-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_3418392-3577364

-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.15275_t
Valid prediction for GeneMark_model.15282_t
Valid prediction for snap_scaffold_4-snap.788-T1
Valid prediction for GeneMark_model.15267_t
Valid prediction for snap_scaffold_4-snap.775-T1
Valid prediction for GlimmerHMM_glimmerT_9253-T1
Valid prediction for GlimmerHMM_glimmerT_9266-T1
Valid prediction for GeneMark_model.15285_t
Valid prediction for GlimmerHMM_glimmerT_9262-T1
Valid prediction for snap_scaffold_4-snap.791-T1
Valid prediction for snap_scaffold_4-snap.768-T1
Valid prediction for GeneMark_model.15261_t
Valid prediction for GeneMark_model.15250_t
Valid prediction for GeneMark_model.15258_t
Valid prediction for GlimmerHMM_glimmerT_9272-T1
Valid prediction for CodingQuarry_transcript_48819-T1
Valid prediction for snap_scaffold_4-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_9254-T1
Valid prediction for GlimmerHMM_glimmerT_9258-T1
Valid prediction for Augustus_model.g6005.t1
Valid prediction for GeneMark_model.15273_t
Valid prediction for GlimmerHMM_glimmerT_9250-T1
Valid prediction for GlimmerHMM_glimmerT_9268-T1
Valid prediction for snap_scaffold_4-snap.781-T1
Valid prediction for pasa_asmbl_42524.p2
Valid prediction for GeneMark_model.15271_t
Valid prediction for Augustus_model.g6015.t1
Valid prediction for snap_scaffold_4-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_9271-T1
Couldn't classify 136370, 136789
Sorry, prediction pasa_asmbl_42525.p2 fails validation.
(ATG)	 CC	136370-136789	AC	ACA
Valid prediction for snap_scaffold_4-snap.770-T1
Valid prediction for snap_scaffold_4-snap.792-T1
Valid prediction for GeneMark_model.15289_t
Valid prediction for snap_scaffold_4-snap.809-T1
Valid prediction for GlimmerHMM_glimmerT_9242-T1
Valid prediction for snap_scaffold_4-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_9273-T1
Valid prediction for GeneMark_model.15292_t
Valid prediction for GeneMark_model.15254_t
Valid prediction for snap_scaffold_4-snap.807-T1
Valid prediction for GeneMark_model.15279_t
Valid prediction for snap_scaffold_4-snap.786-T1
Valid prediction for snap_scaffold_4-snap.801-T1
Valid prediction for GeneMark_model.15287_t
Valid prediction for GeneMark_model.15283_t
Valid prediction for snap_scaffold_4-snap.795-T1
Valid prediction for GlimmerHMM_glimmerT_9263-T1
Valid prediction for Augustus_model.g6009.t1
Valid prediction for snap_scaffold_4-snap.773-T1
Valid prediction for snap_scaffold_4-snap.802-T1
Valid prediction for GeneMark_model.15269_t
Valid prediction for GeneMark_model.15265_t
Valid prediction for GeneMark_model.15278_t
Valid prediction for GeneMark_model.15256_t
Valid prediction for snap_scaffold_4-snap.798-T1
Valid prediction for GeneMark_model.15291_t
Valid prediction for GeneMark_model.15288_t
Valid prediction for Augustus_model.g6013.t1
Valid prediction for GeneMark_model.15252_t
Valid prediction for snap_scaffold_4-snap.799-T1
Valid prediction for snap_scaffold_4-snap.805-T1
Valid prediction for Augustus_model.g6011.t1
Valid prediction for snap_scaffold_4-snap.776-T1
Valid prediction for GeneMark_model.15248_t
Valid prediction for GlimmerHMM_glimmerT_9244-T1
Valid prediction for snap_scaffold_4-snap.796-T1
Valid prediction for Augustus_model.g6014.t1
Valid prediction for GlimmerHMM_glimmerT_9264-T1
Valid prediction for Augustus_model.g6002.t1
Valid prediction for GlimmerHMM_glimmerT_9269-T1
Valid prediction for GeneMark_model.15263_t
Valid prediction for Augustus_model.g5998.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.15274_t
Valid prediction for snap_scaffold_4-snap.787-T1
Valid prediction for GlimmerHMM_glimmerT_9270-T1
Couldn't classify 134971, 135100
Couldn't classify 137054, 137529
Sorry, prediction pasa_asmbl_41185.p1 fails validation.
(GGG)	 AG	134971-135100	GT	AGG
(AAG)	 AG	137054-137529	GG	AGG
-recovered pasa_asmbl_41185.p1, internal, 134971, 135100
Valid prediction for Augustus_model.g5996.t1
Valid prediction for GeneMark_model.15266_t
Valid prediction for GeneMark_model.15290_t
Valid prediction for GeneMark_model.15284_t
Valid prediction for snap_scaffold_4-snap.778-T1
Valid prediction for GeneMark_model.15276_t
Valid prediction for GlimmerHMM_glimmerT_9251-T1
Valid prediction for snap_scaffold_4-snap.774-T1
Valid prediction for GlimmerHMM_glimmerT_9252-T1
Valid prediction for GeneMark_model.15255_t
Valid prediction for HiQ_model.g5995.t1
Valid prediction for Augustus_model.g6004.t1
Valid prediction for snap_scaffold_4-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_9265-T1
Valid prediction for GeneMark_model.15270_t
Valid prediction for Augustus_model.g6007.t1
Valid prediction for GlimmerHMM_glimmerT_9241-T1
Valid prediction for Augustus_model.g5997.t1
Valid prediction for HiQ_model.g6008.t1
Valid prediction for snap_scaffold_4-snap.800-T1
Valid prediction for GlimmerHMM_glimmerT_9257-T1
Valid prediction for GlimmerHMM_glimmerT_9245-T1
Couldn't classify 97375, 97411
Couldn't classify 99366, 99562
Sorry, prediction pasa_asmbl_41189.p1 fails validation.
(GTC)	 AC	97375-97411	GT	AGG
(GGA)	 AG	97999-98106	GT	AGG
(GAG)	 AG	99366-99562	GA	ACG
-recovered pasa_asmbl_41189.p1, internal, 97999, 98106
Valid prediction for Augustus_model.g6012.t1
Valid prediction for GeneMark_model.15286_t
Valid prediction for GlimmerHMM_glimmerT_9260-T1
Valid prediction for snap_scaffold_4-snap.808-T1
Valid prediction for snap_scaffold_4-snap.793-T1
Valid prediction for GeneMark_model.15268_t
Valid prediction for GeneMark_model.15257_t
Valid prediction for GlimmerHMM_glimmerT_9248-T1
Valid prediction for pasa_asmbl_41192.p1
Valid prediction for snap_scaffold_4-snap.806-T1
Valid prediction for snap_scaffold_4-snap.782-T1
Valid prediction for snap_scaffold_4-snap.769-T1
Valid prediction for Augustus_model.g6006.t1
Valid prediction for GeneMark_model.15277_t
Valid prediction for Augustus_model.g6001.t1
Valid prediction for GlimmerHMM_glimmerT_9246-T1
Valid prediction for snap_scaffold_4-snap.790-T1
Valid prediction for Augustus_model.g6000.t1
Valid prediction for GlimmerHMM_glimmerT_9261-T1
Valid prediction for snap_scaffold_4-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_9255-T1
Valid prediction for snap_scaffold_4-snap.777-T1
Valid prediction for Augustus_model.g6010.t1
Valid prediction for Augustus_model.g5999.t1
Valid prediction for snap_scaffold_4-snap.772-T1
Valid prediction for GeneMark_model.15264_t
Valid prediction for GeneMark_model.15253_t
Valid prediction for CodingQuarry_transcript_48816-T1
Valid prediction for GeneMark_model.15251_t
Valid prediction for snap_scaffold_4-snap.810-T1
Valid prediction for snap_scaffold_4-snap.794-T1
Valid prediction for GlimmerHMM_glimmerT_9256-T1
Valid prediction for GeneMark_model.15281_t
Valid prediction for Augustus_model.g6003.t1
Valid prediction for GlimmerHMM_glimmerT_9247-T1
Valid prediction for GeneMark_model.15259_t
Valid prediction for GeneMark_model.15272_t
Couldn't classify 100395, 100973
Sorry, prediction pasa_asmbl_41188.p1 fails validation.
(GTC)	 CC	100395-100973	TA	AGT
Couldn't classify 146190, 146323
Sorry, prediction pasa_asmbl_41184.p1 fails validation.
(CTG)	 CC	146190-146323	GT	CTG
(GGA)	 AG	146870-147174	GT	TAG
(GTG)	 AG	147472-147664	GT	AGG
(GCG)	 AG	147954-148009	GT	GCG
(CCA)	 AG	148462-148523	GT	AGG
(TTA)	 AG	148837-148974	GT	AGG
(GCT)	 AG	149111-149187	GT	AGG
(GTT)	 AG	149386-149401	TG	AGT
-recovered pasa_asmbl_41184.p1, terminal, 149386, 149401
-recovered pasa_asmbl_41184.p1, internal, 146870, 147174
-recovered pasa_asmbl_41184.p1, internal, 147472, 147664
-recovered pasa_asmbl_41184.p1, internal, 147954, 148009
-recovered pasa_asmbl_41184.p1, internal, 148462, 148523
-recovered pasa_asmbl_41184.p1, internal, 148837, 148974
-recovered pasa_asmbl_41184.p1, internal, 149111, 149187
Valid prediction for GeneMark_model.15247_t
Valid prediction for GlimmerHMM_glimmerT_9240-T1
Valid prediction for GeneMark_model.15260_t
Valid prediction for GlimmerHMM_glimmerT_9243-T1
Valid prediction for GeneMark_model.15249_t
Valid prediction for snap_scaffold_4-snap.766-T1
Valid prediction for GlimmerHMM_glimmerT_9274-T1
Valid prediction for CodingQuarry_transcript_48818-T1
Valid prediction for pasa_asmbl_41182.p1
Valid prediction for snap_scaffold_4-snap.780-T1
Valid prediction for snap_scaffold_4-snap.779-T1
Valid prediction for snap_scaffold_4-snap.784-T1
Valid prediction for HiQ_model.g5994.t1
Valid prediction for snap_scaffold_4-snap.771-T1
Valid prediction for GlimmerHMM_glimmerT_9249-T1
Valid prediction for snap_scaffold_4-snap.767-T1
Valid prediction for GeneMark_model.15262_t
Valid prediction for GlimmerHMM_glimmerT_9259-T1
Valid prediction for GlimmerHMM_glimmerT_9267-T1
Valid prediction for snap_scaffold_4-snap.803-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14847, rend_intergenic: 9985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24528, rend_intergenic: 17070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31688, rend_intergenic: 26940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34290, rend_intergenic: 31744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37089, rend_intergenic: 34298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50489, rend_intergenic: 47470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53502, rend_intergenic: 51376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69416, rend_intergenic: 63269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75132, rend_intergenic: 72441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77779, rend_intergenic: 75951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86471, rend_intergenic: 79493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93299, rend_intergenic: 87056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100115, rend_intergenic: 93310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105638, rend_intergenic: 104213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110887, rend_intergenic: 107743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113697, rend_intergenic: 111385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117475, rend_intergenic: 113719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152421, rend_intergenic: 152219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157178, rend_intergenic: 153750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 121766, rend_intergenic: 121763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158973
-exon list size: 674


building trellis

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87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 14847, rend_intergenic: 9985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24528, rend_intergenic: 17070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31688, rend_intergenic: 26940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34290, rend_intergenic: 31744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37089, rend_intergenic: 34298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50489, rend_intergenic: 47470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53502, rend_intergenic: 51376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69416, rend_intergenic: 63269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75132, rend_intergenic: 72441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77779, rend_intergenic: 75951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86471, rend_intergenic: 79493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93299, rend_intergenic: 87056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100115, rend_intergenic: 93310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105638, rend_intergenic: 104213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110887, rend_intergenic: 107743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113697, rend_intergenic: 111385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117475, rend_intergenic: 113719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152421, rend_intergenic: 152219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157178, rend_intergenic: 153750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 121766, rend_intergenic: 121763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 148686 - 158973
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 3 predictions from path traversal
GOT 5prime partial gene.

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