-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_7142588-7312339

-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 GeneMark_model.59738_t
Valid prediction for GeneMark_model.59746_t
Valid prediction for snap_scaffold_14-snap.1513-T1
Valid prediction for CodingQuarry_transcript_15657-T1
Valid prediction for snap_scaffold_14-snap.1512-T1
Valid prediction for GlimmerHMM_glimmerT_34888-T1
Valid prediction for HiQ_model.g23459.t1
Couldn't classify 48194, 48230
Sorry, prediction pasa_asmbl_12108.p1 fails validation.
(GTA)	 CT	48194-48230	GT	CGG
(GTA)	 AG	48497-48603	GT	AGG
(GTG)	 AG	48736-48855	GT	GGG
(GGA)	 AG	49062-49214	AT	AGA
-recovered pasa_asmbl_12108.p1, terminal, 49062, 49214
-recovered pasa_asmbl_12108.p1, internal, 48497, 48603
-recovered pasa_asmbl_12108.p1, internal, 48736, 48855
Valid prediction for GeneMark_model.59736_t
Couldn't classify 101808, 101914
Sorry, prediction pasa_asmbl_12734.p1 fails validation.
(ATG)	 GT	96760-96988	GT	CGG
(CCT)	 AG	99327-99494	GT	AGG
(TCA)	 AG	99738-99874	GT	AGG
(GGT)	 AG	99966-100009	GT	AGG
(ACC)	 AG	100139-100238	GT	AAG
(GTG)	 AG	100330-100410	GT	AGG
(GTC)	 AG	100649-100748	GT	CAG
(ACC)	 AG	100851-100899	GT	AGG
(GAC)	 AG	101001-101340	GT	AGG
(GGG)	 AG	101525-101621	GT	AGG
(ACC)	 AG	101808-101914	GT	AGG
-recovered pasa_asmbl_12734.p1, initial, 96760, 96988
-recovered pasa_asmbl_12734.p1, internal, 99327, 99494
-recovered pasa_asmbl_12734.p1, internal, 99738, 99874
-recovered pasa_asmbl_12734.p1, internal, 99966, 100009
-recovered pasa_asmbl_12734.p1, internal, 100139, 100238
-recovered pasa_asmbl_12734.p1, internal, 100330, 100410
-recovered pasa_asmbl_12734.p1, internal, 100649, 100748
-recovered pasa_asmbl_12734.p1, internal, 100851, 100899
-recovered pasa_asmbl_12734.p1, internal, 101001, 101340
-recovered pasa_asmbl_12734.p1, internal, 101525, 101621
-recovered pasa_asmbl_12734.p1, internal, 101808, 101914
Valid prediction for GlimmerHMM_glimmerT_34895-T1
Valid prediction for GeneMark_model.59749_t
Valid prediction for Augustus_model.g23455.t1
Valid prediction for GeneMark_model.59743_t
Valid prediction for snap_scaffold_14-snap.1515-T1
Couldn't classify 105581, 105701
Sorry, prediction pasa_asmbl_12117.p1 fails validation.
(CCT)	 AG	105581-105701	GT	TGG
(GTT)	 AG	106115-106194	GT	AAG
(TCG)	 AG	106355-106588	GT	TGG
(GTG)	 AG	106790-106909	CC	GAC
-recovered pasa_asmbl_12117.p1, terminal, 106790, 106909
-recovered pasa_asmbl_12117.p1, internal, 105581, 105701
-recovered pasa_asmbl_12117.p1, internal, 106115, 106194
-recovered pasa_asmbl_12117.p1, internal, 106355, 106588
Valid prediction for snap_scaffold_14-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_34889-T1
Valid prediction for pasa_asmbl_12122.p1
Valid prediction for GeneMark_model.59732_t
Valid prediction for snap_scaffold_14-snap.1492-T1
Valid prediction for GeneMark_model.59768_t
Valid prediction for GlimmerHMM_glimmerT_34904-T1
Valid prediction for Augustus_model.g23460.t1
Valid prediction for snap_scaffold_14-snap.1505-T1
Valid prediction for snap_scaffold_14-snap.1501-T1
Valid prediction for Augustus_model.g23472.t1
Valid prediction for snap_scaffold_14-snap.1519-T1
Valid prediction for HiQ_model.g23469.t1
Valid prediction for GeneMark_model.59747_t
Valid prediction for pasa_asmbl_12112.p1
Valid prediction for snap_scaffold_14-snap.1523-T1
Valid prediction for snap_scaffold_14-snap.1495-T1
Valid prediction for GeneMark_model.59751_t
Valid prediction for GeneMark_model.59753_t
Valid prediction for pasa_asmbl_12124.p1
Valid prediction for GeneMark_model.59762_t
Valid prediction for GlimmerHMM_glimmerT_34903-T1
Valid prediction for snap_scaffold_14-snap.1522-T1
Valid prediction for CodingQuarry_transcript_15656-T1
Valid prediction for HiQ_model.g23464.t1
Valid prediction for Augustus_model.g23456.t1
Couldn't classify 66952, 67000
Sorry, prediction pasa_asmbl_12111.p2 fails validation.
(CCA)	 CC	66952-67000	GT	AGG
(ACC)	 AG	67670-67741	GT	AGG
(CTG)	 AG	68055-68187	GT	AAG
(GCT)	 AG	69004-69113	GT	TGG
(AGT)	 AG	69400-69425	GA	AAG
-recovered pasa_asmbl_12111.p2, terminal, 69400, 69425
-recovered pasa_asmbl_12111.p2, internal, 67670, 67741
-recovered pasa_asmbl_12111.p2, internal, 68055, 68187
-recovered pasa_asmbl_12111.p2, internal, 69004, 69113
Valid prediction for GlimmerHMM_glimmerT_34900-T1
Valid prediction for CodingQuarry_transcript_15650-T1
Valid prediction for GeneMark_model.59756_t
Valid prediction for GeneMark_model.59759_t
Valid prediction for Augustus_model.g23458.t1
Valid prediction for GlimmerHMM_glimmerT_34896-T1
Valid prediction for GeneMark_model.59745_t
Valid prediction for GeneMark_model.59741_t
Couldn't classify 44948, 44965
Couldn't classify 47094, 47129
Sorry, prediction pasa_asmbl_12107.p1 fails validation.
(GAA)	 AC	44948-44965	GT	AGG
(TCT)	 AG	45091-45246	GT	AGG
(TAC)	 AG	45372-45521	GT	GGG
(CTG)	 AG	45607-45764	GT	ATG
(GTT)	 AG	46039-46166	GT	GGG
(GTC)	 AG	46346-46448	GT	AGG
(GGG)	 AG	46614-46710	GT	GGG
(GTG)	 AG	47094-47129	GG	GAG
-recovered pasa_asmbl_12107.p1, internal, 45091, 45246
-recovered pasa_asmbl_12107.p1, internal, 45372, 45521
-recovered pasa_asmbl_12107.p1, internal, 45607, 45764
-recovered pasa_asmbl_12107.p1, internal, 46039, 46166
-recovered pasa_asmbl_12107.p1, internal, 46346, 46448
-recovered pasa_asmbl_12107.p1, internal, 46614, 46710
Valid prediction for GlimmerHMM_glimmerT_34894-T1
Valid prediction for GlimmerHMM_glimmerT_34909-T1
Valid prediction for snap_scaffold_14-snap.1514-T1
Valid prediction for GlimmerHMM_glimmerT_34902-T1
Valid prediction for GlimmerHMM_glimmerT_34893-T1
Valid prediction for snap_scaffold_14-snap.1488-T1
Valid prediction for snap_scaffold_14-snap.1494-T1
Valid prediction for GeneMark_model.59748_t
Valid prediction for snap_scaffold_14-snap.1490-T1
Valid prediction for GeneMark_model.59767_t
Couldn't classify 114675, 114994
Couldn't classify 115136, 115244
Sorry, prediction pasa_asmbl_12119.p1 fails validation.
(GAG)	 GG	114675-114994	GT	AGG
(CAG)	 AG	115136-115244	AG	AGA
Valid prediction for Augustus_model.g23454.t1
Valid prediction for Augustus_model.g23467.t1
Valid prediction for HiQ_model.g23466.t1
Valid prediction for GeneMark_model.59755_t
Valid prediction for GeneMark_model.59739_t
Valid prediction for pasa_asmbl_12110.p2
Valid prediction for snap_scaffold_14-snap.1525-T1
Valid prediction for snap_scaffold_14-snap.1502-T1
Valid prediction for snap_scaffold_14-snap.1508-T1
Valid prediction for GeneMark_model.59742_t
Valid prediction for pasa_asmbl_12132.p1
Valid prediction for snap_scaffold_14-snap.1507-T1
Valid prediction for CodingQuarry_transcript_15648-T1
Valid prediction for CodingQuarry_transcript_15649-T1
Valid prediction for snap_scaffold_14-snap.1489-T1
Valid prediction for GlimmerHMM_glimmerT_34885-T1
Valid prediction for GlimmerHMM_glimmerT_34906-T1
Valid prediction for pasa_asmbl_12116.p1
Valid prediction for GlimmerHMM_glimmerT_34910-T1
Valid prediction for snap_scaffold_14-snap.1497-T1
Valid prediction for snap_scaffold_14-snap.1493-T1
Valid prediction for Augustus_model.g23452.t1
Valid prediction for HiQ_model.g23462.t1
Valid prediction for CodingQuarry_transcript_15655-T1
Valid prediction for GeneMark_model.59764_t
Valid prediction for GeneMark_model.59758_t
Valid prediction for GlimmerHMM_glimmerT_34890-T1
Valid prediction for snap_scaffold_14-snap.1517-T1
Valid prediction for GeneMark_model.59735_t
Valid prediction for snap_scaffold_14-snap.1503-T1
Valid prediction for CodingQuarry_transcript_15652-T1
Valid prediction for Augustus_model.g23461.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_14-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_34886-T1
Valid prediction for snap_scaffold_14-snap.1511-T1
Valid prediction for GeneMark_model.59757_t
Valid prediction for GlimmerHMM_glimmerT_34908-T1
Valid prediction for snap_scaffold_14-snap.1499-T1
Valid prediction for HiQ_model.g23470.t1
Valid prediction for CodingQuarry_transcript_15651-T1
Valid prediction for snap_scaffold_14-snap.1524-T1
Couldn't classify 76956, 77329
Sorry, prediction pasa_asmbl_13164.p1 fails validation.
(TTT)	 TA	76956-77329	GT	AGG
(CAA)	 AG	77520-77687	GT	GTG
(GCC)	 AG	77857-77957	GT	TGG
(CCC)	 AG	78074-78243	GT	CTG
(GTA)	 AG	78514-78657	GC	GAG
-recovered pasa_asmbl_13164.p1, terminal, 78514, 78657
-recovered pasa_asmbl_13164.p1, internal, 77520, 77687
-recovered pasa_asmbl_13164.p1, internal, 77857, 77957
-recovered pasa_asmbl_13164.p1, internal, 78074, 78243
-recovered pasa_asmbl_13164.p1, internal, 78514, 78657
Valid prediction for snap_scaffold_14-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_34891-T1
Valid prediction for GeneMark_model.59761_t
Valid prediction for CodingQuarry_transcript_15653-T1
Valid prediction for snap_scaffold_14-snap.1521-T1
Valid prediction for Augustus_model.g23468.t1
Valid prediction for GeneMark_model.59750_t
Valid prediction for Augustus_model.g23453.t1
Valid prediction for GeneMark_model.59734_t
Valid prediction for snap_scaffold_14-snap.1516-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_34899-T1
Valid prediction for GlimmerHMM_glimmerT_34907-T1
Couldn't classify 41046, 41123
Sorry, prediction pasa_asmbl_13168.p1 fails validation.
(GAG)	 CC	41046-41123	GT	AGG
(CGG)	 AG	41276-41340	GT	AGG
(TAA)	 AG	41509-41575	GT	AGG
(GGG)	 AG	41734-41852	GT	CGG
(AGA)	 AG	44001-44081	GT	AGG
(GCA)	 AG	44264-44376	GT	AGG
(ACA)	 AG	44555-44703	GT	GGG
(AAT)	 AG	44887-44998	GT	GGG
(GTG)	 AG	47878-47954	GT	CAG
(GAC)	 AG	48880-48951	GT	CTG
(AAC)	 AG	49099-49253	GT	AAG
(AGC)	 AG	50760-50832	TC	GAT
-recovered pasa_asmbl_13168.p1, terminal, 50760, 50832
-recovered pasa_asmbl_13168.p1, internal, 41276, 41340
-recovered pasa_asmbl_13168.p1, internal, 41509, 41575
-recovered pasa_asmbl_13168.p1, internal, 41734, 41852
-recovered pasa_asmbl_13168.p1, internal, 44001, 44081
-recovered pasa_asmbl_13168.p1, internal, 44264, 44376
-recovered pasa_asmbl_13168.p1, internal, 44555, 44703
-recovered pasa_asmbl_13168.p1, internal, 44887, 44998
-recovered pasa_asmbl_13168.p1, internal, 47878, 47954
-recovered pasa_asmbl_13168.p1, internal, 48880, 48951
-recovered pasa_asmbl_13168.p1, internal, 49099, 49253
Valid prediction for snap_scaffold_14-snap.1518-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.1506-T1
Valid prediction for Augustus_model.g23457.t1
Valid prediction for GeneMark_model.59760_t
Valid prediction for GeneMark_model.59765_t
Valid prediction for Augustus_model.g23463.t1
Valid prediction for pasa_asmbl_13176.p1
Valid prediction for snap_scaffold_14-snap.1526-T1
Valid prediction for pasa_asmbl_13169.p1
Valid prediction for CodingQuarry_transcript_15658-T1
Valid prediction for Augustus_model.g23465.t1
Valid prediction for GlimmerHMM_glimmerT_34912-T1
Valid prediction for CodingQuarry_transcript_15654-T1
Valid prediction for GeneMark_model.59769_t
Valid prediction for snap_scaffold_14-snap.1510-T1
Valid prediction for GlimmerHMM_glimmerT_34901-T1
Valid prediction for GlimmerHMM_glimmerT_34892-T1
Valid prediction for HiQ_model.g23471.t1
Valid prediction for snap_scaffold_14-snap.1520-T1
Valid prediction for snap_scaffold_14-snap.1491-T1
Valid prediction for GlimmerHMM_glimmerT_34911-T1
Valid prediction for GeneMark_model.59733_t
Valid prediction for GlimmerHMM_glimmerT_34905-T1
Valid prediction for snap_scaffold_14-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_34897-T1
Valid prediction for GlimmerHMM_glimmerT_34898-T1
Valid prediction for Augustus_model.g23473.t1
Valid prediction for pasa_asmbl_13172.p1
Valid prediction for HiQ_model.g23474.t1
Valid prediction for GeneMark_model.59754_t
Valid prediction for GlimmerHMM_glimmerT_34913-T1
Valid prediction for GeneMark_model.59752_t
Valid prediction for GeneMark_model.59737_t
Valid prediction for GeneMark_model.59731_t
Valid prediction for GeneMark_model.59744_t
Valid prediction for GlimmerHMM_glimmerT_34887-T1
Couldn't classify 148712, 148895
Sorry, prediction pasa_asmbl_13161.p1 fails validation.
(TGG)	 GC	148712-148895	GT	CCG
(CCT)	 AG	149695-149807	GT	AGG
(ATT)	 AG	150052-150240	GA	AGG
-recovered pasa_asmbl_13161.p1, terminal, 150052, 150240
-recovered pasa_asmbl_13161.p1, internal, 149695, 149807
Valid prediction for GeneMark_model.59763_t
Valid prediction for GeneMark_model.59766_t
Valid prediction for snap_scaffold_14-snap.1509-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21512, rend_intergenic: 19513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47749, rend_intergenic: 41374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62934, rend_intergenic: 53456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79477, rend_intergenic: 77055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88632, rend_intergenic: 83381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136447, rend_intergenic: 129856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 16196, rend_intergenic: 16193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 49214, rend_intergenic: 49211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169752
-exon list size: 529


building trellis

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75.7    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 21512, rend_intergenic: 19513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47749, rend_intergenic: 41374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62934, rend_intergenic: 53456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79477, rend_intergenic: 77055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88632, rend_intergenic: 83381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136447, rend_intergenic: 129856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 16196, rend_intergenic: 16193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 49214, rend_intergenic: 49211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12255
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 - 10263
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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 - 10211
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

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