-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_7638439-7740065

-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 GlimmerHMM_glimmerT_54522-T1
Valid prediction for snap_scaffold_25-snap.1661-T1
Valid prediction for snap_scaffold_25-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_54536-T1
Valid prediction for Augustus_model.g36184.t1
Valid prediction for snap_scaffold_25-snap.1649-T1
Valid prediction for snap_scaffold_25-snap.1657-T1
Valid prediction for GlimmerHMM_glimmerT_54526-T1
Valid prediction for Augustus_model.g36177.t1
Valid prediction for snap_scaffold_25-snap.1660-T1
Valid prediction for snap_scaffold_25-snap.1668-T1
Valid prediction for snap_scaffold_25-snap.1655-T1
Valid prediction for GlimmerHMM_glimmerT_54528-T1
Valid prediction for GlimmerHMM_glimmerT_54534-T1
Valid prediction for HiQ_model.g36178.t1
Couldn't classify 95795, 95910
Sorry, prediction pasa_asmbl_33676.p1 fails validation.
(TTG)	 AC	95795-95910	GT	ACG
(TCT)	 AG	96045-96135	GT	CGG
(AAA)	 AG	96724-96769	GT	AGG
(AGG)	 AG	96863-96971	GT	AGG
(TGG)	 AG	97183-97290	GT	AGG
(GCT)	 AG	97633-97743	GT	AGG
(GAA)	 AG	97880-97957	GT	AGG
(GTT)	 AG	98167-98352	GT	AGG
(GGC)	 AG	98589-98694	TC	AGT
-recovered pasa_asmbl_33676.p1, terminal, 98589, 98694
-recovered pasa_asmbl_33676.p1, internal, 96045, 96135
-recovered pasa_asmbl_33676.p1, internal, 96724, 96769
-recovered pasa_asmbl_33676.p1, internal, 96863, 96971
-recovered pasa_asmbl_33676.p1, internal, 97183, 97290
-recovered pasa_asmbl_33676.p1, internal, 97633, 97743
-recovered pasa_asmbl_33676.p1, internal, 97880, 97957
-recovered pasa_asmbl_33676.p1, internal, 98167, 98352
Valid prediction for GlimmerHMM_glimmerT_54537-T1
Valid prediction for GlimmerHMM_glimmerT_54529-T1
Valid prediction for snap_scaffold_25-snap.1664-T1
Valid prediction for Augustus_model.g36188.t1
Valid prediction for snap_scaffold_25-snap.1650-T1
Valid prediction for snap_scaffold_25-snap.1644-T1
Valid prediction for snap_scaffold_25-snap.1647-T1
Valid prediction for pasa_asmbl_33675.p1
Valid prediction for snap_scaffold_25-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_54543-T1
Valid prediction for snap_scaffold_25-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_54538-T1
Valid prediction for snap_scaffold_25-snap.1665-T1
Valid prediction for CodingQuarry_transcript_38787-T1
Valid prediction for CodingQuarry_transcript_38790-T1
Valid prediction for Augustus_model.g36181.t1
Valid prediction for GlimmerHMM_glimmerT_54525-T1
Valid prediction for snap_scaffold_25-snap.1670-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_25-snap.1651-T1
Valid prediction for CodingQuarry_transcript_38789-T1
Valid prediction for snap_scaffold_25-snap.1652-T1
Couldn't classify 37892, 38419
Sorry, prediction pasa_asmbl_34404.p2 fails validation.
(GAG)	 AT	37892-38419	GG	GAG
Couldn't classify 7775, 7857
Sorry, prediction pasa_asmbl_34405.p1 fails validation.
(AGT)	 GA	7775-7857	GT	GAG
(CAT)	 AG	8363-8637	GT	AGG
(GAG)	 AG	8903-8979	GT	AGG
(GTG)	 AG	9299-9551	GT	TGG
(GCC)	 AG	9734-10038	GA	AAG
-recovered pasa_asmbl_34405.p1, terminal, 9734, 10038
-recovered pasa_asmbl_34405.p1, internal, 8363, 8637
-recovered pasa_asmbl_34405.p1, internal, 8903, 8979
-recovered pasa_asmbl_34405.p1, internal, 9299, 9551
Valid prediction for pasa_asmbl_34402.p1
Valid prediction for snap_scaffold_25-snap.1658-T1
Valid prediction for snap_scaffold_25-snap.1662-T1
Valid prediction for pasa_asmbl_34597.p1
Valid prediction for GlimmerHMM_glimmerT_54523-T1
Valid prediction for Augustus_model.g36180.t1
Valid prediction for GlimmerHMM_glimmerT_54539-T1
Valid prediction for GlimmerHMM_glimmerT_54535-T1
Valid prediction for GlimmerHMM_glimmerT_54541-T1
Valid prediction for GlimmerHMM_glimmerT_54542-T1
Valid prediction for snap_scaffold_25-snap.1663-T1
Valid prediction for snap_scaffold_25-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_54527-T1
Valid prediction for CodingQuarry_transcript_38788-T1
Valid prediction for snap_scaffold_25-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_54530-T1
Valid prediction for HiQ_model.g36179.t1
Valid prediction for snap_scaffold_25-snap.1648-T1
Valid prediction for snap_scaffold_25-snap.1653-T1
Valid prediction for GlimmerHMM_glimmerT_54540-T1
Valid prediction for Augustus_model.g36185.t1
Valid prediction for snap_scaffold_25-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_54524-T1
Valid prediction for Augustus_model.g36183.t1
Valid prediction for snap_scaffold_25-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_54533-T1
Valid prediction for Augustus_model.g36187.t1
Valid prediction for snap_scaffold_25-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_54531-T1
Valid prediction for snap_scaffold_25-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_54532-T1
Valid prediction for Augustus_model.g36186.t1
Valid prediction for Augustus_model.g36182.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 31670, rend_intergenic: 31667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 60827, rend_intergenic: 60824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6313, rend_intergenic: 2357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13641, rend_intergenic: 9121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52816, rend_intergenic: 49743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53124, rend_intergenic: 52956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66356, rend_intergenic: 53403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68988, rend_intergenic: 66882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83582, rend_intergenic: 77872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98694, rend_intergenic: 94331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 101627
-exon list size: 216


building trellis

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33.0    
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39.0    
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39.9    
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45.0    
45.4    
45.9    
46.3    
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47.2    
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48.2    
48.6    
49.1    
49.5    
50.0    
50.5    
50.9    
51.4    
51.8    
52.3    
52.8    
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54.6    
55.0    
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56.4    
56.9    
57.3    
57.8    
58.3    
58.7    
59.2    
59.6    
60.1    
60.6    
61.0    
61.5    
61.9    
62.4    
62.8    
63.3    
63.8    
64.2    
64.7    
65.1    
65.6    
66.1    
66.5    
67.0    
67.4    
67.9    
68.3    
68.8    
69.3    
69.7    
70.2    
70.6    
71.1    
71.6    
72.0    
72.5    
72.9    
73.4    
73.9    
74.3    
74.8    
75.2    
75.7    
76.1    
76.6    
77.1    
77.5    
78.0    
78.4    
78.9    
79.4    
79.8    
80.3    
80.7    
81.2    
81.7    
82.1    
82.6    
83.0    
83.5    
83.9    
84.4    
84.9    
85.3    
85.8    
86.2    
86.7    
87.2    
87.6    
88.1    
88.5    
89.0    
89.4    
89.9    
90.4    
90.8    
91.3    
91.7    
92.2    
92.7    
93.1    
93.6    
94.0    
94.5    
95.0    
95.4    
95.9    
96.3    
96.8    
97.2    
97.7    
98.2    
98.6    
99.1    
99.5    
-found 20 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 31670, rend_intergenic: 31667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 60827, rend_intergenic: 60824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6313, rend_intergenic: 2357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13641, rend_intergenic: 9121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52816, rend_intergenic: 49743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53124, rend_intergenic: 52956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66356, rend_intergenic: 53403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68988, rend_intergenic: 66882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83582, rend_intergenic: 77872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98694, rend_intergenic: 94331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support