-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_7462420-7665050

-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 snap_scaffold_19-snap.1516-T1
Valid prediction for Augustus_model.g30281.t1
Valid prediction for pasa_asmbl_22276.p1
Valid prediction for GeneMark_model.79297_t
Valid prediction for Augustus_model.g30278.t1
Valid prediction for GlimmerHMM_glimmerT_45414-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.79303_t
Valid prediction for GlimmerHMM_glimmerT_45394-T1
Valid prediction for GeneMark_model.79327_t
Valid prediction for GeneMark_model.79320_t
Valid prediction for snap_scaffold_19-snap.1514-T1
Valid prediction for HiQ_model.g30268.t1
Valid prediction for Augustus_model.g30283.t1
Valid prediction for Augustus_model.g30261.t1
Valid prediction for GlimmerHMM_glimmerT_45392-T1
Valid prediction for HiQ_model.g30257.t1
Valid prediction for GlimmerHMM_glimmerT_45400-T1
Valid prediction for GeneMark_model.79310_t
Valid prediction for snap_scaffold_19-snap.1491-T1
Valid prediction for GlimmerHMM_glimmerT_45418-T1
Valid prediction for pasa_asmbl_22285.p1
Valid prediction for GlimmerHMM_glimmerT_45399-T1
Valid prediction for snap_scaffold_19-snap.1509-T1
Valid prediction for Augustus_model.g30259.t1
Valid prediction for GeneMark_model.79341_t
Valid prediction for GlimmerHMM_glimmerT_45419-T1
Valid prediction for snap_scaffold_19-snap.1493-T1
Valid prediction for HiQ_model.g30280.t1
Valid prediction for snap_scaffold_19-snap.1487-T1
Valid prediction for snap_scaffold_19-snap.1496-T1
Valid prediction for GeneMark_model.79319_t
Valid prediction for Augustus_model.g30258.t1
Valid prediction for GlimmerHMM_glimmerT_45423-T1
Valid prediction for snap_scaffold_19-snap.1480-T1
Couldn't classify 40809, 42020
Sorry, prediction pasa_asmbl_22267.p1 fails validation.
(CCT)	 TA	40809-42020	GT	AGG
(ATC)	 AG	42473-42580	GT	AGG
-recovered pasa_asmbl_22267.p1, terminal, 42473, 42580
-recovered pasa_asmbl_22267.p1, internal, 42473, 42580
Valid prediction for snap_scaffold_19-snap.1507-T1
Valid prediction for snap_scaffold_19-snap.1486-T1
Valid prediction for snap_scaffold_19-snap.1506-T1
Valid prediction for Augustus_model.g30269.t1
Valid prediction for pasa_asmbl_22277.p1
Valid prediction for GeneMark_model.79308_t
Valid prediction for snap_scaffold_19-snap.1485-T1
Valid prediction for snap_scaffold_19-snap.1497-T1
Valid prediction for CodingQuarry_transcript_25649-T1
Valid prediction for Augustus_model.g30260.t1
Valid prediction for GlimmerHMM_glimmerT_45395-T1
Valid prediction for GeneMark_model.79330_t
Valid prediction for CodingQuarry_transcript_25655-T1
Valid prediction for GeneMark_model.79306_t
Valid prediction for CodingQuarry_transcript_25650-T1
Valid prediction for CodingQuarry_transcript_25653-T1
Valid prediction for GeneMark_model.79312_t
Valid prediction for GeneMark_model.79331_t
Valid prediction for GlimmerHMM_glimmerT_45403-T1
Valid prediction for GlimmerHMM_glimmerT_45420-T1
Valid prediction for HiQ_model.g30277.t1
Valid prediction for GlimmerHMM_glimmerT_45427-T1
Couldn't classify 98703, 99122
Sorry, prediction pasa_asmbl_22270.p1 fails validation.
(TGT)	 CA	98703-99122	GT	AGG
(CTA)	 AG	99299-99432	GT	AAG
(ATC)	 AG	99703-99754	GT	AGG
(GAG)	 AG	100152-100271	GT	AGG
(ATG)	 AG	100573-100741	GT	AGG
(ATG)	 AG	101417-101554	GT	AGG
(AAA)	 AG	101912-101988	TG	AGT
-recovered pasa_asmbl_22270.p1, initial, 100573, 100741
add_exon() Sorry, pasa_asmbl_22270.p1 101417-101554-initial-1 is invalid.
-recovered pasa_asmbl_22270.p1, initial, 101417, 101554
-recovered pasa_asmbl_22270.p1, terminal, 101912, 101988
-recovered pasa_asmbl_22270.p1, internal, 99299, 99432
-recovered pasa_asmbl_22270.p1, internal, 99703, 99754
-recovered pasa_asmbl_22270.p1, internal, 100152, 100271
-recovered pasa_asmbl_22270.p1, internal, 100573, 100741
-recovered pasa_asmbl_22270.p1, internal, 101417, 101554
Valid prediction for Augustus_model.g30263.t1
Valid prediction for snap_scaffold_19-snap.1502-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.79324_t
Valid prediction for GlimmerHMM_glimmerT_45401-T1
Valid prediction for HiQ_model.g30275.t1
Valid prediction for snap_scaffold_19-snap.1508-T1
Valid prediction for GeneMark_model.79317_t
Valid prediction for GeneMark_model.79301_t
Valid prediction for snap_scaffold_19-snap.1505-T1
Valid prediction for GlimmerHMM_glimmerT_45404-T1
Valid prediction for snap_scaffold_19-snap.1495-T1
Valid prediction for GeneMark_model.79335_t
Valid prediction for GeneMark_model.79337_t
Valid prediction for GlimmerHMM_glimmerT_45426-T1
Valid prediction for GlimmerHMM_glimmerT_45408-T1
Valid prediction for CodingQuarry_transcript_25654-T1
Valid prediction for GeneMark_model.79298_t
Valid prediction for snap_scaffold_19-snap.1484-T1
Valid prediction for snap_scaffold_19-snap.1512-T1
Valid prediction for pasa_asmbl_22287.p1
Valid prediction for HiQ_model.g30270.t1
Valid prediction for snap_scaffold_19-snap.1478-T1
Valid prediction for GlimmerHMM_glimmerT_45405-T1
Valid prediction for GlimmerHMM_glimmerT_45406-T1
Couldn't classify 110959, 111054
Couldn't classify 114939, 114965
Sorry, prediction pasa_asmbl_22273.p1 fails validation.
(AGA)	 GG	110959-111054	GT	CAG
(GCG)	 AG	111467-111585	GT	AAG
(GTG)	 AG	112587-112716	GT	AGG
(GTT)	 AG	112819-112898	GT	AGG
(ACA)	 AG	113111-113274	GT	AGG
(ACA)	 AG	114355-114413	GT	AGG
(GGA)	 AG	114939-114965	AG	GGA
-recovered pasa_asmbl_22273.p1, internal, 111467, 111585
-recovered pasa_asmbl_22273.p1, internal, 112587, 112716
-recovered pasa_asmbl_22273.p1, internal, 112819, 112898
-recovered pasa_asmbl_22273.p1, internal, 113111, 113274
-recovered pasa_asmbl_22273.p1, internal, 114355, 114413
Valid prediction for snap_scaffold_19-snap.1473-T1
Valid prediction for snap_scaffold_19-snap.1510-T1
Valid prediction for GeneMark_model.79339_t
Valid prediction for snap_scaffold_19-snap.1476-T1
Valid prediction for snap_scaffold_19-snap.1481-T1
Valid prediction for Augustus_model.g30266.t1
Valid prediction for Augustus_model.g30284.t1
Valid prediction for snap_scaffold_19-snap.1490-T1
Couldn't classify 34115, 34195
Couldn't classify 39658, 39682
Sorry, prediction pasa_asmbl_22264.p1 fails validation.
(GGG)	 GA	34115-34195	GT	AGG
(GCC)	 AG	35727-35816	GT	AGG
(TCG)	 AG	38616-38736	GT	GGG
(TAG)	 AG	38958-39103	GT	TGG
(GCC)	 AG	39360-39562	GT	AGG
(GGG)	 AG	39658-39682	GA	GTG
-recovered pasa_asmbl_22264.p1, internal, 35727, 35816
-recovered pasa_asmbl_22264.p1, internal, 38616, 38736
-recovered pasa_asmbl_22264.p1, internal, 38958, 39103
-recovered pasa_asmbl_22264.p1, internal, 39360, 39562
Couldn't classify 40127, 40394
Sorry, prediction pasa_asmbl_22266.p2 fails validation.
(ATG)	 TG	39740-39767	GT	AAG
(TGA)	 AG	39885-40026	GT	ACG
(AAA)	 AG	40127-40394	TT	CCT
-recovered pasa_asmbl_22266.p2, initial, 39740, 39767
-recovered pasa_asmbl_22266.p2, internal, 39885, 40026
Valid prediction for snap_scaffold_19-snap.1482-T1
Valid prediction for GeneMark_model.79329_t
Valid prediction for GlimmerHMM_glimmerT_45397-T1
Valid prediction for Augustus_model.g30286.t1
Valid prediction for snap_scaffold_19-snap.1494-T1
Valid prediction for snap_scaffold_19-snap.1518-T1
Valid prediction for GeneMark_model.79323_t
Valid prediction for Augustus_model.g30276.t1
Valid prediction for Augustus_model.g30265.t1
Valid prediction for GlimmerHMM_glimmerT_45417-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 GlimmerHMM_glimmerT_45412-T1
Valid prediction for GeneMark_model.79321_t
Valid prediction for GeneMark_model.79333_t
Valid prediction for GeneMark_model.79313_t
Valid prediction for GlimmerHMM_glimmerT_45422-T1
Valid prediction for GeneMark_model.79309_t
Valid prediction for snap_scaffold_19-snap.1519-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.79304_t
Valid prediction for snap_scaffold_19-snap.1517-T1
Valid prediction for snap_scaffold_19-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_45391-T1
Valid prediction for HiQ_model.g30272.t1
Valid prediction for snap_scaffold_19-snap.1503-T1
Valid prediction for Augustus_model.g30264.t1
Valid prediction for GeneMark_model.79300_t
Valid prediction for Augustus_model.g30267.t1
Valid prediction for Augustus_model.g30271.t1
Couldn't classify 70299, 70418
Sorry, prediction pasa_asmbl_21457.p1 fails validation.
(CTT)	 AA	70299-70418	GT	TGG
(CAA)	 AG	70556-70936	AC	AAA
-recovered pasa_asmbl_21457.p1, terminal, 70556, 70936
Valid prediction for GeneMark_model.79314_t
Valid prediction for snap_scaffold_19-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_45421-T1
Valid prediction for GlimmerHMM_glimmerT_45410-T1
Valid prediction for GeneMark_model.79326_t
Valid prediction for GeneMark_model.79302_t
Valid prediction for GlimmerHMM_glimmerT_45425-T1
Valid prediction for GeneMark_model.79338_t
Valid prediction for pasa_asmbl_21454.p1
Valid prediction for Augustus_model.g30282.t1
Valid prediction for GeneMark_model.79340_t
Valid prediction for Augustus_model.g30285.t1
Valid prediction for snap_scaffold_19-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_45402-T1
Valid prediction for GeneMark_model.79322_t
Valid prediction for CodingQuarry_transcript_25651-T1
Valid prediction for GeneMark_model.79305_t
Valid prediction for GeneMark_model.79336_t
Valid prediction for GeneMark_model.79328_t
Valid prediction for Augustus_model.g30262.t1
Valid prediction for snap_scaffold_19-snap.1488-T1
Valid prediction for snap_scaffold_19-snap.1479-T1
Valid prediction for Augustus_model.g30279.t1
Valid prediction for snap_scaffold_19-snap.1477-T1
Valid prediction for snap_scaffold_19-snap.1472-T1
Valid prediction for GeneMark_model.79325_t
Valid prediction for snap_scaffold_19-snap.1513-T1
Valid prediction for GeneMark_model.79332_t
Valid prediction for GeneMark_model.79299_t
Valid prediction for GlimmerHMM_glimmerT_45413-T1
Valid prediction for snap_scaffold_19-snap.1504-T1
Valid prediction for Augustus_model.g30274.t1
Valid prediction for GlimmerHMM_glimmerT_45409-T1
Valid prediction for snap_scaffold_19-snap.1501-T1
Valid prediction for snap_scaffold_19-snap.1489-T1
Valid prediction for snap_scaffold_19-snap.1483-T1
Valid prediction for GlimmerHMM_glimmerT_45393-T1
Valid prediction for GlimmerHMM_glimmerT_45424-T1
Valid prediction for snap_scaffold_19-snap.1515-T1
Valid prediction for snap_scaffold_19-snap.1499-T1
Valid prediction for GlimmerHMM_glimmerT_45396-T1
Valid prediction for GeneMark_model.79311_t
Valid prediction for GlimmerHMM_glimmerT_45407-T1
Valid prediction for GlimmerHMM_glimmerT_45416-T1
Valid prediction for GeneMark_model.79307_t
Valid prediction for GeneMark_model.79334_t
Valid prediction for GlimmerHMM_glimmerT_45415-T1
Valid prediction for snap_scaffold_19-snap.1474-T1
Valid prediction for snap_scaffold_19-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_45411-T1
Valid prediction for snap_scaffold_19-snap.1475-T1
Couldn't classify 63187, 63195
Couldn't classify 65463, 65501
Sorry, prediction pasa_asmbl_21458.p1 fails validation.
(ATT)	 GC	63187-63195	GT	AGG
(GAA)	 AG	63284-63415	GT	TGG
(GTC)	 AG	63579-63640	GT	GAG
(GTA)	 AG	63727-63856	GT	TGG
(GGG)	 AG	64163-64324	GT	TGG
(GCT)	 AG	64640-64683	GT	AGG
(GAG)	 AG	65093-65231	GT	AGG
(GTG)	 AG	65463-65501	TA	CCT
-recovered pasa_asmbl_21458.p1, internal, 63284, 63415
-recovered pasa_asmbl_21458.p1, internal, 63579, 63640
-recovered pasa_asmbl_21458.p1, internal, 63727, 63856
-recovered pasa_asmbl_21458.p1, internal, 64163, 64324
-recovered pasa_asmbl_21458.p1, internal, 64640, 64683
-recovered pasa_asmbl_21458.p1, internal, 65093, 65231
Valid prediction for GlimmerHMM_glimmerT_45398-T1
Valid prediction for Augustus_model.g30273.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 167828, rend_intergenic: 167825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21569, rend_intergenic: 15045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23021, rend_intergenic: 21936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25300, rend_intergenic: 23157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27597, rend_intergenic: 26863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29167, rend_intergenic: 27897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40909, rend_intergenic: 29193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58934, rend_intergenic: 57195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198101, rend_intergenic: 195398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202631
-exon list size: 637


building trellis

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73.1    
73.2    
73.4    
73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 43 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 167828, rend_intergenic: 167825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21569, rend_intergenic: 15045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23021, rend_intergenic: 21936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25300, rend_intergenic: 23157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27597, rend_intergenic: 26863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29167, rend_intergenic: 27897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40909, rend_intergenic: 29193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58934, rend_intergenic: 57195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198101, rend_intergenic: 195398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support