243
Valid prediction for snap_scaffold_12-snap.2253-T1
Valid prediction for pasa_asmbl_8869.p1
Valid prediction for GlimmerHMM_glimmerT_30161-T1
Valid prediction for snap_scaffold_12-snap.2243-T1
Valid prediction for snap_scaffold_12-snap.2264-T1
Valid prediction for snap_scaffold_12-snap.2259-T1
Valid prediction for CodingQuarry_transcript_10411-T1
Valid prediction for CodingQuarry_transcript_10415-T1
Valid prediction for GlimmerHMM_glimmerT_30162-T1
Valid prediction for GlimmerHMM_glimmerT_30156-T1
Valid prediction for GlimmerHMM_glimmerT_30159-T1
Valid prediction for pasa_asmbl_8859.p1
Valid prediction for CodingQuarry_transcript_10412-T1
Valid prediction for snap_scaffold_12-snap.2254-T1
Valid prediction for GlimmerHMM_glimmerT_30168-T1
Valid prediction for snap_scaffold_12-snap.2248-T1
Valid prediction for Augustus_model.g19961.t1
Valid prediction for snap_scaffold_12-snap.2240-T1
Valid prediction for Augustus_model.g19958.t1
Valid prediction for CodingQuarry_transcript_10409-T1
Valid prediction for Augustus_model.g19967.t1
Couldn't classify 60516, 60576
Couldn't classify 64895, 65924
Sorry, prediction pasa_asmbl_8871.p1 fails validation.
(GAG)	 AT	60516-60576	GT	GGG
(GCT)	 AG	60704-60849	GT	AGG
(GTG)	 AG	61070-61212	GT	AGG
(GAC)	 AG	61378-61591	GT	AGG
(ACT)	 AG	61898-62073	GT	AGG
(GGG)	 AG	62198-62360	GT	AGG
(GGT)	 AG	62678-62773	GT	AGG
(GAG)	 AG	62896-63012	GT	AGG
(TCC)	 AG	63172-63340	GT	AGG
(AAG)	 AG	63474-63670	GT	AGG
(GTG)	 AG	63886-64244	GT	AAG
(GGT)	 AG	64356-64508	GT	AGG
(GTC)	 AG	64640-64789	GT	AGG
(AGG)	 AG	64895-65924	CC	CCC
-recovered pasa_asmbl_8871.p1, internal, 60704, 60849
-recovered pasa_asmbl_8871.p1, internal, 61070, 61212
-recovered pasa_asmbl_8871.p1, internal, 61378, 61591
-recovered pasa_asmbl_8871.p1, internal, 61898, 62073
-recovered pasa_asmbl_8871.p1, internal, 62198, 62360
-recovered pasa_asmbl_8871.p1, internal, 62678, 62773
-recovered pasa_asmbl_8871.p1, internal, 62896, 63012
-recovered pasa_asmbl_8871.p1, internal, 63172, 63340
-recovered pasa_asmbl_8871.p1, internal, 63474, 63670
-recovered pasa_asmbl_8871.p1, internal, 63886, 64244
-recovered pasa_asmbl_8871.p1, internal, 64356, 64508
-recovered pasa_asmbl_8871.p1, internal, 64640, 64789
Valid prediction for GlimmerHMM_glimmerT_30172-T1
Valid prediction for HiQ_model.g19966.t1
Valid prediction for snap_scaffold_12-snap.2247-T1
Couldn't classify 36414, 36720
Sorry, prediction pasa_asmbl_8874.p1 fails validation.
(GCT)	 TG	36414-36720	GT	AGG
(ATG)	 AG	37208-37390	GT	AGG
(CTA)	 AG	37547-37664	GT	AAG
(GAC)	 AG	37825-37926	GT	AGG
(TGA)	 AG	38144-38267	GT	AGG
(GTG)	 AG	38531-38592	GT	GAG
(TGA)	 AG	38751-38886	GT	AGG
(CTC)	 AG	38977-39078	GT	AGG
(GCA)	 AG	39163-39279	GT	AGG
(GAG)	 AG	39381-39548	GT	AGG
(GAC)	 AG	39629-39726	GT	AGG
(GTT)	 AG	39813-39932	GT	AGG
(GCT)	 AG	40005-40134	GT	CGG
(GAG)	 AG	40229-40323	GT	CAG
(GTC)	 AG	40429-40477	GT	AGG
(GGC)	 AG	40581-40658	GT	AGG
(CAC)	 AG	40770-40910	CA	GAC
add_exon() Sorry, pasa_asmbl_8874.p1 37208-37390-initial-1 is invalid.
-recovered pasa_asmbl_8874.p1, initial, 37208, 37390
-recovered pasa_asmbl_8874.p1, terminal, 40770, 40910
-recovered pasa_asmbl_8874.p1, internal, 37208, 37390
-recovered pasa_asmbl_8874.p1, internal, 37547, 37664
-recovered pasa_asmbl_8874.p1, internal, 37825, 37926
-recovered pasa_asmbl_8874.p1, internal, 38144, 38267
-recovered pasa_asmbl_8874.p1, internal, 38531, 38592
-recovered pasa_asmbl_8874.p1, internal, 38751, 38886
-recovered pasa_asmbl_8874.p1, internal, 38977, 39078
-recovered pasa_asmbl_8874.p1, internal, 39163, 39279
-recovered pasa_asmbl_8874.p1, internal, 39381, 39548
-recovered pasa_asmbl_8874.p1, internal, 39629, 39726
-recovered pasa_asmbl_8874.p1, internal, 39813, 39932
-recovered pasa_asmbl_8874.p1, internal, 40005, 40134
-recovered pasa_asmbl_8874.p1, internal, 40229, 40323
-recovered pasa_asmbl_8874.p1, internal, 40429, 40477
-recovered pasa_asmbl_8874.p1, internal, 40581, 40658

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26087, rend_intergenic: 22327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42915, rend_intergenic: 38851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50765, rend_intergenic: 46429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59549, rend_intergenic: 50949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66953, rend_intergenic: 62531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92325, rend_intergenic: 77454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120635, rend_intergenic: 102690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135573, rend_intergenic: 131633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157565, rend_intergenic: 141536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171983
-exon list size: 413


building trellis

0.2    
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1.0    
1.2    
1.4    
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13.5    
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14.5    
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14.9    
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15.9    
16.1    
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17.6    
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24.6    
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25.5    
25.8    
26.0    
26.3    
26.5    
26.7    
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27.5    
27.7    
28.0    
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28.9    
29.2    
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29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.6    
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32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
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34.5    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.1    
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36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
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41.4    
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41.9    
42.2    
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42.7    
42.9    
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43.6    
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44.6    
44.8    
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47.0    
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48.0    
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97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 26087, rend_intergenic: 22327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42915, rend_intergenic: 38851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50765, rend_intergenic: 46429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59549, rend_intergenic: 50949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66953, rend_intergenic: 62531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92325, rend_intergenic: 77454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120635, rend_intergenic: 102690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135573, rend_intergenic: 131633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157565, rend_intergenic: 141536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support