-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_1721756-1857215

-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.g2194.t1
Valid prediction for snap_scaffold_2-snap.428-T1
Valid prediction for snap_scaffold_2-snap.411-T1
Valid prediction for Augustus_model.g2205.t1
Valid prediction for Augustus_model.g2196.t1
Valid prediction for GlimmerHMM_glimmerT_3263-T1
Valid prediction for Augustus_model.g2195.t1
Valid prediction for snap_scaffold_2-snap.416-T1
Valid prediction for Augustus_model.g2200.t1
Valid prediction for snap_scaffold_2-snap.407-T1
Valid prediction for snap_scaffold_2-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_3253-T1
Valid prediction for snap_scaffold_2-snap.409-T1
Valid prediction for snap_scaffold_2-snap.401-T1
Valid prediction for snap_scaffold_2-snap.420-T1
Valid prediction for GlimmerHMM_glimmerT_3256-T1
Valid prediction for snap_scaffold_2-snap.426-T1
Valid prediction for snap_scaffold_2-snap.414-T1
Valid prediction for snap_scaffold_2-snap.413-T1
Valid prediction for snap_scaffold_2-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_3254-T1
Couldn't classify 119127, 119245
Couldn't classify 126433, 126500
Sorry, prediction pasa_asmbl_24222.p1 fails validation.
(GCA)	 CA	119127-119245	GT	AGG
(GAT)	 AG	121763-121895	GT	AGG
(ATG)	 AG	123614-123758	GT	TGG
(CTT)	 AG	125062-125127	GT	AGG
(GTA)	 AG	125591-125680	GT	AGG
(ACA)	 AG	126065-126202	GT	AGG
(ATA)	 AG	126433-126500	TC	GCT
-recovered pasa_asmbl_24222.p1, initial, 123614, 123758
-recovered pasa_asmbl_24222.p1, internal, 121763, 121895
-recovered pasa_asmbl_24222.p1, internal, 123614, 123758
-recovered pasa_asmbl_24222.p1, internal, 125062, 125127
-recovered pasa_asmbl_24222.p1, internal, 125591, 125680
-recovered pasa_asmbl_24222.p1, internal, 126065, 126202
Couldn't classify 127430, 127553
Couldn't classify 128838, 128959
Sorry, prediction pasa_asmbl_24223.p1 fails validation.
(ATC)	 AC	127430-127553	GT	AGG
(ATA)	 AG	127775-127900	GT	CGG
(ACG)	 AG	128128-128247	GT	AGG
(ATA)	 AG	128345-128476	GT	GGG
(ACG)	 AG	128838-128959	AC	AGA
-recovered pasa_asmbl_24223.p1, internal, 127775, 127900
-recovered pasa_asmbl_24223.p1, internal, 128128, 128247
-recovered pasa_asmbl_24223.p1, internal, 128345, 128476
Valid prediction for Augustus_model.g2204.t1
Valid prediction for snap_scaffold_2-snap.432-T1
Valid prediction for GlimmerHMM_glimmerT_3269-T1
Valid prediction for GlimmerHMM_glimmerT_3255-T1
Valid prediction for snap_scaffold_2-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_3258-T1
Valid prediction for GlimmerHMM_glimmerT_3271-T1
Valid prediction for snap_scaffold_2-snap.410-T1
Valid prediction for snap_scaffold_2-snap.423-T1
Valid prediction for GlimmerHMM_glimmerT_3272-T1
Valid prediction for snap_scaffold_2-snap.405-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 73391, 73474
Couldn't classify 74156, 74267
Sorry, prediction pasa_asmbl_22870.p1 fails validation.
(CCA)	 CC	73391-73474	GT	TGG
(GTG)	 AG	73830-73954	GT	CGG
(GTC)	 AG	74156-74267	AA	GCA
-recovered pasa_asmbl_22870.p1, internal, 73830, 73954
Valid prediction for pasa_asmbl_22866.p1
Valid prediction for GlimmerHMM_glimmerT_3266-T1
Valid prediction for snap_scaffold_2-snap.400-T1
Valid prediction for HiQ_model.g2197.t1
Valid prediction for GlimmerHMM_glimmerT_3261-T1
Valid prediction for snap_scaffold_2-snap.429-T1
Valid prediction for GlimmerHMM_glimmerT_3259-T1
Valid prediction for GlimmerHMM_glimmerT_3260-T1
Valid prediction for Augustus_model.g2203.t1
Valid prediction for snap_scaffold_2-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_3270-T1
Valid prediction for Augustus_model.g2201.t1
Valid prediction for GlimmerHMM_glimmerT_3264-T1
Valid prediction for Augustus_model.g2198.t1
Valid prediction for snap_scaffold_2-snap.404-T1
Valid prediction for snap_scaffold_2-snap.424-T1
Valid prediction for GlimmerHMM_glimmerT_3257-T1
Valid prediction for Augustus_model.g2199.t1
Valid prediction for snap_scaffold_2-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_3265-T1
Valid prediction for CodingQuarry_transcript_28467-T1
Couldn't classify 86216, 86377
Couldn't classify 87955, 88190
Sorry, prediction pasa_asmbl_22869.p1 fails validation.
(GAG)	 GA	86216-86377	GT	TGG
(TGG)	 AG	86556-86849	GT	AGG
(GTG)	 AG	87315-87513	GT	AGG
(GAG)	 AG	87955-88190	CT	CCC
add_exon() Sorry, pasa_asmbl_22869.p1 87315-87513-terminal-3 is invalid.
-recovered pasa_asmbl_22869.p1, terminal, 87315, 87513
-recovered pasa_asmbl_22869.p1, internal, 86556, 86849
-recovered pasa_asmbl_22869.p1, internal, 87315, 87513
Valid prediction for snap_scaffold_2-snap.402-T1
Valid prediction for snap_scaffold_2-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_3262-T1
Couldn't classify 33930, 34001
Couldn't classify 34743, 34817
Sorry, prediction pasa_asmbl_24056.p1 fails validation.
(GTA)	 AA	33930-34001	GT	AGG
(CTG)	 AG	34086-34202	GT	AGG
(CCT)	 AG	34318-34395	GT	AGG
(GCA)	 AG	34743-34817	CT	AGC
-recovered pasa_asmbl_24056.p1, internal, 34086, 34202
-recovered pasa_asmbl_24056.p1, internal, 34318, 34395
Valid prediction for Augustus_model.g2202.t1
Valid prediction for GlimmerHMM_glimmerT_3268-T1
Valid prediction for snap_scaffold_2-snap.403-T1
Valid prediction for snap_scaffold_2-snap.433-T1
Valid prediction for GlimmerHMM_glimmerT_3267-T1
Valid prediction for snap_scaffold_2-snap.418-T1
Valid prediction for snap_scaffold_2-snap.427-T1
Valid prediction for snap_scaffold_2-snap.415-T1
Valid prediction for snap_scaffold_2-snap.406-T1
Valid prediction for snap_scaffold_2-snap.431-T1
Valid prediction for snap_scaffold_2-snap.408-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.430-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12595, rend_intergenic: 10140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25661, rend_intergenic: 12945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30122, rend_intergenic: 25759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67283, rend_intergenic: 40127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81997, rend_intergenic: 78059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91976, rend_intergenic: 87798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119635, rend_intergenic: 118726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131199, rend_intergenic: 121532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131847, rend_intergenic: 131206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133967, rend_intergenic: 132639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 135460
-exon list size: 325


building trellis

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40.7    
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43.4    
43.7    
44.0    
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44.6    
45.0    
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45.6    
45.9    
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46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
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52.6    
52.9    
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54.4    
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55.7    
56.0    
56.3    
56.6    
56.9    
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58.1    
58.4    
58.7    
59.0    
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59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
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63.0    
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63.6    
63.9    
64.2    
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67.0    
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69.1    
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69.7    
70.0    
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70.6    
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77.4    
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78.0    
78.3    
78.6    
78.9    
79.2    
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80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
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84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 12595, rend_intergenic: 10140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25661, rend_intergenic: 12945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30122, rend_intergenic: 25759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67283, rend_intergenic: 40127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81997, rend_intergenic: 78059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91976, rend_intergenic: 87798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119635, rend_intergenic: 118726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131199, rend_intergenic: 121532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131847, rend_intergenic: 131206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133967, rend_intergenic: 132639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11131
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 10139
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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