-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_6109298-6365390

-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 HiQ_model.g29326.t1
Valid prediction for Augustus_model.g29313.t1
Valid prediction for GlimmerHMM_glimmerT_44236-T1
Valid prediction for Augustus_model.g29315.t1
Valid prediction for GlimmerHMM_glimmerT_44240-T1
Valid prediction for snap_scaffold_19-snap.1282-T1
Valid prediction for snap_scaffold_19-snap.1288-T1
Valid prediction for snap_scaffold_19-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_44231-T1
Valid prediction for Augustus_model.g29311.t1
Valid prediction for pasa_asmbl_21400.p1
Couldn't classify 59971, 60543
Sorry, prediction pasa_asmbl_21389.p1 fails validation.
(TTC)	 CC	59971-60543	CT	AAC
Valid prediction for snap_scaffold_19-snap.1273-T1
Couldn't classify 108798, 108840
Couldn't classify 112183, 112367
Sorry, prediction pasa_asmbl_21403.p2 fails validation.
(CTG)	 CC	108798-108840	GT	AGG
(GGG)	 AG	111617-111832	GT	AGG
(GGG)	 AG	112183-112367	CT	CAC
-recovered pasa_asmbl_21403.p2, internal, 111617, 111832
Valid prediction for snap_scaffold_19-snap.1267-T1
Valid prediction for snap_scaffold_19-snap.1285-T1
Valid prediction for Augustus_model.g29330.t1
Valid prediction for GlimmerHMM_glimmerT_44227-T1
Valid prediction for HiQ_model.g29327.t1
Valid prediction for snap_scaffold_19-snap.1284-T1
Valid prediction for snap_scaffold_19-snap.1295-T1
Valid prediction for snap_scaffold_19-snap.1286-T1
Valid prediction for snap_scaffold_19-snap.1289-T1
Valid prediction for snap_scaffold_19-snap.1266-T1
Valid prediction for GlimmerHMM_glimmerT_44228-T1
Valid prediction for CodingQuarry_transcript_25676-T1
Valid prediction for snap_scaffold_19-snap.1271-T1
Valid prediction for GlimmerHMM_glimmerT_44230-T1
Valid prediction for HiQ_model.g29323.t1
Valid prediction for snap_scaffold_19-snap.1291-T1
Valid prediction for snap_scaffold_19-snap.1290-T1
Valid prediction for snap_scaffold_19-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_44219-T1
Valid prediction for GlimmerHMM_glimmerT_44225-T1
Valid prediction for pasa_asmbl_21404.p1
Valid prediction for GlimmerHMM_glimmerT_44238-T1
Valid prediction for Augustus_model.g29322.t1
Valid prediction for CodingQuarry_transcript_25674-T1
Valid prediction for snap_scaffold_19-snap.1292-T1
Valid prediction for GlimmerHMM_glimmerT_44216-T1
Valid prediction for CodingQuarry_transcript_25675-T1
Valid prediction for snap_scaffold_19-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_44224-T1
Valid prediction for Augustus_model.g29325.t1
Valid prediction for HiQ_model.g29329.t1
Valid prediction for snap_scaffold_19-snap.1278-T1
Valid prediction for snap_scaffold_19-snap.1305-T1
Valid prediction for CodingQuarry_transcript_25679-T1
Valid prediction for GlimmerHMM_glimmerT_44223-T1
Valid prediction for Augustus_model.g29312.t1
Couldn't classify 74448, 74624
Sorry, prediction pasa_asmbl_21965.p1 fails validation.
(ATG)	 AG	72922-73230	GT	AGG
(GCC)	 AG	74193-74366	GT	AGG
(CTG)	 AG	74448-74624	AG	AGA
-recovered pasa_asmbl_21965.p1, initial, 72922, 73230
-recovered pasa_asmbl_21965.p1, internal, 72922, 73230
-recovered pasa_asmbl_21965.p1, internal, 74193, 74366
Valid prediction for pasa_asmbl_21920.p1
Valid prediction for snap_scaffold_19-snap.1272-T1
Valid prediction for CodingQuarry_transcript_25677-T1
Valid prediction for snap_scaffold_19-snap.1269-T1
Valid prediction for HiQ_model.g29321.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: -)Couldn't classify 222674, 222845
Couldn't classify 223056, 224164
Sorry, prediction pasa_asmbl_22192.p1 fails validation.
(CAG)	 CA	222674-222845	GT	AGG
(GTG)	 AG	223056-224164	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_44229-T1
Valid prediction for Augustus_model.g29316.t1
Valid prediction for snap_scaffold_19-snap.1299-T1
Couldn't classify 224291, 224986
Sorry, prediction pasa_asmbl_22191.p1 fails validation.
(GGT)	 TT	224291-224986	AC	AAA
Valid prediction for snap_scaffold_19-snap.1283-T1
Valid prediction for GlimmerHMM_glimmerT_44217-T1
Valid prediction for snap_scaffold_19-snap.1301-T1
Valid prediction for snap_scaffold_19-snap.1270-T1
Valid prediction for GlimmerHMM_glimmerT_44233-T1
Valid prediction for snap_scaffold_19-snap.1297-T1
Valid prediction for Augustus_model.g29336.t1
Valid prediction for GlimmerHMM_glimmerT_44220-T1
Valid prediction for GlimmerHMM_glimmerT_44237-T1
Valid prediction for Augustus_model.g29314.t1
Valid prediction for HiQ_model.g29328.t1
Valid prediction for GlimmerHMM_glimmerT_44226-T1
Valid prediction for snap_scaffold_19-snap.1300-T1
Valid prediction for snap_scaffold_19-snap.1302-T1
Valid prediction for Augustus_model.g29332.t1
Valid prediction for snap_scaffold_19-snap.1275-T1
Valid prediction for snap_scaffold_19-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_44239-T1
Valid prediction for snap_scaffold_19-snap.1294-T1
Valid prediction for snap_scaffold_19-snap.1268-T1
Valid prediction for Augustus_model.g29318.t1
Couldn't classify 123940, 124002
Sorry, prediction pasa_asmbl_22199.p1 fails validation.
(GAT)	 CA	123940-124002	GT	AGG
(TTC)	 AG	124362-124433	GT	AGG
(TTT)	 AG	124542-124640	GT	AAG
(GAC)	 AG	124788-124925	GT	GTG
(GCT)	 AG	125149-125265	GT	GAG
(ATT)	 AG	125475-125552	GT	CGG
(GCA)	 AG	126370-126520	GT	AGG
(ACG)	 AG	126607-126701	GT	AGG
(GAG)	 AG	127250-127321	TA	GAT
-recovered pasa_asmbl_22199.p1, terminal, 127250, 127321
-recovered pasa_asmbl_22199.p1, internal, 124362, 124433
-recovered pasa_asmbl_22199.p1, internal, 124542, 124640
-recovered pasa_asmbl_22199.p1, internal, 124788, 124925
-recovered pasa_asmbl_22199.p1, internal, 125149, 125265
-recovered pasa_asmbl_22199.p1, internal, 125475, 125552
-recovered pasa_asmbl_22199.p1, internal, 126370, 126520
-recovered pasa_asmbl_22199.p1, internal, 126607, 126701
Valid prediction for snap_scaffold_19-snap.1287-T1
Valid prediction for snap_scaffold_19-snap.1280-T1
Valid prediction for HiQ_model.g29334.t1
Valid prediction for CodingQuarry_transcript_25678-T1
Valid prediction for GlimmerHMM_glimmerT_44222-T1
Valid prediction for CodingQuarry_transcript_25680-T1
Valid prediction for pasa_asmbl_22189.p1
Valid prediction for snap_scaffold_19-snap.1281-T1
Valid prediction for snap_scaffold_19-snap.1304-T1
Valid prediction for CodingQuarry_transcript_25671-T1
Valid prediction for Augustus_model.g29335.t1
Valid prediction for Augustus_model.g29331.t1
Valid prediction for GlimmerHMM_glimmerT_44221-T1
Couldn't classify 149771, 149914
Sorry, prediction pasa_asmbl_22197.p1 fails validation.
(AGG)	 TC	149771-149914	GT	GGG
(TTT)	 AG	150036-150153	GT	AGG
(ACA)	 AG	150294-150437	GT	AGG
(ATG)	 AG	150623-150924	AG	GAA
add_exon() Sorry, pasa_asmbl_22197.p1 150036-150153-terminal-3 is invalid.
-recovered pasa_asmbl_22197.p1, terminal, 150036, 150153
-recovered pasa_asmbl_22197.p1, terminal, 150623, 150924
-recovered pasa_asmbl_22197.p1, internal, 150036, 150153
-recovered pasa_asmbl_22197.p1, internal, 150294, 150437
Valid prediction for snap_scaffold_19-snap.1306-T1
Valid prediction for snap_scaffold_19-snap.1277-T1
Valid prediction for Augustus_model.g29333.t1
Valid prediction for snap_scaffold_19-snap.1298-T1
Valid prediction for snap_scaffold_19-snap.1274-T1
Valid prediction for Augustus_model.g29324.t1
Valid prediction for snap_scaffold_19-snap.1276-T1
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_44235-T1
Valid prediction for GlimmerHMM_glimmerT_44234-T1
Valid prediction for HiQ_model.g29317.t1
Valid prediction for GlimmerHMM_glimmerT_44218-T1
Valid prediction for Augustus_model.g29319.t1
Valid prediction for GlimmerHMM_glimmerT_44232-T1
Valid prediction for Augustus_model.g29320.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15546, rend_intergenic: 8015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19415, rend_intergenic: 16251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60491, rend_intergenic: 59387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226260, rend_intergenic: 212727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256093
-exon list size: 417


building trellis

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29.6    
29.8    
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30.5    
30.8    
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32.9    
33.2    
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33.9    
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34.6    
34.8    
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35.6    
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36.0    
36.3    
36.5    
36.8    
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37.5    
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37.9    
38.2    
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38.7    
38.9    
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39.4    
39.6    
39.9    
40.1    
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40.6    
40.8    
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44.2    
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45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.5    
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48.4    
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49.6    
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50.6    
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51.6    
51.8    
52.0    
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52.7    
53.0    
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74.2    
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76.4    
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77.1    
77.3    
77.6    
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78.0    
78.3    
78.5    
78.8    
79.0    
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80.0    
80.2    
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81.1    
81.4    
81.6    
81.9    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
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84.0    
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87.4    
87.6    
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88.1    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.5    
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90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 15546, rend_intergenic: 8015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19415, rend_intergenic: 16251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60491, rend_intergenic: 59387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226260, rend_intergenic: 212727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support