-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_2581098-2761205

-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 HiQ_model.g19685.t1
Valid prediction for GlimmerHMM_glimmerT_29579-T1
Valid prediction for Augustus_model.g19693.t1
Valid prediction for Augustus_model.g19682.t1
Couldn't classify 76997, 77198
Sorry, prediction pasa_asmbl_8468.p1 fails validation.
(GGC)	 AG	76997-77198	GT	AGG
(ATC)	 AG	78571-78701	GT	AGG
(CTG)	 AG	80493-80611	GT	CGG
(AGC)	 AG	81341-81602	TT	AAT
-recovered pasa_asmbl_8468.p1, terminal, 81341, 81602
-recovered pasa_asmbl_8468.p1, internal, 76997, 77198
-recovered pasa_asmbl_8468.p1, internal, 78571, 78701
-recovered pasa_asmbl_8468.p1, internal, 80493, 80611
Valid prediction for snap_scaffold_12-snap.536-T1
Valid prediction for GeneMark_model.51132_t
Valid prediction for GeneMark_model.51102_t
Valid prediction for GlimmerHMM_glimmerT_29585-T1
Valid prediction for Augustus_model.g19690.t1
Valid prediction for GeneMark_model.51129_t
Valid prediction for Augustus_model.g19694.t1
Valid prediction for snap_scaffold_12-snap.530-T1
Valid prediction for Augustus_model.g19683.t1
Valid prediction for Augustus_model.g19688.t1
Valid prediction for snap_scaffold_12-snap.550-T1
Valid prediction for Augustus_model.g19689.t1
Valid prediction for GeneMark_model.51100_t
Valid prediction for GeneMark_model.51107_t
Valid prediction for GeneMark_model.51122_t
Valid prediction for HiQ_model.g19687.t1
Valid prediction for snap_scaffold_12-snap.562-T1
Valid prediction for snap_scaffold_12-snap.543-T1
Valid prediction for snap_scaffold_12-snap.551-T1
Valid prediction for snap_scaffold_12-snap.555-T1
Valid prediction for Augustus_model.g19692.t1
Couldn't classify 125438, 125557
Couldn't classify 128560, 128623
Sorry, prediction pasa_asmbl_8477.p1 fails validation.
(GCC)	 GG	125438-125557	GT	CGG
(CAA)	 AG	125777-125840	GT	CAG
(ATG)	 AG	126038-126127	GT	AGG
(CCA)	 AG	126944-127173	GT	GGG
(TTG)	 AG	127622-127696	GT	AGG
(GGC)	 AG	127902-127965	GT	CGG
(GTG)	 AG	128185-128344	GT	AGG
(GTG)	 AG	128560-128623	CT	GGC
add_exon() Sorry, pasa_asmbl_8477.p1 126038-126127-initial-1 is invalid.
-recovered pasa_asmbl_8477.p1, initial, 126038, 126127
-recovered pasa_asmbl_8477.p1, internal, 125777, 125840
-recovered pasa_asmbl_8477.p1, internal, 126038, 126127
-recovered pasa_asmbl_8477.p1, internal, 126944, 127173
-recovered pasa_asmbl_8477.p1, internal, 127622, 127696
-recovered pasa_asmbl_8477.p1, internal, 127902, 127965
-recovered pasa_asmbl_8477.p1, internal, 128185, 128344
Valid prediction for snap_scaffold_12-snap.534-T1
Valid prediction for GeneMark_model.51116_t
Couldn't classify 82831, 83271
Sorry, prediction pasa_asmbl_8473.p1 fails validation.
(TCC)	 CC	82831-83271	TG	GAT
Couldn't classify 84888, 85076
Sorry, prediction pasa_asmbl_8476.p1 fails validation.
(GTG)	 GT	84888-85076	GT	AGG
(GTG)	 AG	85563-85698	GT	CTG
(TCC)	 AG	85961-86058	GT	ACG
(TTC)	 AG	87186-87255	GT	TGG
(ACA)	 AG	88108-88188	GT	AGG
(ATC)	 AG	88566-88675	GT	ACG
(GTG)	 AG	89603-89662	GT	ACG
(GCT)	 AG	90081-90149	GT	TGG
(CTC)	 AG	90472-90548	GT	GGG
(GAT)	 AG	92062-92237	GT	AGG
(GTC)	 AG	94778-95112	AG	GAA
-recovered pasa_asmbl_8476.p1, terminal, 94778, 95112
-recovered pasa_asmbl_8476.p1, internal, 85563, 85698
-recovered pasa_asmbl_8476.p1, internal, 85961, 86058
-recovered pasa_asmbl_8476.p1, internal, 87186, 87255
-recovered pasa_asmbl_8476.p1, internal, 88108, 88188
-recovered pasa_asmbl_8476.p1, internal, 88566, 88675
-recovered pasa_asmbl_8476.p1, internal, 89603, 89662
-recovered pasa_asmbl_8476.p1, internal, 90081, 90149
-recovered pasa_asmbl_8476.p1, internal, 90472, 90548
-recovered pasa_asmbl_8476.p1, internal, 92062, 92237
Valid prediction for snap_scaffold_12-snap.540-T1
Valid prediction for GeneMark_model.51105_t
Valid prediction for GeneMark_model.51099_t
Valid prediction for GlimmerHMM_glimmerT_29586-T1
Valid prediction for snap_scaffold_12-snap.528-T1
Valid prediction for GeneMark_model.51123_t
Valid prediction for GeneMark_model.51133_t
Valid prediction for snap_scaffold_12-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_29580-T1
Valid prediction for snap_scaffold_12-snap.558-T1
Valid prediction for GlimmerHMM_glimmerT_29581-T1
Valid prediction for snap_scaffold_12-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_29587-T1
Valid prediction for Augustus_model.g19684.t1
Valid prediction for snap_scaffold_12-snap.541-T1
Valid prediction for snap_scaffold_12-snap.538-T1
Valid prediction for Augustus_model.g19691.t1
Valid prediction for snap_scaffold_12-snap.546-T1
Valid prediction for GeneMark_model.51135_t
Valid prediction for GeneMark_model.51112_t
Valid prediction for GlimmerHMM_glimmerT_29583-T1
Valid prediction for snap_scaffold_12-snap.525-T1
Valid prediction for snap_scaffold_12-snap.533-T1
Valid prediction for GeneMark_model.51128_t
Valid prediction for GeneMark_model.51103_t
Valid prediction for GlimmerHMM_glimmerT_29590-T1
Valid prediction for snap_scaffold_12-snap.544-T1
Valid prediction for GlimmerHMM_glimmerT_29576-T1
Valid prediction for snap_scaffold_12-snap.554-T1
Valid prediction for GeneMark_model.51118_t
Valid prediction for GlimmerHMM_glimmerT_29574-T1
Valid prediction for Augustus_model.g19696.t1
Valid prediction for GeneMark_model.51126_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_12-snap.561-T1
Valid prediction for snap_scaffold_12-snap.548-T1
Valid prediction for snap_scaffold_12-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_29577-T1
Valid prediction for snap_scaffold_12-snap.559-T1
Valid prediction for snap_scaffold_12-snap.526-T1
Valid prediction for snap_scaffold_12-snap.527-T1
Valid prediction for GeneMark_model.51110_t
Valid prediction for GeneMark_model.51108_t
Valid prediction for GlimmerHMM_glimmerT_29588-T1
Valid prediction for GeneMark_model.51134_t
Valid prediction for GlimmerHMM_glimmerT_29589-T1
Valid prediction for GeneMark_model.51111_t
Valid prediction for GeneMark_model.51124_t
Valid prediction for snap_scaffold_12-snap.557-T1
Valid prediction for Augustus_model.g19697.t1
Valid prediction for GlimmerHMM_glimmerT_29582-T1
Valid prediction for GeneMark_model.51101_t
Valid prediction for snap_scaffold_12-snap.556-T1
Valid prediction for snap_scaffold_12-snap.529-T1
Valid prediction for GlimmerHMM_glimmerT_29584-T1
Couldn't classify 6056, 6086
Couldn't classify 6914, 7041
Sorry, prediction pasa_asmbl_8301.p1 fails validation.
(AAG)	 CG	6056-6086	GT	TGG
(ATG)	 AG	6191-6294	GT	AAG
(GAG)	 AG	6637-6760	GT	TGG
(GTA)	 AG	6914-7041	GT	AGG
add_exon() Sorry, pasa_asmbl_8301.p1 6191-6294-initial-1 is invalid.
-recovered pasa_asmbl_8301.p1, initial, 6191, 6294
-recovered pasa_asmbl_8301.p1, internal, 6191, 6294
-recovered pasa_asmbl_8301.p1, internal, 6637, 6760
-recovered pasa_asmbl_8301.p1, internal, 6914, 7041
Valid prediction for snap_scaffold_12-snap.549-T1
Valid prediction for GlimmerHMM_glimmerT_29591-T1
Valid prediction for snap_scaffold_12-snap.535-T1
Valid prediction for GeneMark_model.51130_t
Valid prediction for Augustus_model.g19686.t1
Valid prediction for GeneMark_model.51136_t
Valid prediction for GlimmerHMM_glimmerT_29592-T1
Valid prediction for GlimmerHMM_glimmerT_29578-T1
Valid prediction for GeneMark_model.51119_t
Valid prediction for GeneMark_model.51131_t
Valid prediction for snap_scaffold_12-snap.547-T1
Valid prediction for GeneMark_model.51125_t
Valid prediction for GeneMark_model.51121_t
Valid prediction for GeneMark_model.51117_t
Couldn't classify 8171, 8206
Couldn't classify 9290, 9337
Sorry, prediction pasa_asmbl_8292.p1 fails validation.
(CGT)	 AA	8171-8206	GT	AGG
(GGT)	 AG	8650-8884	GT	TGG
(ATT)	 AG	9043-9149	GC	AGG
(TTG)	 AG	9290-9337	AC	TCA
-recovered pasa_asmbl_8292.p1, internal, 8650, 8884
-recovered pasa_asmbl_8292.p1, internal, 9043, 9149
Valid prediction for GeneMark_model.51115_t
Valid prediction for GeneMark_model.51106_t
Valid prediction for GeneMark_model.51120_t
Valid prediction for snap_scaffold_12-snap.542-T1
Valid prediction for snap_scaffold_12-snap.552-T1
Valid prediction for snap_scaffold_12-snap.553-T1
Valid prediction for GeneMark_model.51109_t
Valid prediction for snap_scaffold_12-snap.531-T1
Valid prediction for GeneMark_model.51127_t
Valid prediction for GeneMark_model.51104_t
Valid prediction for GeneMark_model.51113_t
Valid prediction for Augustus_model.g19695.t1
Valid prediction for snap_scaffold_12-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_29575-T1
Valid prediction for snap_scaffold_12-snap.539-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32661, rend_intergenic: 31390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43772, rend_intergenic: 38510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45673, rend_intergenic: 44940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50297, rend_intergenic: 46840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74518, rend_intergenic: 68776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81446, rend_intergenic: 79770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91512, rend_intergenic: 89083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92971, rend_intergenic: 92063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107130, rend_intergenic: 104665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117075, rend_intergenic: 114645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136289, rend_intergenic: 131201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179137, rend_intergenic: 174965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180108
-exon list size: 589


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 32661, rend_intergenic: 31390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43772, rend_intergenic: 38510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45673, rend_intergenic: 44940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50297, rend_intergenic: 46840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74518, rend_intergenic: 68776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81446, rend_intergenic: 79770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91512, rend_intergenic: 89083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92971, rend_intergenic: 92063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107130, rend_intergenic: 104665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117075, rend_intergenic: 114645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136289, rend_intergenic: 131201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179137, rend_intergenic: 174965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support