-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_16247810-16403871

-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.58014_t
Valid prediction for snap_scaffold_13-snap.3206-T1
Valid prediction for GeneMark_model.58034_t
Valid prediction for GlimmerHMM_glimmerT_33778-T1
Valid prediction for snap_scaffold_13-snap.3215-T1
Valid prediction for GlimmerHMM_glimmerT_33776-T1
Valid prediction for snap_scaffold_13-snap.3208-T1
Valid prediction for CodingQuarry_transcript_13323-T1
Valid prediction for snap_scaffold_13-snap.3191-T1
Valid prediction for GlimmerHMM_glimmerT_33789-T1
Valid prediction for snap_scaffold_13-snap.3200-T1
Valid prediction for Augustus_model.g22697.t1
Valid prediction for GeneMark_model.58040_t
Valid prediction for GeneMark_model.58012_t
Valid prediction for snap_scaffold_13-snap.3211-T1
Valid prediction for snap_scaffold_13-snap.3188-T1
Valid prediction for Augustus_model.g22689.t1
Valid prediction for GeneMark_model.58025_t
Valid prediction for Augustus_model.g22692.t1
Valid prediction for GeneMark_model.58031_t
Valid prediction for GeneMark_model.58003_t
Valid prediction for CodingQuarry_transcript_13322-T1
Valid prediction for snap_scaffold_13-snap.3195-T1
Valid prediction for GeneMark_model.58006_t
Valid prediction for GeneMark_model.58037_t
Valid prediction for GeneMark_model.58007_t
Valid prediction for GlimmerHMM_glimmerT_33781-T1
Valid prediction for GlimmerHMM_glimmerT_33797-T1
Valid prediction for snap_scaffold_13-snap.3210-T1
Valid prediction for snap_scaffold_13-snap.3203-T1
Valid prediction for GlimmerHMM_glimmerT_33791-T1
Valid prediction for snap_scaffold_13-snap.3205-T1
Valid prediction for HiQ_model.g22682.t1
Valid prediction for GlimmerHMM_glimmerT_33793-T1
Valid prediction for snap_scaffold_13-snap.3197-T1
Couldn't classify 35886, 36492
Couldn't classify 36631, 36716
Sorry, prediction pasa_asmbl_11546.p1 fails validation.
(AGC)	 CT	35886-36492	GT	AGG
(GGT)	 AG	36631-36716	AC	CCA
Valid prediction for GeneMark_model.58008_t
Valid prediction for snap_scaffold_13-snap.3201-T1
Valid prediction for GlimmerHMM_glimmerT_33795-T1
Valid prediction for snap_scaffold_13-snap.3193-T1
Valid prediction for GeneMark_model.58020_t
Valid prediction for snap_scaffold_13-snap.3221-T1
Valid prediction for pasa_asmbl_11543.p1
Valid prediction for snap_scaffold_13-snap.3199-T1
Valid prediction for snap_scaffold_13-snap.3213-T1
Valid prediction for GeneMark_model.58027_t
Valid prediction for HiQ_model.g22687.t1
Valid prediction for GeneMark_model.58001_t
Valid prediction for GeneMark_model.58029_t
Valid prediction for GeneMark_model.58010_t
Valid prediction for snap_scaffold_13-snap.3218-T1
Valid prediction for GlimmerHMM_glimmerT_33799-T1
Valid prediction for snap_scaffold_13-snap.3216-T1
Valid prediction for GeneMark_model.58022_t
Valid prediction for GeneMark_model.58023_t
Valid prediction for GlimmerHMM_glimmerT_33773-T1
Valid prediction for GlimmerHMM_glimmerT_33785-T1
Valid prediction for GeneMark_model.58016_t
Valid prediction for GeneMark_model.58033_t
Valid prediction for snap_scaffold_13-snap.3222-T1
Valid prediction for GeneMark_model.57998_t
Valid prediction for GeneMark_model.58039_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 GlimmerHMM_glimmerT_33788-T1
Valid prediction for CodingQuarry_transcript_13324-T1
Valid prediction for GlimmerHMM_glimmerT_33796-T1
Valid prediction for Augustus_model.g22686.t1
Valid prediction for Augustus_model.g22693.t1
Valid prediction for GlimmerHMM_glimmerT_33794-T1
Valid prediction for snap_scaffold_13-snap.3196-T1
Valid prediction for GeneMark_model.58004_t
Valid prediction for GeneMark_model.58028_t
Valid prediction for GlimmerHMM_glimmerT_33774-T1
Valid prediction for GlimmerHMM_glimmerT_33790-T1
Valid prediction for snap_scaffold_13-snap.3189-T1
Valid prediction for snap_scaffold_13-snap.3194-T1
Valid prediction for Augustus_model.g22684.t1
Couldn't classify 23351, 23406
Sorry, prediction GeneMark_model.58036_t fails validation.
(ATG)	 AG	20533-20727	GT	AGG
(GCA)	 AG	21616-21717	GT	TGG
(GAA)	 AG	22614-22746	GT	AGG
(AGG)	 AG	23351-23406	GT	AGG
-recovered GeneMark_model.58036_t, initial, 20533, 20727
-recovered GeneMark_model.58036_t, internal, 20533, 20727
-recovered GeneMark_model.58036_t, internal, 21616, 21717
-recovered GeneMark_model.58036_t, internal, 22614, 22746
-recovered GeneMark_model.58036_t, internal, 23351, 23406
Valid prediction for snap_scaffold_13-snap.3220-T1
Valid prediction for Augustus_model.g22694.t1
Couldn't classify 37252, 37314
Sorry, prediction pasa_asmbl_10270.p1 fails validation.
(ATG)	 AC	34589-34720	GT	GGG
(GTG)	 AG	36360-36542	GT	AGG
(GAG)	 AG	36633-36707	GT	AGG
(GCC)	 AG	36935-37024	GT	GTG
(TGT)	 AG	37252-37314	TG	ACT
-recovered pasa_asmbl_10270.p1, initial, 34589, 34720
-recovered pasa_asmbl_10270.p1, internal, 36360, 36542
-recovered pasa_asmbl_10270.p1, internal, 36633, 36707
-recovered pasa_asmbl_10270.p1, internal, 36935, 37024
Valid prediction for GeneMark_model.58000_t
Valid prediction for snap_scaffold_13-snap.3192-T1
Valid prediction for GeneMark_model.58017_t
Couldn't classify 141619, 142179
Sorry, prediction pasa_asmbl_10256.p1 fails validation.
(CGC)	 GC	141619-142179	CC	CTC
Valid prediction for GlimmerHMM_glimmerT_33782-T1
Valid prediction for Augustus_model.g22695.t1
Valid prediction for GeneMark_model.58041_t
Couldn't classify 126761, 126788
Couldn't classify 129063, 129100
Sorry, prediction pasa_asmbl_10261.p1 fails validation.
(CAG)	 AA	126761-126788	GT	AGG
(GAG)	 AG	127392-127514	GT	CAG
(CCC)	 AG	127640-127761	GT	AGG
(GTG)	 AG	127853-128013	GT	AGG
(TCT)	 AG	128249-128355	GT	CGG
(ATG)	 AG	128447-128638	GT	AGG
(ATG)	 AG	129063-129100	CT	CCC
-recovered pasa_asmbl_10261.p1, initial, 128447, 128638
-recovered pasa_asmbl_10261.p1, internal, 127392, 127514
-recovered pasa_asmbl_10261.p1, internal, 127640, 127761
-recovered pasa_asmbl_10261.p1, internal, 127853, 128013
-recovered pasa_asmbl_10261.p1, internal, 128249, 128355
-recovered pasa_asmbl_10261.p1, internal, 128447, 128638
Valid prediction for snap_scaffold_13-snap.3202-T1
Valid prediction for GeneMark_model.58038_t
Valid prediction for snap_scaffold_13-snap.3212-T1
Valid prediction for GlimmerHMM_glimmerT_33783-T1
Valid prediction for snap_scaffold_13-snap.3198-T1
Valid prediction for GlimmerHMM_glimmerT_33780-T1
Valid prediction for GeneMark_model.58009_t
Couldn't classify 78094, 78327
Sorry, prediction pasa_asmbl_10263.p1 fails validation.
(ATG)	 AC	76813-76843	GT	CGG
(GGT)	 AG	77591-77643	GT	AGG
(GAA)	 AG	77791-77907	GT	AGG
(CTG)	 AG	78094-78327	TG	GGT
-recovered pasa_asmbl_10263.p1, initial, 76813, 76843
-recovered pasa_asmbl_10263.p1, internal, 77591, 77643
-recovered pasa_asmbl_10263.p1, internal, 77791, 77907
Valid prediction for GeneMark_model.57997_t
Valid prediction for GlimmerHMM_glimmerT_33787-T1
Valid prediction for GeneMark_model.58032_t
Valid prediction for GeneMark_model.58015_t
Valid prediction for Augustus_model.g22685.t1
Valid prediction for GeneMark_model.58019_t
Valid prediction for Augustus_model.g22690.t1
Valid prediction for Augustus_model.g22696.t1
Valid prediction for snap_scaffold_13-snap.3204-T1
Valid prediction for GeneMark_model.57996_t
Valid prediction for snap_scaffold_13-snap.3190-T1
Valid prediction for HiQ_model.g22691.t1
Valid prediction for GeneMark_model.58005_t
Valid prediction for HiQ_model.g22683.t1
Valid prediction for snap_scaffold_13-snap.3207-T1
Valid prediction for GeneMark_model.58002_t
Couldn't classify 115869, 116044
Couldn't classify 116986, 117119
Sorry, prediction pasa_asmbl_10305.p1 fails validation.
(AGG)	 CC	115869-116044	GT	AAG
(CAC)	 AG	116606-116652	GT	ATG
(ATG)	 AG	116986-117119	CA	CAC
-recovered pasa_asmbl_10305.p1, internal, 116606, 116652
Valid prediction for GeneMark_model.58011_t
Valid prediction for GlimmerHMM_glimmerT_33792-T1
Valid prediction for Augustus_model.g22688.t1
Valid prediction for snap_scaffold_13-snap.3217-T1
Valid prediction for GlimmerHMM_glimmerT_33775-T1
Valid prediction for GlimmerHMM_glimmerT_33777-T1
Valid prediction for GeneMark_model.58013_t
Valid prediction for GeneMark_model.58021_t
Valid prediction for GeneMark_model.57999_t
Couldn't classify 33205, 33268
Sorry, prediction GeneMark_model.58035_t fails validation.
(GGA)	 AG	33205-33268	GT	GAG
(AAC)	 AG	33334-33985	GT	TGG
(TGG)	 AG	34685-34720	GT	GGG
(TGG)	 AG	35652-35687	GT	GGG
(GTG)	 AG	36360-36542	GT	AGG
(GAG)	 AG	36633-36707	GT	AGG
(CAG)	 AG	36764-36784	AA	GAA
-recovered GeneMark_model.58035_t, terminal, 36764, 36784
-recovered GeneMark_model.58035_t, internal, 33205, 33268
-recovered GeneMark_model.58035_t, internal, 33334, 33985
-recovered GeneMark_model.58035_t, internal, 34685, 34720
-recovered GeneMark_model.58035_t, internal, 35652, 35687
-recovered GeneMark_model.58035_t, internal, 36360, 36542
-recovered GeneMark_model.58035_t, internal, 36633, 36707
Valid prediction for snap_scaffold_13-snap.3214-T1
Valid prediction for snap_scaffold_13-snap.3219-T1
Couldn't classify 149832, 150022
Sorry, prediction pasa_asmbl_10297.p1 fails validation.
(ATG)	 AG	149350-149461	GT	AGG
(GTC)	 AG	149832-150022	CC	CCC
-recovered pasa_asmbl_10297.p1, initial, 149350, 149461
-recovered pasa_asmbl_10297.p1, internal, 149350, 149461
Valid prediction for GeneMark_model.58026_t
Valid prediction for snap_scaffold_13-snap.3209-T1
Valid prediction for GlimmerHMM_glimmerT_33798-T1
Valid prediction for GlimmerHMM_glimmerT_33779-T1
Valid prediction for GeneMark_model.58030_t
Valid prediction for GlimmerHMM_glimmerT_33784-T1
Valid prediction for GlimmerHMM_glimmerT_33786-T1
Valid prediction for GeneMark_model.58024_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 16075, rend_intergenic: 16072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 122076, rend_intergenic: 122073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9645, rend_intergenic: 4028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14585, rend_intergenic: 10750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30706, rend_intergenic: 22023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49305, rend_intergenic: 46037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52515, rend_intergenic: 50556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69943, rend_intergenic: 63624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74241, rend_intergenic: 71368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79250, rend_intergenic: 76336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90305, rend_intergenic: 88769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93782, rend_intergenic: 90771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104362, rend_intergenic: 95515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106264, rend_intergenic: 104869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112481, rend_intergenic: 107392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115596, rend_intergenic: 112985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121474, rend_intergenic: 117927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134466, rend_intergenic: 122073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142325, rend_intergenic: 135832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149042, rend_intergenic: 147654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156062
-exon list size: 619


building trellis

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82.4    
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    
84.9    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.7    
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 34 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 16075, rend_intergenic: 16072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 122076, rend_intergenic: 122073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9645, rend_intergenic: 4028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14585, rend_intergenic: 10750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30706, rend_intergenic: 22023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49305, rend_intergenic: 46037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52515, rend_intergenic: 50556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69943, rend_intergenic: 63624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74241, rend_intergenic: 71368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79250, rend_intergenic: 76336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90305, rend_intergenic: 88769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93782, rend_intergenic: 90771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104362, rend_intergenic: 95515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106264, rend_intergenic: 104869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112481, rend_intergenic: 107392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115596, rend_intergenic: 112985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121474, rend_intergenic: 117927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134466, rend_intergenic: 122073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142325, rend_intergenic: 135832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149042, rend_intergenic: 147654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support