-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_209806-404271

-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_15-snap.76-T1
Valid prediction for GeneMark_model.62263_t
Valid prediction for GeneMark_model.62281_t
Valid prediction for GlimmerHMM_glimmerT_36209-T1
Valid prediction for snap_scaffold_15-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_36196-T1
Valid prediction for GeneMark_model.62285_t
Valid prediction for GlimmerHMM_glimmerT_36221-T1
Valid prediction for snap_scaffold_15-snap.52-T1
Couldn't classify 186156, 186246
Sorry, prediction pasa_asmbl_13915.p1 fails validation.
(TTT)	 AG	186156-186246	GT	GAG
(CTA)	 AG	186678-186745	GT	AGG
(AGA)	 AG	186878-186942	GT	AGG
(CAA)	 AG	187090-187207	GT	AGG
(TTC)	 AG	187372-187514	GT	AGG
(GAT)	 AG	187607-187703	GT	ATG
(AGC)	 AG	188237-188353	GT	TGG
(GTG)	 AG	188481-188605	GT	AGG
(CTG)	 AG	188709-188775	GT	AGG
(GAA)	 AG	189513-189624	GT	AGG
(GTG)	 AG	190073-190169	GT	GAG
(CTC)	 AG	190335-190458	GT	AGG
(GAC)	 AG	190607-190849	CA	AAC
-recovered pasa_asmbl_13915.p1, terminal, 190607, 190849
-recovered pasa_asmbl_13915.p1, internal, 186156, 186246
-recovered pasa_asmbl_13915.p1, internal, 186678, 186745
-recovered pasa_asmbl_13915.p1, internal, 186878, 186942
-recovered pasa_asmbl_13915.p1, internal, 187090, 187207
-recovered pasa_asmbl_13915.p1, internal, 187372, 187514
-recovered pasa_asmbl_13915.p1, internal, 187607, 187703
-recovered pasa_asmbl_13915.p1, internal, 188237, 188353
-recovered pasa_asmbl_13915.p1, internal, 188481, 188605
-recovered pasa_asmbl_13915.p1, internal, 188709, 188775
-recovered pasa_asmbl_13915.p1, internal, 189513, 189624
-recovered pasa_asmbl_13915.p1, internal, 190073, 190169
-recovered pasa_asmbl_13915.p1, internal, 190335, 190458
Valid prediction for HiQ_model.g24356.t1
Valid prediction for GeneMark_model.62269_t
Valid prediction for snap_scaffold_15-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_36212-T1
Valid prediction for GeneMark_model.62296_t
Valid prediction for GlimmerHMM_glimmerT_36201-T1
Valid prediction for snap_scaffold_15-snap.47-T1
Valid prediction for CodingQuarry_transcript_17848-T1
Valid prediction for GlimmerHMM_glimmerT_36204-T1
Valid prediction for GeneMark_model.62299_t
Valid prediction for snap_scaffold_15-snap.55-T1
Valid prediction for GeneMark_model.62267_t
Valid prediction for snap_scaffold_15-snap.56-T1
Valid prediction for GeneMark_model.62261_t
Valid prediction for Augustus_model.g24350.t1
Valid prediction for snap_scaffold_15-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_36192-T1
Valid prediction for snap_scaffold_15-snap.58-T1
Valid prediction for GeneMark_model.62265_t
Valid prediction for GeneMark_model.62288_t
Valid prediction for Augustus_model.g24349.t1
Valid prediction for GeneMark_model.62258_t
Valid prediction for GlimmerHMM_glimmerT_36195-T1
Valid prediction for GlimmerHMM_glimmerT_36202-T1
Valid prediction for GeneMark_model.62272_t
Valid prediction for pasa_asmbl_13904.p1
Valid prediction for GlimmerHMM_glimmerT_36191-T1
Valid prediction for pasa_asmbl_13913.p1
Valid prediction for GeneMark_model.62302_t
Valid prediction for GeneMark_model.62290_t
Valid prediction for HiQ_model.g24354.t1
Valid prediction for snap_scaffold_15-snap.79-T1
Valid prediction for Augustus_model.g24348.t1
Valid prediction for GlimmerHMM_glimmerT_36219-T1
Valid prediction for Augustus_model.g24355.t1
Valid prediction for GeneMark_model.62304_t
Valid prediction for snap_scaffold_15-snap.61-T1
Valid prediction for GlimmerHMM_glimmerT_36216-T1
Valid prediction for GlimmerHMM_glimmerT_36218-T1
Valid prediction for snap_scaffold_15-snap.53-T1
Valid prediction for snap_scaffold_15-snap.70-T1
Valid prediction for GlimmerHMM_glimmerT_36214-T1
Valid prediction for CodingQuarry_transcript_17844-T1
Valid prediction for snap_scaffold_15-snap.51-T1
Valid prediction for GlimmerHMM_glimmerT_36200-T1
Valid prediction for GeneMark_model.62283_t
Valid prediction for Augustus_model.g24346.t1
Valid prediction for snap_scaffold_15-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_36217-T1
Valid prediction for snap_scaffold_15-snap.62-T1
Valid prediction for GeneMark_model.62275_t
Valid prediction for HiQ_model.g24358.t1
Couldn't classify 125832, 126025
Couldn't classify 131044, 131212
Sorry, prediction pasa_asmbl_13899.p1 fails validation.
(ACG)	 AG	125832-126025	GT	TGG
(CCA)	 AG	127785-127953	GT	AGG
(GAC)	 AG	128611-128717	GT	AGG
(GAG)	 AG	131044-131212	TG	GTT
-recovered pasa_asmbl_13899.p1, terminal, 128611, 128717
-recovered pasa_asmbl_13899.p1, internal, 125832, 126025
-recovered pasa_asmbl_13899.p1, internal, 127785, 127953
-recovered pasa_asmbl_13899.p1, internal, 128611, 128717
Valid prediction for snap_scaffold_15-snap.63-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.68-T1
Valid prediction for GlimmerHMM_glimmerT_36211-T1
Valid prediction for CodingQuarry_transcript_17847-T1
Valid prediction for GeneMark_model.62253_t
Valid prediction for GeneMark_model.62271_t
Valid prediction for GlimmerHMM_glimmerT_36193-T1
Valid prediction for GeneMark_model.62276_t
Valid prediction for snap_scaffold_15-snap.78-T1
Valid prediction for GeneMark_model.62298_t
Valid prediction for snap_scaffold_15-snap.73-T1
Valid prediction for snap_scaffold_15-snap.45-T1
Valid prediction for GlimmerHMM_glimmerT_36203-T1
Couldn't classify 140055, 140184
Couldn't classify 149351, 149607
Sorry, prediction pasa_asmbl_13902.p1 fails validation.
(AGG)	 CC	140055-140184	GT	AGG
(GCA)	 AG	140329-140465	GT	AGG
(GGT)	 AG	141824-141929	GT	TGG
(GGA)	 AG	143465-143622	GT	AGG
(GTG)	 AG	145350-145527	GT	AGG
(CTT)	 AG	145965-145982	GT	AGG
(AGT)	 AG	146353-146530	GT	AGG
(CAT)	 AG	146619-146787	GT	AGG
(GGG)	 AG	146942-147127	GT	CGG
(GTA)	 AG	147994-148099	GT	AGG
(AGC)	 AG	149351-149607	TG	GGT
-recovered pasa_asmbl_13902.p1, internal, 140329, 140465
-recovered pasa_asmbl_13902.p1, internal, 141824, 141929
-recovered pasa_asmbl_13902.p1, internal, 143465, 143622
-recovered pasa_asmbl_13902.p1, internal, 145350, 145527
-recovered pasa_asmbl_13902.p1, internal, 145965, 145982
-recovered pasa_asmbl_13902.p1, internal, 146353, 146530
-recovered pasa_asmbl_13902.p1, internal, 146619, 146787
-recovered pasa_asmbl_13902.p1, internal, 146942, 147127
-recovered pasa_asmbl_13902.p1, internal, 147994, 148099
Valid prediction for snap_scaffold_15-snap.83-T1
Valid prediction for GeneMark_model.62266_t
Valid prediction for GeneMark_model.62279_t
Valid prediction for snap_scaffold_15-snap.60-T1
Couldn't classify 133191, 133351
Couldn't classify 137685, 137766
Sorry, prediction pasa_asmbl_13901.p1 fails validation.
(GGA)	 CA	133191-133351	GT	TGG
(GTA)	 AG	133531-133684	GT	CCG
(GTG)	 AG	133832-133939	GC	AGG
(AAC)	 AG	134638-134690	GT	AGG
(CAT)	 AG	135896-135991	GT	AGG
(GTT)	 AG	137685-137766	GT	AGG
-recovered pasa_asmbl_13901.p1, internal, 133531, 133684
-recovered pasa_asmbl_13901.p1, internal, 133832, 133939
-recovered pasa_asmbl_13901.p1, internal, 134638, 134690
-recovered pasa_asmbl_13901.p1, internal, 135896, 135991
-recovered pasa_asmbl_13901.p1, internal, 137685, 137766
Valid prediction for GeneMark_model.62255_t
Valid prediction for GlimmerHMM_glimmerT_36207-T1
Valid prediction for Augustus_model.g24347.t1
Valid prediction for GlimmerHMM_glimmerT_36213-T1
Valid prediction for snap_scaffold_15-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_36199-T1
Valid prediction for snap_scaffold_15-snap.77-T1
Valid prediction for GeneMark_model.62273_t
Valid prediction for snap_scaffold_15-snap.82-T1
Valid prediction for Augustus_model.g24345.t1
Valid prediction for GeneMark_model.62287_t
Valid prediction for GeneMark_model.62257_t
Valid prediction for GlimmerHMM_glimmerT_36190-T1
Valid prediction for GeneMark_model.62300_t
Couldn't classify 171053, 171331
Sorry, prediction pasa_asmbl_13907.p1 fails validation.
(GAG)	 GA	171053-171331	GT	GGG
(GTG)	 AG	172677-173259	GT	TGG
(GTG)	 AG	173608-173790	GT	AGG
(GAT)	 AG	174012-174118	GT	AGG
(GTG)	 AG	174213-174731	CG	AGC
-recovered pasa_asmbl_13907.p1, terminal, 174213, 174731
-recovered pasa_asmbl_13907.p1, internal, 172677, 173259
-recovered pasa_asmbl_13907.p1, internal, 173608, 173790
-recovered pasa_asmbl_13907.p1, internal, 174012, 174118
Valid prediction for GlimmerHMM_glimmerT_36205-T1
Valid prediction for Augustus_model.g24351.t1
Valid prediction for GeneMark_model.62292_t
Valid prediction for Augustus_model.g24352.t1
Valid prediction for pasa_asmbl_13914.p1
Valid prediction for CodingQuarry_transcript_17845-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 GeneMark_model.62294_t
Valid prediction for snap_scaffold_15-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_36197-T1
Valid prediction for GeneMark_model.62264_t
Valid prediction for GeneMark_model.62268_t
Valid prediction for GeneMark_model.62301_t
Valid prediction for CodingQuarry_transcript_17846-T1
Valid prediction for GeneMark_model.62256_t
Valid prediction for snap_scaffold_15-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_36210-T1
Valid prediction for GeneMark_model.62270_t
Valid prediction for GeneMark_model.62303_t
Valid prediction for snap_scaffold_15-snap.48-T1
Valid prediction for snap_scaffold_15-snap.71-T1
Valid prediction for snap_scaffold_15-snap.72-T1
Valid prediction for GeneMark_model.62289_t
Valid prediction for GlimmerHMM_glimmerT_36220-T1
Valid prediction for GeneMark_model.62278_t
Valid prediction for snap_scaffold_15-snap.81-T1
Valid prediction for GeneMark_model.62291_t
Valid prediction for GeneMark_model.62262_t
Valid prediction for HiQ_model.g24357.t1
Valid prediction for GeneMark_model.62259_t
Valid prediction for snap_scaffold_15-snap.75-T1
Valid prediction for snap_scaffold_15-snap.64-T1
Valid prediction for HiQ_model.g24353.t1
Valid prediction for GeneMark_model.62277_t
Valid prediction for snap_scaffold_15-snap.44-T1
Valid prediction for snap_scaffold_15-snap.50-T1
Valid prediction for GeneMark_model.62284_t
Valid prediction for GeneMark_model.62295_t
Valid prediction for GeneMark_model.62274_t
Valid prediction for GeneMark_model.62282_t
Valid prediction for GlimmerHMM_glimmerT_36194-T1
Valid prediction for GeneMark_model.62260_t
Valid prediction for snap_scaffold_15-snap.67-T1
Valid prediction for pasa_asmbl_14931.p1
Valid prediction for GeneMark_model.62297_t
Valid prediction for snap_scaffold_15-snap.66-T1
Valid prediction for GeneMark_model.62254_t
Valid prediction for snap_scaffold_15-snap.57-T1
Valid prediction for GlimmerHMM_glimmerT_36208-T1
Valid prediction for snap_scaffold_15-snap.54-T1
Valid prediction for GeneMark_model.62293_t
Valid prediction for GlimmerHMM_glimmerT_36198-T1
Valid prediction for snap_scaffold_15-snap.69-T1
Valid prediction for GeneMark_model.62286_t
Valid prediction for pasa_asmbl_14929.p1
Valid prediction for GlimmerHMM_glimmerT_36215-T1
Valid prediction for GlimmerHMM_glimmerT_36206-T1
Valid prediction for GeneMark_model.62280_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 117463, rend_intergenic: 117460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48424, rend_intergenic: 3087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52887, rend_intergenic: 51824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55979, rend_intergenic: 52928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73542, rend_intergenic: 68009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82457, rend_intergenic: 80786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98479, rend_intergenic: 85828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125335, rend_intergenic: 112622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129436, rend_intergenic: 127858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132019, rend_intergenic: 129582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151715, rend_intergenic: 133670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194466
-exon list size: 709


building trellis

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68.6    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 117463, rend_intergenic: 117460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48424, rend_intergenic: 3087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52887, rend_intergenic: 51824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55979, rend_intergenic: 52928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73542, rend_intergenic: 68009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82457, rend_intergenic: 80786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98479, rend_intergenic: 85828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125335, rend_intergenic: 112622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129436, rend_intergenic: 127858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132019, rend_intergenic: 129582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151715, rend_intergenic: 133670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10614
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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