-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_5419376-5607263

-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.82361_t
Couldn't classify 122178, 122263
Couldn't classify 126973, 127006
Sorry, prediction pasa_asmbl_25776.p1 fails validation.
(CTG)	 GC	122178-122263	GT	AGG
(GTA)	 AG	122358-122420	GT	AGG
(TAA)	 AG	122522-122624	GT	AGG
(TAC)	 AG	122733-122822	GT	AAG
(CAA)	 AG	122923-123025	GT	TGG
(ACG)	 AG	123150-123324	GT	AGG
(GTG)	 AG	123515-123571	GT	AGG
(GTT)	 AG	123728-123850	GT	AGG
(GTT)	 AG	124084-124203	GT	AGG
(CGT)	 AG	124332-124494	GT	AGG
(GAG)	 AG	124736-124882	GT	AGG
(CAG)	 AG	125094-125237	GT	AGG
(AGG)	 AG	125369-125619	GT	AGG
(AGA)	 AG	125780-125948	GT	AGG
(GAA)	 AG	126072-126225	GT	GAG
(ACG)	 AG	126486-126651	GT	CGG
(GGC)	 AG	126973-127006	GC	TGG
-recovered pasa_asmbl_25776.p1, internal, 122358, 122420
-recovered pasa_asmbl_25776.p1, internal, 122522, 122624
-recovered pasa_asmbl_25776.p1, internal, 122733, 122822
-recovered pasa_asmbl_25776.p1, internal, 122923, 123025
-recovered pasa_asmbl_25776.p1, internal, 123150, 123324
-recovered pasa_asmbl_25776.p1, internal, 123515, 123571
-recovered pasa_asmbl_25776.p1, internal, 123728, 123850
-recovered pasa_asmbl_25776.p1, internal, 124084, 124203
-recovered pasa_asmbl_25776.p1, internal, 124332, 124494
-recovered pasa_asmbl_25776.p1, internal, 124736, 124882
-recovered pasa_asmbl_25776.p1, internal, 125094, 125237
-recovered pasa_asmbl_25776.p1, internal, 125369, 125619
-recovered pasa_asmbl_25776.p1, internal, 125780, 125948
-recovered pasa_asmbl_25776.p1, internal, 126072, 126225
-recovered pasa_asmbl_25776.p1, internal, 126486, 126651
-recovered pasa_asmbl_25776.p1, internal, 126973, 127006
Valid prediction for GeneMark_model.82355_t
Valid prediction for snap_scaffold_20-snap.1213-T1
Valid prediction for snap_scaffold_20-snap.1204-T1
Valid prediction for Augustus_model.g31436.t1
Valid prediction for snap_scaffold_20-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_47118-T1
Valid prediction for GeneMark_model.82370_t
Valid prediction for GeneMark_model.82336_t
Valid prediction for Augustus_model.g31432.t1
Valid prediction for GlimmerHMM_glimmerT_47123-T1
Valid prediction for GeneMark_model.82357_t
Couldn't classify 118728, 118793
Couldn't classify 121755, 121763
Sorry, prediction pasa_asmbl_25774.p1 fails validation.
(CTC)	 AC	118728-118793	GT	GGG
(GTG)	 AG	118957-119208	GT	AGG
(GTG)	 AG	119431-119556	GT	AGG
(AAG)	 AG	119746-119940	GT	TCG
(ATT)	 AG	120143-120313	GT	CGG
(GCC)	 AG	120449-120662	GT	AGG
(ATG)	 AG	121019-121171	GT	GGG
(GCG)	 AG	121416-121528	GT	CAG
(GTT)	 AG	121755-121763	GG	AGG
add_exon() Sorry, pasa_asmbl_25774.p1 121019-121171-initial-1 is invalid.
-recovered pasa_asmbl_25774.p1, initial, 121019, 121171
-recovered pasa_asmbl_25774.p1, internal, 118957, 119208
-recovered pasa_asmbl_25774.p1, internal, 119431, 119556
-recovered pasa_asmbl_25774.p1, internal, 119746, 119940
-recovered pasa_asmbl_25774.p1, internal, 120143, 120313
-recovered pasa_asmbl_25774.p1, internal, 120449, 120662
-recovered pasa_asmbl_25774.p1, internal, 121019, 121171
-recovered pasa_asmbl_25774.p1, internal, 121416, 121528
Valid prediction for GlimmerHMM_glimmerT_47133-T1
Valid prediction for snap_scaffold_20-snap.1208-T1
Valid prediction for GlimmerHMM_glimmerT_47114-T1
Valid prediction for GeneMark_model.82367_t
Couldn't classify 116290, 116406
Sorry, prediction pasa_asmbl_25773.p1 fails validation.
(ATG)	 CA	115887-116132	GT	AAG
(AAT)	 AG	116290-116406	GC	ACG
-recovered pasa_asmbl_25773.p1, initial, 115887, 116132
-recovered pasa_asmbl_25773.p1, internal, 116290, 116406
Valid prediction for GlimmerHMM_glimmerT_47135-T1
Valid prediction for GlimmerHMM_glimmerT_47132-T1
Valid prediction for GlimmerHMM_glimmerT_47121-T1
Valid prediction for GlimmerHMM_glimmerT_47122-T1
Valid prediction for pasa_asmbl_25769.p1
Valid prediction for snap_scaffold_20-snap.1211-T1
Valid prediction for GeneMark_model.82346_t
Valid prediction for Augustus_model.g31430.t1
Valid prediction for Augustus_model.g31425.t1
Valid prediction for Augustus_model.g31439.t1
Valid prediction for GlimmerHMM_glimmerT_47128-T1
Valid prediction for GlimmerHMM_glimmerT_47130-T1
Valid prediction for snap_scaffold_20-snap.1201-T1
Valid prediction for GeneMark_model.82338_t
Valid prediction for GeneMark_model.82374_t
Valid prediction for snap_scaffold_20-snap.1227-T1
Valid prediction for snap_scaffold_20-snap.1228-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_30446-T1
Valid prediction for GeneMark_model.82350_t
Valid prediction for pasa_asmbl_26324.p1
Valid prediction for snap_scaffold_20-snap.1199-T1
Valid prediction for pasa_asmbl_25778.p1
Valid prediction for snap_scaffold_20-snap.1232-T1
Valid prediction for GlimmerHMM_glimmerT_47119-T1
Valid prediction for snap_scaffold_20-snap.1212-T1
Valid prediction for snap_scaffold_20-snap.1233-T1
Valid prediction for snap_scaffold_20-snap.1224-T1
Valid prediction for snap_scaffold_20-snap.1202-T1
Valid prediction for GeneMark_model.82353_t
Valid prediction for pasa_asmbl_26343.p1
Valid prediction for GeneMark_model.82343_t
Valid prediction for GlimmerHMM_glimmerT_47127-T1
Valid prediction for CodingQuarry_transcript_30447-T1
Valid prediction for HiQ_model.g31441.t1
Valid prediction for Augustus_model.g31422.t1
Valid prediction for GlimmerHMM_glimmerT_47140-T1
Valid prediction for GeneMark_model.82348_t
Valid prediction for GeneMark_model.82340_t
Valid prediction for snap_scaffold_20-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_47116-T1
Valid prediction for Augustus_model.g31434.t1
Valid prediction for snap_scaffold_20-snap.1207-T1
Valid prediction for snap_scaffold_20-snap.1226-T1
Valid prediction for GeneMark_model.82352_t
Valid prediction for GeneMark_model.82341_t
Valid prediction for HiQ_model.g31427.t1
Valid prediction for GeneMark_model.82359_t
Valid prediction for CodingQuarry_transcript_30450-T1
Valid prediction for GeneMark_model.82372_t
Valid prediction for GlimmerHMM_glimmerT_47117-T1
Valid prediction for GeneMark_model.82363_t
Valid prediction for snap_scaffold_20-snap.1197-T1
Valid prediction for snap_scaffold_20-snap.1200-T1
Valid prediction for snap_scaffold_20-snap.1214-T1
Valid prediction for snap_scaffold_20-snap.1217-T1
Valid prediction for GeneMark_model.82339_t
Valid prediction for Augustus_model.g31428.t1
Valid prediction for snap_scaffold_20-snap.1198-T1
Valid prediction for snap_scaffold_20-snap.1215-T1
Valid prediction for GeneMark_model.82345_t
Valid prediction for GeneMark_model.82347_t
Valid prediction for Augustus_model.g31429.t1
Valid prediction for GlimmerHMM_glimmerT_47137-T1
Valid prediction for GlimmerHMM_glimmerT_47126-T1
Valid prediction for HiQ_model.g31424.t1
Valid prediction for Augustus_model.g31442.t1
Valid prediction for GlimmerHMM_glimmerT_47139-T1
Valid prediction for GeneMark_model.82366_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.1220-T1
Valid prediction for snap_scaffold_20-snap.1206-T1
Valid prediction for snap_scaffold_20-snap.1209-T1
Valid prediction for Augustus_model.g31435.t1
Valid prediction for GlimmerHMM_glimmerT_47125-T1
Valid prediction for HiQ_model.g31431.t1
Valid prediction for pasa_asmbl_26694.p1
Valid prediction for snap_scaffold_20-snap.1203-T1
Valid prediction for GeneMark_model.82354_t
Valid prediction for GeneMark_model.82344_t
Valid prediction for Augustus_model.g31445.t1
Valid prediction for GlimmerHMM_glimmerT_47143-T1
Valid prediction for GeneMark_model.82369_t
Valid prediction for GlimmerHMM_glimmerT_47124-T1
Valid prediction for snap_scaffold_20-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_47134-T1
Valid prediction for GlimmerHMM_glimmerT_47120-T1
Valid prediction for HiQ_model.g31423.t1
Valid prediction for snap_scaffold_20-snap.1223-T1
Valid prediction for snap_scaffold_20-snap.1216-T1
Valid prediction for GeneMark_model.82337_t
Valid prediction for snap_scaffold_20-snap.1234-T1
Valid prediction for snap_scaffold_20-snap.1221-T1
Valid prediction for Augustus_model.g31446.t1
Couldn't classify 118811, 119016
Sorry, prediction pasa_asmbl_26683.p1 fails validation.
(TCC)	 AT	118811-119016	GT	AGG
(GGG)	 AG	119428-119523	GT	GGG
(ACC)	 AG	119839-119930	GT	AGG
(AAA)	 AG	120331-120388	GT	AGG
(CTG)	 AG	121232-121325	GT	AGG
(GGA)	 AG	121443-121496	GT	ATG
(GGG)	 AG	121788-121871	GT	ATG
(AAA)	 AG	121990-122031	GT	AGG
(CAT)	 AG	122140-122247	GT	CGG
(ACG)	 AG	122682-122748	GT	AGG
(GCT)	 AG	122908-123078	GT	CTG
(CCC)	 AG	123950-124001	GT	AAG
(GCA)	 AG	124664-124724	GT	AGG
(AAA)	 AG	125142-125318	GT	TGG
(ATG)	 AG	125610-125843	GG	GAG
-recovered pasa_asmbl_26683.p1, terminal, 125610, 125843
-recovered pasa_asmbl_26683.p1, internal, 119428, 119523
-recovered pasa_asmbl_26683.p1, internal, 119839, 119930
-recovered pasa_asmbl_26683.p1, internal, 120331, 120388
-recovered pasa_asmbl_26683.p1, internal, 121232, 121325
-recovered pasa_asmbl_26683.p1, internal, 121443, 121496
-recovered pasa_asmbl_26683.p1, internal, 121788, 121871
-recovered pasa_asmbl_26683.p1, internal, 121990, 122031
-recovered pasa_asmbl_26683.p1, internal, 122140, 122247
-recovered pasa_asmbl_26683.p1, internal, 122682, 122748
-recovered pasa_asmbl_26683.p1, internal, 122908, 123078
-recovered pasa_asmbl_26683.p1, internal, 123950, 124001
-recovered pasa_asmbl_26683.p1, internal, 124664, 124724
-recovered pasa_asmbl_26683.p1, internal, 125142, 125318
Valid prediction for Augustus_model.g31433.t1
Valid prediction for GlimmerHMM_glimmerT_47144-T1
Valid prediction for Augustus_model.g31444.t1
Valid prediction for GlimmerHMM_glimmerT_47142-T1
Valid prediction for Augustus_model.g31438.t1
Valid prediction for GeneMark_model.82371_t
Valid prediction for GeneMark_model.82335_t
Valid prediction for GlimmerHMM_glimmerT_47129-T1
Valid prediction for CodingQuarry_transcript_30448-T1
Valid prediction for HiQ_model.g31437.t1
Valid prediction for Augustus_model.g31440.t1
Couldn't classify 175872, 175959
Sorry, prediction pasa_asmbl_26680.p1 fails validation.
(GTT)	 AC	175872-175959	GT	TGG
(GGA)	 AG	176229-176309	GT	TGG
(TCA)	 AG	176387-176511	GT	ATG
(CCT)	 AG	176690-176823	GT	AAG
(GTA)	 AG	177000-177102	GT	CTG
(TAC)	 AG	177872-177976	AG	GAA
-recovered pasa_asmbl_26680.p1, terminal, 177872, 177976
-recovered pasa_asmbl_26680.p1, internal, 176229, 176309
-recovered pasa_asmbl_26680.p1, internal, 176387, 176511
-recovered pasa_asmbl_26680.p1, internal, 176690, 176823
-recovered pasa_asmbl_26680.p1, internal, 177000, 177102
Valid prediction for CodingQuarry_transcript_30449-T1
Valid prediction for Augustus_model.g31426.t1
Valid prediction for GeneMark_model.82342_t
Valid prediction for GeneMark_model.82349_t
Valid prediction for GeneMark_model.82362_t
Valid prediction for HiQ_model.g31443.t1
Valid prediction for GeneMark_model.82356_t
Valid prediction for GlimmerHMM_glimmerT_47131-T1
Valid prediction for GlimmerHMM_glimmerT_47136-T1
Valid prediction for snap_scaffold_20-snap.1229-T1
Valid prediction for snap_scaffold_20-snap.1210-T1
Valid prediction for GeneMark_model.82375_t
Valid prediction for GlimmerHMM_glimmerT_47138-T1
Valid prediction for GeneMark_model.82358_t
Valid prediction for snap_scaffold_20-snap.1230-T1
Valid prediction for snap_scaffold_20-snap.1222-T1
Valid prediction for snap_scaffold_20-snap.1231-T1
Valid prediction for GeneMark_model.82364_t
Valid prediction for GeneMark_model.82360_t
Valid prediction for snap_scaffold_20-snap.1205-T1
Valid prediction for GlimmerHMM_glimmerT_47141-T1
Valid prediction for GeneMark_model.82373_t
Valid prediction for pasa_asmbl_26693.p1
Valid prediction for CodingQuarry_transcript_30451-T1
Valid prediction for GlimmerHMM_glimmerT_47115-T1
Valid prediction for GeneMark_model.82351_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 53221, rend_intergenic: 43308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66509, rend_intergenic: 62046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73415, rend_intergenic: 68927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107740, rend_intergenic: 104502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130256, rend_intergenic: 128600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146892, rend_intergenic: 142965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175851, rend_intergenic: 163406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187888
-exon list size: 625


building trellis

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70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 53221, rend_intergenic: 43308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66509, rend_intergenic: 62046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73415, rend_intergenic: 68927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107740, rend_intergenic: 104502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130256, rend_intergenic: 128600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146892, rend_intergenic: 142965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175851, rend_intergenic: 163406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support