-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_5919276-6075944

-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_20-snap.1351-T1
Valid prediction for GeneMark_model.82523_t
Valid prediction for GeneMark_model.82496_t
Valid prediction for snap_scaffold_20-snap.1335-T1
Valid prediction for GlimmerHMM_glimmerT_47218-T1
Valid prediction for HiQ_model.g31486.t1
Valid prediction for GeneMark_model.82489_t
Valid prediction for GeneMark_model.82525_t
Valid prediction for CodingQuarry_transcript_30463-T1
Valid prediction for GeneMark_model.82481_t
Valid prediction for GeneMark_model.82507_t
Valid prediction for snap_scaffold_20-snap.1344-T1
Valid prediction for GeneMark_model.82505_t
Valid prediction for snap_scaffold_20-snap.1329-T1
Valid prediction for GeneMark_model.82514_t
Valid prediction for snap_scaffold_20-snap.1330-T1
Valid prediction for snap_scaffold_20-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_47203-T1
Valid prediction for GlimmerHMM_glimmerT_47213-T1
Valid prediction for GeneMark_model.82521_t
Valid prediction for snap_scaffold_20-snap.1317-T1
Valid prediction for snap_scaffold_20-snap.1342-T1
Valid prediction for GeneMark_model.82469_t
Valid prediction for GeneMark_model.82508_t
Valid prediction for snap_scaffold_20-snap.1336-T1
Valid prediction for snap_scaffold_20-snap.1346-T1
Valid prediction for snap_scaffold_20-snap.1338-T1
Valid prediction for snap_scaffold_20-snap.1337-T1
Valid prediction for GeneMark_model.82487_t
Valid prediction for snap_scaffold_20-snap.1340-T1
Valid prediction for snap_scaffold_20-snap.1339-T1
Valid prediction for GlimmerHMM_glimmerT_47221-T1
Valid prediction for GeneMark_model.82509_t
Valid prediction for GeneMark_model.82494_t
Valid prediction for snap_scaffold_20-snap.1325-T1
Valid prediction for GeneMark_model.82471_t
Valid prediction for snap_scaffold_20-snap.1328-T1
Valid prediction for GeneMark_model.82483_t
Valid prediction for GeneMark_model.82513_t
Valid prediction for GeneMark_model.82527_t
Valid prediction for GeneMark_model.82477_t
Valid prediction for GeneMark_model.82479_t
Valid prediction for snap_scaffold_20-snap.1334-T1
Valid prediction for snap_scaffold_20-snap.1333-T1
Valid prediction for GeneMark_model.82518_t
Valid prediction for GeneMark_model.82473_t
Valid prediction for snap_scaffold_20-snap.1323-T1
Valid prediction for GeneMark_model.82503_t
Valid prediction for snap_scaffold_20-snap.1349-T1
Valid prediction for GlimmerHMM_glimmerT_47205-T1
Valid prediction for GeneMark_model.82500_t
Valid prediction for GeneMark_model.82520_t
Valid prediction for GeneMark_model.82482_t
Valid prediction for GeneMark_model.82491_t
Valid prediction for GeneMark_model.82474_t
Valid prediction for GeneMark_model.82498_t
Valid prediction for GeneMark_model.82516_t
Valid prediction for snap_scaffold_20-snap.1352-T1
Valid prediction for GeneMark_model.82511_t

-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_20-snap.1324-T1
Valid prediction for GlimmerHMM_glimmerT_47220-T1
Valid prediction for Augustus_model.g31489.t1
Valid prediction for GeneMark_model.82501_t
Valid prediction for GeneMark_model.82515_t
Valid prediction for snap_scaffold_20-snap.1326-T1
Valid prediction for GeneMark_model.82490_t
Valid prediction for Augustus_model.g31495.t1
Valid prediction for GlimmerHMM_glimmerT_47215-T1
Valid prediction for GlimmerHMM_glimmerT_47208-T1
Valid prediction for pasa_asmbl_26717.p1
Valid prediction for GeneMark_model.82522_t
Couldn't classify 93006, 93014
Couldn't classify 100328, 100434
Sorry, prediction pasa_asmbl_26730.p1 fails validation.
(CCC)	 GG	93006-93014	GT	AGG
(GCT)	 AG	93326-93436	GT	AGG
(ATC)	 AG	96201-96306	GT	AGG
(GCG)	 AG	97749-97863	GT	TGG
(CTT)	 AG	98396-98520	GT	AGG
(ATG)	 AG	100328-100434	GC	AGG
add_exon() Sorry, pasa_asmbl_26730.p1 100328-100434-initial-1 is invalid.
-recovered pasa_asmbl_26730.p1, initial, 100328, 100434
-recovered pasa_asmbl_26730.p1, internal, 93326, 93436
-recovered pasa_asmbl_26730.p1, internal, 96201, 96306
-recovered pasa_asmbl_26730.p1, internal, 97749, 97863
-recovered pasa_asmbl_26730.p1, internal, 98396, 98520
-recovered pasa_asmbl_26730.p1, internal, 100328, 100434
Valid prediction for GeneMark_model.82517_t
Valid prediction for GeneMark_model.82528_t
Valid prediction for GeneMark_model.82472_t
Valid prediction for GlimmerHMM_glimmerT_47214-T1
Valid prediction for GeneMark_model.82504_t
Valid prediction for GeneMark_model.82480_t
Valid prediction for Augustus_model.g31496.t1
Valid prediction for snap_scaffold_20-snap.1316-T1
Couldn't classify 113968, 114067
Couldn't classify 117172, 117440
Sorry, prediction pasa_asmbl_26728.p1 fails validation.
(CCA)	 TC	113968-114067	GT	CTG
(GTC)	 AG	114220-114243	GT	ATG
(TGT)	 AG	115741-116037	GT	AGG
(GCC)	 AG	116279-116572	GT	AGG
(AGT)	 AG	116687-116965	GT	TGG
(AAA)	 AG	117172-117440	GG	AGG
-recovered pasa_asmbl_26728.p1, internal, 114220, 114243
-recovered pasa_asmbl_26728.p1, internal, 115741, 116037
-recovered pasa_asmbl_26728.p1, internal, 116279, 116572
-recovered pasa_asmbl_26728.p1, internal, 116687, 116965
Valid prediction for GeneMark_model.82497_t
Valid prediction for GeneMark_model.82506_t
Couldn't classify 118549, 118693
Couldn't classify 118965, 119242
Sorry, prediction pasa_asmbl_27242.p1 fails validation.
(GTT)	 AC	118549-118693	GT	AGG
(TGC)	 AG	118965-119242	GG	AGG
Valid prediction for CodingQuarry_transcript_30462-T1
Valid prediction for GeneMark_model.82519_t
Valid prediction for Augustus_model.g31494.t1
Valid prediction for HiQ_model.g31488.t1
Valid prediction for GlimmerHMM_glimmerT_47216-T1
Valid prediction for GlimmerHMM_glimmerT_47211-T1
Valid prediction for CodingQuarry_transcript_30461-T1
Valid prediction for Augustus_model.g31485.t1
Valid prediction for snap_scaffold_20-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_47204-T1
Valid prediction for GlimmerHMM_glimmerT_47224-T1
Valid prediction for snap_scaffold_20-snap.1322-T1
Valid prediction for Augustus_model.g31493.t1
Valid prediction for CodingQuarry_transcript_30464-T1
Valid prediction for GeneMark_model.82495_t
Valid prediction for HiQ_model.g31487.t1
Valid prediction for GlimmerHMM_glimmerT_47219-T1
Valid prediction for snap_scaffold_20-snap.1348-T1
Valid prediction for GlimmerHMM_glimmerT_47217-T1
Valid prediction for snap_scaffold_20-snap.1327-T1
Valid prediction for GeneMark_model.82467_t
Valid prediction for pasa_asmbl_26710.p1
Valid prediction for snap_scaffold_20-snap.1341-T1
Valid prediction for GeneMark_model.82493_t
Valid prediction for GeneMark_model.82484_t
Valid prediction for Augustus_model.g31490.t1
Valid prediction for GlimmerHMM_glimmerT_47222-T1
Couldn't classify 123683, 123872
Sorry, prediction pasa_asmbl_26725.p1 fails validation.
(TCA)	 TT	123683-123872	GT	AGG
(TCC)	 AG	124671-124733	GT	GGG
(GTG)	 AG	126246-126268	GT	ATG
(GGT)	 AG	127431-127529	CA	AAC
-recovered pasa_asmbl_26725.p1, terminal, 127431, 127529
-recovered pasa_asmbl_26725.p1, internal, 124671, 124733
-recovered pasa_asmbl_26725.p1, internal, 126246, 126268
Valid prediction for GeneMark_model.82512_t
Valid prediction for GeneMark_model.82492_t
Valid prediction for GeneMark_model.82475_t
Valid prediction for GeneMark_model.82488_t
Couldn't classify 131140, 131437
Sorry, prediction pasa_asmbl_26719.p1 fails validation.
(CCT)	 AC	131140-131437	GT	TTG
(ATG)	 AG	133074-133291	CA	AGC
-recovered pasa_asmbl_26719.p1, terminal, 133074, 133291
Valid prediction for snap_scaffold_20-snap.1315-T1
Valid prediction for GlimmerHMM_glimmerT_47212-T1
Valid prediction for GeneMark_model.82486_t
Couldn't classify 106010, 106057
Sorry, prediction pasa_asmbl_26729.p1 fails validation.
(GTC)	 AC	106010-106057	GT	AGG
(GAC)	 AG	107144-107271	GT	TGG
(TCG)	 AG	108524-108610	GT	AGG
(CGT)	 AG	109059-109175	GT	TGG
(TGG)	 AG	109436-109565	GT	GGG
(CCT)	 AG	110257-110325	CA	AAC
-recovered pasa_asmbl_26729.p1, terminal, 110257, 110325
-recovered pasa_asmbl_26729.p1, internal, 107144, 107271
-recovered pasa_asmbl_26729.p1, internal, 108524, 108610
-recovered pasa_asmbl_26729.p1, internal, 109059, 109175
-recovered pasa_asmbl_26729.p1, internal, 109436, 109565
Valid prediction for snap_scaffold_20-snap.1331-T1
Valid prediction for GeneMark_model.82476_t
Valid prediction for GeneMark_model.82499_t
Valid prediction for CodingQuarry_transcript_30465-T1
Valid prediction for snap_scaffold_20-snap.1320-T1
Valid prediction for GeneMark_model.82502_t
Valid prediction for GeneMark_model.82485_t
Valid prediction for snap_scaffold_20-snap.1332-T1
Valid prediction for GlimmerHMM_glimmerT_47209-T1
Valid prediction for snap_scaffold_20-snap.1343-T1
Valid prediction for snap_scaffold_20-snap.1347-T1
Valid prediction for GeneMark_model.82524_t
Valid prediction for GeneMark_model.82470_t
Valid prediction for pasa_asmbl_26715.p1
Valid prediction for snap_scaffold_20-snap.1321-T1
Couldn't classify 80178, 80285
Couldn't classify 80943, 81064
Sorry, prediction pasa_asmbl_26731.p1 fails validation.
(TTC)	 CG	80178-80285	GT	AGG
(GAG)	 AG	80588-80708	GT	AGG
(AGC)	 AG	80943-81064	CT	ACC
-recovered pasa_asmbl_26731.p1, internal, 80588, 80708
Valid prediction for Augustus_model.g31491.t1
Valid prediction for Augustus_model.g31492.t1
Valid prediction for GlimmerHMM_glimmerT_47210-T1
Valid prediction for Augustus_model.g31497.t1
Valid prediction for GeneMark_model.82526_t
Valid prediction for GlimmerHMM_glimmerT_47223-T1
Valid prediction for GlimmerHMM_glimmerT_47206-T1
Valid prediction for GeneMark_model.82510_t
Valid prediction for GeneMark_model.82478_t
Valid prediction for GeneMark_model.82468_t
Valid prediction for snap_scaffold_20-snap.1319-T1
Valid prediction for GlimmerHMM_glimmerT_47207-T1
Valid prediction for snap_scaffold_20-snap.1318-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45974, rend_intergenic: 29617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49744, rend_intergenic: 49668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56376, rend_intergenic: 49927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66462, rend_intergenic: 56398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70410, rend_intergenic: 66500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113437, rend_intergenic: 71624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118228, rend_intergenic: 116534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123290, rend_intergenic: 118452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124484, rend_intergenic: 123572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131535, rend_intergenic: 124996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137234, rend_intergenic: 135293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144142, rend_intergenic: 141573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156669
-exon list size: 785


building trellis

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73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 45974, rend_intergenic: 29617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49744, rend_intergenic: 49668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56376, rend_intergenic: 49927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66462, rend_intergenic: 56398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70410, rend_intergenic: 66500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113437, rend_intergenic: 71624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118228, rend_intergenic: 116534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123290, rend_intergenic: 118452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124484, rend_intergenic: 123572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131535, rend_intergenic: 124996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137234, rend_intergenic: 135293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144142, rend_intergenic: 141573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support