-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_19071136-19277550

-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_3-snap.3762-T1
Valid prediction for GlimmerHMM_glimmerT_8467-T1
Valid prediction for GlimmerHMM_glimmerT_8461-T1
Valid prediction for GlimmerHMM_glimmerT_8458-T1
Valid prediction for snap_scaffold_3-snap.3759-T1
Valid prediction for GlimmerHMM_glimmerT_8451-T1
Valid prediction for GlimmerHMM_glimmerT_8448-T1
Valid prediction for Augustus_model.g5553.t1
Couldn't classify 68924, 69041
Couldn't classify 72102, 72150
Sorry, prediction pasa_asmbl_40765.p1 fails validation.
(TCC)	 TC	68924-69041	GT	GGG
(AGA)	 AG	69221-69376	GT	TGG
(TGT)	 AG	70765-70925	GT	AGG
(GGC)	 AG	71197-71399	GT	AGG
(AGG)	 AG	72102-72150	GG	TGG
-recovered pasa_asmbl_40765.p1, internal, 69221, 69376
-recovered pasa_asmbl_40765.p1, internal, 70765, 70925
-recovered pasa_asmbl_40765.p1, internal, 71197, 71399
Valid prediction for GlimmerHMM_glimmerT_8471-T1
Valid prediction for snap_scaffold_3-snap.3770-T1
Valid prediction for snap_scaffold_3-snap.3769-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8446-T1
Valid prediction for snap_scaffold_3-snap.3788-T1
Valid prediction for snap_scaffold_3-snap.3777-T1
Valid prediction for snap_scaffold_3-snap.3748-T1
Valid prediction for snap_scaffold_3-snap.3793-T1
Valid prediction for GlimmerHMM_glimmerT_8447-T1
Valid prediction for GlimmerHMM_glimmerT_8449-T1
Valid prediction for snap_scaffold_3-snap.3789-T1
Valid prediction for snap_scaffold_3-snap.3754-T1
Valid prediction for snap_scaffold_3-snap.3787-T1
Valid prediction for GlimmerHMM_glimmerT_8462-T1
Valid prediction for Augustus_model.g5561.t1
Valid prediction for snap_scaffold_3-snap.3790-T1
Couldn't classify 56977, 57070
Couldn't classify 60962, 61018
Sorry, prediction pasa_asmbl_40763.p1 fails validation.
(GAG)	 CA	56977-57070	GT	GGG
(CTG)	 AG	57174-57235	GT	AGG
(GAG)	 AG	57589-57654	GT	AGG
(GCT)	 AG	58457-58522	GT	AGG
(GAT)	 AG	59077-59121	GT	AGG
(GAG)	 AG	59401-59427	GT	TGG
(GAA)	 AG	60619-60684	GT	AGG
(GAG)	 AG	60962-61018	AG	GGA
-recovered pasa_asmbl_40763.p1, internal, 57174, 57235
-recovered pasa_asmbl_40763.p1, internal, 57589, 57654
-recovered pasa_asmbl_40763.p1, internal, 58457, 58522
-recovered pasa_asmbl_40763.p1, internal, 59077, 59121
-recovered pasa_asmbl_40763.p1, internal, 59401, 59427
-recovered pasa_asmbl_40763.p1, internal, 60619, 60684
Valid prediction for snap_scaffold_3-snap.3765-T1
Valid prediction for snap_scaffold_3-snap.3753-T1
Valid prediction for Augustus_model.g5555.t1
Valid prediction for snap_scaffold_3-snap.3752-T1
Valid prediction for GlimmerHMM_glimmerT_8445-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g5556.t1
Valid prediction for GlimmerHMM_glimmerT_8456-T1
Valid prediction for GlimmerHMM_glimmerT_8441-T1
Valid prediction for pasa_asmbl_40761.p1
Valid prediction for snap_scaffold_3-snap.3763-T1
Valid prediction for GlimmerHMM_glimmerT_8454-T1
Valid prediction for GlimmerHMM_glimmerT_8442-T1
Valid prediction for snap_scaffold_3-snap.3785-T1
Valid prediction for snap_scaffold_3-snap.3782-T1
Valid prediction for snap_scaffold_3-snap.3780-T1
Valid prediction for snap_scaffold_3-snap.3791-T1
Valid prediction for snap_scaffold_3-snap.3749-T1
Couldn't classify 65511, 65545
Couldn't classify 67592, 67797
Sorry, prediction pasa_asmbl_40764.p1 fails validation.
(GTC)	 TG	65511-65545	GT	AGG
(TGA)	 AG	66274-66348	GT	AAG
(ACT)	 AG	66471-66708	GT	AGG
(GAT)	 AG	66994-67056	GT	GGG
(CAG)	 AG	67184-67328	GT	AGG
(GCC)	 AG	67592-67797	AA	GCA
-recovered pasa_asmbl_40764.p1, internal, 66274, 66348
-recovered pasa_asmbl_40764.p1, internal, 66471, 66708
-recovered pasa_asmbl_40764.p1, internal, 66994, 67056
-recovered pasa_asmbl_40764.p1, internal, 67184, 67328
Valid prediction for snap_scaffold_3-snap.3784-T1
Valid prediction for Augustus_model.g5552.t1
Valid prediction for GlimmerHMM_glimmerT_8473-T1
Valid prediction for snap_scaffold_3-snap.3775-T1
Valid prediction for GlimmerHMM_glimmerT_8455-T1
Valid prediction for GlimmerHMM_glimmerT_8459-T1
Valid prediction for CodingQuarry_transcript_46483-T1
Valid prediction for snap_scaffold_3-snap.3792-T1
Valid prediction for snap_scaffold_3-snap.3773-T1
Valid prediction for Augustus_model.g5565.t1
Valid prediction for snap_scaffold_3-snap.3756-T1
Valid prediction for GlimmerHMM_glimmerT_8474-T1
Valid prediction for snap_scaffold_3-snap.3767-T1
Valid prediction for snap_scaffold_3-snap.3795-T1
Valid prediction for GlimmerHMM_glimmerT_8464-T1
Valid prediction for snap_scaffold_3-snap.3779-T1
Valid prediction for GlimmerHMM_glimmerT_8472-T1
Valid prediction for snap_scaffold_3-snap.3758-T1
Valid prediction for GlimmerHMM_glimmerT_8457-T1
Valid prediction for snap_scaffold_3-snap.3776-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 snap_scaffold_3-snap.3781-T1
Valid prediction for snap_scaffold_3-snap.3783-T1
Valid prediction for snap_scaffold_3-snap.3766-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8452-T1
Valid prediction for GlimmerHMM_glimmerT_8440-T1
Valid prediction for snap_scaffold_3-snap.3797-T1
Valid prediction for GlimmerHMM_glimmerT_8468-T1
Valid prediction for Augustus_model.g5563.t1
Valid prediction for GlimmerHMM_glimmerT_8470-T1
Valid prediction for snap_scaffold_3-snap.3750-T1
Valid prediction for GlimmerHMM_glimmerT_8450-T1
Valid prediction for GlimmerHMM_glimmerT_8444-T1
Valid prediction for Augustus_model.g5554.t1
Valid prediction for snap_scaffold_3-snap.3778-T1
Valid prediction for GlimmerHMM_glimmerT_8475-T1
Valid prediction for snap_scaffold_3-snap.3751-T1
Valid prediction for snap_scaffold_3-snap.3760-T1
Valid prediction for snap_scaffold_3-snap.3794-T1
Valid prediction for snap_scaffold_3-snap.3771-T1
Valid prediction for GlimmerHMM_glimmerT_8443-T1
Valid prediction for snap_scaffold_3-snap.3786-T1
Valid prediction for Augustus_model.g5551.t1
Valid prediction for snap_scaffold_3-snap.3768-T1
Valid prediction for Augustus_model.g5558.t1
Valid prediction for GlimmerHMM_glimmerT_8469-T1
Valid prediction for Augustus_model.g5560.t1
Valid prediction for snap_scaffold_3-snap.3761-T1
Valid prediction for snap_scaffold_3-snap.3774-T1
Valid prediction for snap_scaffold_3-snap.3755-T1
Valid prediction for GlimmerHMM_glimmerT_8453-T1
Valid prediction for snap_scaffold_3-snap.3757-T1
Valid prediction for GlimmerHMM_glimmerT_8465-T1
Valid prediction for GlimmerHMM_glimmerT_8463-T1
Valid prediction for Augustus_model.g5559.t1
Valid prediction for Augustus_model.g5564.t1
Valid prediction for snap_scaffold_3-snap.3796-T1
Valid prediction for Augustus_model.g5562.t1
Valid prediction for Augustus_model.g5557.t1
Valid prediction for GlimmerHMM_glimmerT_8460-T1
Valid prediction for GlimmerHMM_glimmerT_8466-T1
Valid prediction for snap_scaffold_3-snap.3772-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3764-T1
Valid prediction for Augustus_model.g5566.t1
Couldn't classify 113137, 113271
Sorry, prediction pasa_asmbl_39640.p1 fails validation.
(GCG)	 CA	113137-113271	GT	AGG
(ATA)	 AG	113441-113564	GT	AGG
(GTG)	 AG	114006-114181	GT	TCG
(GTC)	 AG	114376-114508	GT	GGG
(GAA)	 AG	116384-116475	GT	AGG
(AAG)	 AG	116906-117052	GT	ACG
(GAC)	 AG	117762-117862	GT	AGG
(GCA)	 AG	118087-119515	AG	AGA
-recovered pasa_asmbl_39640.p1, terminal, 118087, 119515
-recovered pasa_asmbl_39640.p1, internal, 113441, 113564
-recovered pasa_asmbl_39640.p1, internal, 114006, 114181
-recovered pasa_asmbl_39640.p1, internal, 114376, 114508
-recovered pasa_asmbl_39640.p1, internal, 116384, 116475
-recovered pasa_asmbl_39640.p1, internal, 116906, 117052
-recovered pasa_asmbl_39640.p1, internal, 117762, 117862

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15046, rend_intergenic: 11886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25036, rend_intergenic: 22016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29935, rend_intergenic: 26438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33712, rend_intergenic: 31201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43135, rend_intergenic: 38722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43933, rend_intergenic: 43235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51094, rend_intergenic: 47341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55621, rend_intergenic: 51900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56138, rend_intergenic: 55649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61072, rend_intergenic: 58752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63710, rend_intergenic: 61227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75450, rend_intergenic: 65376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102786, rend_intergenic: 87316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112312, rend_intergenic: 102973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116535, rend_intergenic: 112333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118054, rend_intergenic: 116732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126190, rend_intergenic: 122986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131406, rend_intergenic: 126727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136636, rend_intergenic: 135202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177822, rend_intergenic: 136860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185980, rend_intergenic: 178041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186533, rend_intergenic: 186180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204838, rend_intergenic: 186854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206415
-exon list size: 480


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 15046, rend_intergenic: 11886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25036, rend_intergenic: 22016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29935, rend_intergenic: 26438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33712, rend_intergenic: 31201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43135, rend_intergenic: 38722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43933, rend_intergenic: 43235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51094, rend_intergenic: 47341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55621, rend_intergenic: 51900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56138, rend_intergenic: 55649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61072, rend_intergenic: 58752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63710, rend_intergenic: 61227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75450, rend_intergenic: 65376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102786, rend_intergenic: 87316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112312, rend_intergenic: 102973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116535, rend_intergenic: 112333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118054, rend_intergenic: 116732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126190, rend_intergenic: 122986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131406, rend_intergenic: 126727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136636, rend_intergenic: 135202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177822, rend_intergenic: 136860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185980, rend_intergenic: 178041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186533, rend_intergenic: 186180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204838, rend_intergenic: 186854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support