-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_7339385-7606203

-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.g28422.t1
Valid prediction for Augustus_model.g28421.t1
Valid prediction for snap_scaffold_18-snap.1557-T1
Valid prediction for CodingQuarry_transcript_23818-T1
Valid prediction for snap_scaffold_18-snap.1552-T1
Couldn't classify 118339, 118464
Sorry, prediction pasa_asmbl_20741.p1 fails validation.
(CAA)	 AG	118339-118464	GT	ACG
(TAT)	 AG	121061-121132	GT	GGG
(AAA)	 AG	122631-122717	GT	AGG
(AAC)	 AG	122937-123074	GT	TGG
(AAC)	 AG	123190-123387	CC	AAC
-recovered pasa_asmbl_20741.p1, terminal, 123190, 123387
-recovered pasa_asmbl_20741.p1, internal, 118339, 118464
-recovered pasa_asmbl_20741.p1, internal, 121061, 121132
-recovered pasa_asmbl_20741.p1, internal, 122631, 122717
-recovered pasa_asmbl_20741.p1, internal, 122937, 123074
Valid prediction for Augustus_model.g28414.t1
Valid prediction for pasa_asmbl_20747.p1
Valid prediction for Augustus_model.g28420.t1
Valid prediction for Augustus_model.g28419.t1
Valid prediction for GlimmerHMM_glimmerT_42632-T1
Valid prediction for Augustus_model.g28418.t1
Valid prediction for snap_scaffold_18-snap.1560-T1
Valid prediction for snap_scaffold_18-snap.1576-T1
Valid prediction for GlimmerHMM_glimmerT_42640-T1
Valid prediction for snap_scaffold_18-snap.1548-T1
Valid prediction for GlimmerHMM_glimmerT_42642-T1
Valid prediction for GlimmerHMM_glimmerT_42627-T1
Valid prediction for snap_scaffold_18-snap.1575-T1
Valid prediction for snap_scaffold_18-snap.1567-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g28426.t1
Valid prediction for snap_scaffold_18-snap.1578-T1
Valid prediction for GlimmerHMM_glimmerT_42623-T1
Valid prediction for snap_scaffold_18-snap.1572-T1
Valid prediction for GlimmerHMM_glimmerT_42629-T1
Valid prediction for snap_scaffold_18-snap.1566-T1
Valid prediction for GlimmerHMM_glimmerT_42647-T1
Valid prediction for snap_scaffold_18-snap.1554-T1
Valid prediction for snap_scaffold_18-snap.1571-T1
Valid prediction for GlimmerHMM_glimmerT_42638-T1
Valid prediction for HiQ_model.g28431.t1
Valid prediction for GlimmerHMM_glimmerT_42628-T1
Couldn't classify 73210, 73509
Sorry, prediction pasa_asmbl_20739.p1 fails validation.
(CCA)	 CG	73210-73509	AG	GGA
Valid prediction for snap_scaffold_18-snap.1574-T1
Valid prediction for GlimmerHMM_glimmerT_42624-T1
Valid prediction for Augustus_model.g28413.t1
Valid prediction for Augustus_model.g28425.t1
Valid prediction for snap_scaffold_18-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_42622-T1
Valid prediction for Augustus_model.g28416.t1
Valid prediction for GlimmerHMM_glimmerT_42625-T1
Valid prediction for GlimmerHMM_glimmerT_42633-T1
Valid prediction for Augustus_model.g28417.t1
Valid prediction for snap_scaffold_18-snap.1582-T1
Valid prediction for Augustus_model.g28424.t1
Valid prediction for CodingQuarry_transcript_23816-T1
Valid prediction for snap_scaffold_18-snap.1558-T1
Valid prediction for snap_scaffold_18-snap.1570-T1
Valid prediction for Augustus_model.g28439.t1
Valid prediction for snap_scaffold_18-snap.1549-T1
Valid prediction for Augustus_model.g28441.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 85005, 85093
Couldn't classify 86771, 86853
Sorry, prediction pasa_asmbl_19954.p1 fails validation.
(GGA)	 CA	85005-85093	GT	CGG
(AAA)	 AG	85269-85351	GT	AGG
(AAA)	 AG	85673-85768	GT	TGG
(ATG)	 AG	86771-86853	AG	GCA
-recovered pasa_asmbl_19954.p1, internal, 85269, 85351
-recovered pasa_asmbl_19954.p1, internal, 85673, 85768
Valid prediction for Augustus_model.g28435.t1
Valid prediction for snap_scaffold_18-snap.1577-T1
Valid prediction for GlimmerHMM_glimmerT_42635-T1
Valid prediction for GlimmerHMM_glimmerT_42626-T1
Valid prediction for GlimmerHMM_glimmerT_42641-T1
Valid prediction for GlimmerHMM_glimmerT_42644-T1
Valid prediction for GlimmerHMM_glimmerT_42634-T1
Valid prediction for snap_scaffold_18-snap.1586-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_42643-T1
Valid prediction for Augustus_model.g28440.t1
Couldn't classify 61596, 62108
Sorry, prediction pasa_asmbl_21076.p1 fails validation.
(GTC)	 TG	61596-62108	GA	ATG
Valid prediction for GlimmerHMM_glimmerT_42631-T1
Valid prediction for snap_scaffold_18-snap.1562-T1
Valid prediction for Augustus_model.g28430.t1
Valid prediction for snap_scaffold_18-snap.1590-T1
Couldn't classify 115169, 115480
Sorry, prediction pasa_asmbl_19940.p1 fails validation.
(CTC)	 AC	115169-115480	TA	AAT
Valid prediction for snap_scaffold_18-snap.1561-T1
Valid prediction for Augustus_model.g28432.t1
Valid prediction for Augustus_model.g28433.t1
Valid prediction for snap_scaffold_18-snap.1569-T1
Valid prediction for snap_scaffold_18-snap.1551-T1
Valid prediction for GlimmerHMM_glimmerT_42636-T1
Valid prediction for snap_scaffold_18-snap.1585-T1
Valid prediction for snap_scaffold_18-snap.1589-T1
Valid prediction for Augustus_model.g28438.t1
Valid prediction for Augustus_model.g28427.t1
Couldn't classify 98317, 98397
Couldn't classify 103241, 103366
Sorry, prediction pasa_asmbl_19945.p1 fails validation.
(CAC)	 CA	98317-98397	GT	GGG
(GTG)	 AG	98707-98832	GT	AGG
(GTG)	 AG	99382-99522	GT	AGG
(TTG)	 AG	99613-99738	GT	AGG
(CTG)	 AG	100017-100175	GT	TTG
(GTG)	 AG	101828-101956	GT	AGG
(CTG)	 AG	102158-102283	GT	GGG
(CTG)	 AG	102870-102995	GT	AGG
(GTG)	 AG	103241-103366	GT	AGG
-recovered pasa_asmbl_19945.p1, internal, 98707, 98832
-recovered pasa_asmbl_19945.p1, internal, 99382, 99522
-recovered pasa_asmbl_19945.p1, internal, 99613, 99738
-recovered pasa_asmbl_19945.p1, internal, 100017, 100175
-recovered pasa_asmbl_19945.p1, internal, 101828, 101956
-recovered pasa_asmbl_19945.p1, internal, 102158, 102283
-recovered pasa_asmbl_19945.p1, internal, 102870, 102995
-recovered pasa_asmbl_19945.p1, internal, 103241, 103366
Valid prediction for snap_scaffold_18-snap.1583-T1
Valid prediction for Augustus_model.g28436.t1
Valid prediction for snap_scaffold_18-snap.1588-T1
Valid prediction for snap_scaffold_18-snap.1556-T1
Valid prediction for snap_scaffold_18-snap.1584-T1
Valid prediction for Augustus_model.g28428.t1
Couldn't classify 96046, 96085
Sorry, prediction pasa_asmbl_19948.p1 fails validation.
(CTG)	 AA	96046-96085	GT	AGG
(GTT)	 AG	96257-96495	GT	AGG
(GTT)	 AG	96816-97022	CA	AGC
-recovered pasa_asmbl_19948.p1, terminal, 96816, 97022
-recovered pasa_asmbl_19948.p1, internal, 96257, 96495
Valid prediction for snap_scaffold_18-snap.1579-T1
Valid prediction for snap_scaffold_18-snap.1550-T1
Valid prediction for snap_scaffold_18-snap.1568-T1
Couldn't classify 106461, 106619
Sorry, prediction pasa_asmbl_19942.p1 fails validation.
(ACT)	 AA	106461-106619	GT	GGG
(GTG)	 AG	107759-107890	GT	AGG
(GTG)	 AG	108301-108426	GT	AGG
(GTG)	 AG	109981-110106	GT	GGG
(CTC)	 AG	112922-113089	AC	AAA
-recovered pasa_asmbl_19942.p1, terminal, 112922, 113089
-recovered pasa_asmbl_19942.p1, internal, 107759, 107890
-recovered pasa_asmbl_19942.p1, internal, 108301, 108426
-recovered pasa_asmbl_19942.p1, internal, 109981, 110106
Valid prediction for HiQ_model.g28434.t1
Valid prediction for GlimmerHMM_glimmerT_42646-T1
Valid prediction for snap_scaffold_18-snap.1559-T1
Valid prediction for HiQ_model.g28429.t1
Valid prediction for GlimmerHMM_glimmerT_42639-T1
Valid prediction for snap_scaffold_18-snap.1581-T1
Couldn't classify 95456, 95469
Sorry, prediction pasa_asmbl_19950.p1 fails validation.
(ATG)	 GG	94238-94375	GT	AGG
(CCT)	 AG	94738-94927	GT	AGG
(TCC)	 AG	95147-95344	GT	TGG
(AGT)	 AG	95456-95469	GG	GGG
-recovered pasa_asmbl_19950.p1, initial, 94238, 94375
-recovered pasa_asmbl_19950.p1, internal, 94738, 94927
-recovered pasa_asmbl_19950.p1, internal, 95147, 95344
Valid prediction for GlimmerHMM_glimmerT_42645-T1
Valid prediction for snap_scaffold_18-snap.1587-T1
Valid prediction for snap_scaffold_18-snap.1580-T1
Valid prediction for snap_scaffold_18-snap.1565-T1
Valid prediction for snap_scaffold_18-snap.1564-T1
Valid prediction for CodingQuarry_transcript_23817-T1
Valid prediction for GlimmerHMM_glimmerT_42637-T1
Valid prediction for snap_scaffold_18-snap.1555-T1
Valid prediction for GlimmerHMM_glimmerT_42630-T1
Valid prediction for Augustus_model.g28423.t1
Valid prediction for Augustus_model.g28415.t1
Valid prediction for snap_scaffold_18-snap.1553-T1
Valid prediction for snap_scaffold_18-snap.1573-T1
Valid prediction for Augustus_model.g28437.t1
Valid prediction for pasa_asmbl_19955.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16468, rend_intergenic: 12504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20550, rend_intergenic: 17524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21377, rend_intergenic: 21126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33090, rend_intergenic: 22133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65409, rend_intergenic: 59707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80599, rend_intergenic: 68977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108482, rend_intergenic: 99060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 266819
-exon list size: 355


building trellis

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27.7    
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28.3    
28.6    
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29.1    
29.4    
29.7    
30.0    
30.3    
30.5    
30.8    
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31.4    
31.7    
31.9    
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32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
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38.4    
38.7    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
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42.6    
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43.1    
43.4    
43.7    
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45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
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50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
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52.1    
52.4    
52.7    
52.9    
53.2    
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54.1    
54.3    
54.6    
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55.2    
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56.6    
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58.0    
58.3    
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63.6    
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64.1    
64.4    
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65.0    
65.3    
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65.8    
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83.2    
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84.0    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.1    
96.4    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 16468, rend_intergenic: 12504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20550, rend_intergenic: 17524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21377, rend_intergenic: 21126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33090, rend_intergenic: 22133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65409, rend_intergenic: 59707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80599, rend_intergenic: 68977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108482, rend_intergenic: 99060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support