-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_20253857-20446723

-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 GlimmerHMM_glimmerT_5784-T1
Valid prediction for GlimmerHMM_glimmerT_5810-T1
Valid prediction for snap_scaffold_2-snap.3983-T1
Valid prediction for snap_scaffold_2-snap.3980-T1
Couldn't classify 6127, 6219
Sorry, prediction pasa_asmbl_25314.p1 fails validation.
(ATG)	 TA	5131-5548	GT	CGG
(ATC)	 AG	5831-5940	GT	AGG
(GCT)	 AG	6127-6219	GT	GGG
-recovered pasa_asmbl_25314.p1, initial, 5131, 5548
-recovered pasa_asmbl_25314.p1, internal, 5831, 5940
-recovered pasa_asmbl_25314.p1, internal, 6127, 6219
Valid prediction for snap_scaffold_2-snap.3984-T1
Valid prediction for snap_scaffold_2-snap.3988-T1
Valid prediction for snap_scaffold_2-snap.3974-T1
Valid prediction for GlimmerHMM_glimmerT_5799-T1
Valid prediction for GlimmerHMM_glimmerT_5776-T1
Valid prediction for CodingQuarry_transcript_28883-T1
Valid prediction for GlimmerHMM_glimmerT_5802-T1
Valid prediction for snap_scaffold_2-snap.3966-T1
Valid prediction for pasa_asmbl_25319.p1
Valid prediction for snap_scaffold_2-snap.3960-T1
Valid prediction for GlimmerHMM_glimmerT_5780-T1
Valid prediction for CodingQuarry_transcript_28884-T1
Valid prediction for GlimmerHMM_glimmerT_5786-T1
Valid prediction for pasa_asmbl_25321.p1
Valid prediction for GlimmerHMM_glimmerT_5775-T1
Valid prediction for GlimmerHMM_glimmerT_5805-T1
Valid prediction for GlimmerHMM_glimmerT_5793-T1
Valid prediction for snap_scaffold_2-snap.3969-T1
Valid prediction for pasa_asmbl_25324.p1
Valid prediction for snap_scaffold_2-snap.3996-T1
Valid prediction for GlimmerHMM_glimmerT_5807-T1
Couldn't classify 56566, 56829
Couldn't classify 56923, 57034
Sorry, prediction CodingQuarry_transcript_28881-T1 fails validation.
(ATG)	 AG	55468-55571	GT	GGG
(ACT)	 AG	55741-55840	GT	ATG
(GTG)	 AG	55920-56043	GT	CAG
(ACT)	 AG	56151-56298	GT	AGG
(GCA)	 AG	56566-56829	GG	AAG
(GGA)	 GG	56923-57034	CA	GAC
-recovered CodingQuarry_transcript_28881-T1, initial, 55468, 55571
-recovered CodingQuarry_transcript_28881-T1, internal, 55468, 55571
-recovered CodingQuarry_transcript_28881-T1, internal, 55741, 55840
-recovered CodingQuarry_transcript_28881-T1, internal, 55920, 56043
-recovered CodingQuarry_transcript_28881-T1, internal, 56151, 56298
Valid prediction for GlimmerHMM_glimmerT_5794-T1
Valid prediction for snap_scaffold_2-snap.3994-T1
Valid prediction for snap_scaffold_2-snap.3982-T1
Couldn't classify 169290, 169512
Sorry, prediction pasa_asmbl_25327.p1 fails validation.
(GGT)	 CA	169290-169512	GT	AGG
(CTG)	 AG	169597-169751	GT	AGG
(GCT)	 AG	170014-170162	GT	AGG
(GTA)	 AG	170252-170336	GT	AGG
(ATT)	 AG	170556-170622	GT	AGG
(GTT)	 AG	170757-170804	GT	TGG
(AGG)	 AG	170974-171113	GT	CGG
(GCA)	 AG	171201-171410	AG	AAA
-recovered pasa_asmbl_25327.p1, terminal, 170556, 170622
-recovered pasa_asmbl_25327.p1, terminal, 171201, 171410
-recovered pasa_asmbl_25327.p1, internal, 169597, 169751
-recovered pasa_asmbl_25327.p1, internal, 170014, 170162
-recovered pasa_asmbl_25327.p1, internal, 170252, 170336
-recovered pasa_asmbl_25327.p1, internal, 170556, 170622
-recovered pasa_asmbl_25327.p1, internal, 170757, 170804
-recovered pasa_asmbl_25327.p1, internal, 170974, 171113
Valid prediction for snap_scaffold_2-snap.3973-T1
Valid prediction for GlimmerHMM_glimmerT_5809-T1
Valid prediction for snap_scaffold_2-snap.3977-T1
Valid prediction for snap_scaffold_2-snap.3979-T1
Valid prediction for snap_scaffold_2-snap.3990-T1
Valid prediction for snap_scaffold_2-snap.3961-T1
Valid prediction for GlimmerHMM_glimmerT_5800-T1
Valid prediction for snap_scaffold_2-snap.3975-T1
Valid prediction for snap_scaffold_2-snap.4000-T1
Valid prediction for GlimmerHMM_glimmerT_5783-T1
Valid prediction for CodingQuarry_transcript_28880-T1
Valid prediction for CodingQuarry_transcript_28882-T1
Valid prediction for CodingQuarry_transcript_28885-T1
Valid prediction for GlimmerHMM_glimmerT_5778-T1
Valid prediction for GlimmerHMM_glimmerT_5789-T1
Valid prediction for snap_scaffold_2-snap.3964-T1
Valid prediction for GlimmerHMM_glimmerT_5797-T1
Valid prediction for GlimmerHMM_glimmerT_5785-T1
Valid prediction for GlimmerHMM_glimmerT_5801-T1
Valid prediction for GlimmerHMM_glimmerT_5803-T1
Valid prediction for snap_scaffold_2-snap.3999-T1
Valid prediction for snap_scaffold_2-snap.3967-T1
Valid prediction for GlimmerHMM_glimmerT_5787-T1
Valid prediction for snap_scaffold_2-snap.3993-T1
Valid prediction for GlimmerHMM_glimmerT_5792-T1
Valid prediction for snap_scaffold_2-snap.3971-T1
Valid prediction for snap_scaffold_2-snap.3986-T1
Valid prediction for GlimmerHMM_glimmerT_5804-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_2-snap.3959-T1
Valid prediction for GlimmerHMM_glimmerT_5788-T1
Couldn't classify 14917, 14946
Sorry, prediction pasa_asmbl_23989.p1 fails validation.
(ATG)	 CA	12301-12379	GT	GGG
(AGC)	 AG	13105-13320	GT	ACG
(GAC)	 AG	13425-13531	GT	GGG
(TTT)	 AG	13650-13758	GT	AGG
(AGT)	 AG	13894-14010	GT	TGG
(GTC)	 AG	14167-14228	GT	AGG
(GTT)	 AG	14917-14946	TG	ACT
-recovered pasa_asmbl_23989.p1, initial, 12301, 12379
-recovered pasa_asmbl_23989.p1, internal, 13105, 13320
-recovered pasa_asmbl_23989.p1, internal, 13425, 13531
-recovered pasa_asmbl_23989.p1, internal, 13650, 13758
-recovered pasa_asmbl_23989.p1, internal, 13894, 14010
-recovered pasa_asmbl_23989.p1, internal, 14167, 14228
Valid prediction for snap_scaffold_2-snap.3981-T1
Valid prediction for snap_scaffold_2-snap.3976-T1
Valid prediction for GlimmerHMM_glimmerT_5782-T1
Couldn't classify 116182, 116248
Couldn't classify 117842, 117936
Sorry, prediction pasa_asmbl_23897.p1 fails validation.
(GAG)	 AG	116182-116248	GT	GAG
(CTG)	 AG	117192-117377	GT	AGG
(ATC)	 AG	117842-117936	CC	GAC
add_exon() Sorry, pasa_asmbl_23897.p1 116182-116248-terminal-3 is invalid.
-recovered pasa_asmbl_23897.p1, terminal, 116182, 116248
-recovered pasa_asmbl_23897.p1, internal, 116182, 116248
-recovered pasa_asmbl_23897.p1, internal, 117192, 117377
Valid prediction for CodingQuarry_transcript_28886-T1
Valid prediction for GlimmerHMM_glimmerT_5790-T1
Valid prediction for GlimmerHMM_glimmerT_5806-T1
Valid prediction for snap_scaffold_2-snap.3968-T1
Valid prediction for snap_scaffold_2-snap.3965-T1
Valid prediction for snap_scaffold_2-snap.3991-T1
Valid prediction for GlimmerHMM_glimmerT_5781-T1
Valid prediction for snap_scaffold_2-snap.3992-T1
Valid prediction for pasa_asmbl_23899.p1
Valid prediction for GlimmerHMM_glimmerT_5777-T1
Valid prediction for GlimmerHMM_glimmerT_5791-T1
Valid prediction for snap_scaffold_2-snap.3989-T1
Valid prediction for GlimmerHMM_glimmerT_5796-T1
Valid prediction for GlimmerHMM_glimmerT_5798-T1
Valid prediction for snap_scaffold_2-snap.3963-T1
Valid prediction for GlimmerHMM_glimmerT_5808-T1
Valid prediction for CodingQuarry_transcript_28887-T1
Valid prediction for snap_scaffold_2-snap.3962-T1
Valid prediction for GlimmerHMM_glimmerT_5779-T1
Valid prediction for snap_scaffold_2-snap.3987-T1
Couldn't classify 16139, 16160
Sorry, prediction pasa_asmbl_23903.p1 fails validation.
(GAA)	 GG	16139-16160	GT	CAG
(ACC)	 AG	16235-16376	GT	AGG
(TAT)	 AG	16484-16667	GT	CTG
(GGT)	 AG	16840-16939	GT	AGG
(GTG)	 AG	17102-17220	GT	TGG
(AGT)	 AG	17408-17445	GT	GCG
(GCC)	 AG	17532-17644	GT	GGG
(CTG)	 AG	17779-17927	GT	AGG
(TAT)	 AG	18050-18144	GT	AGG
(TGT)	 AG	18411-18489	GT	ACG
(GAT)	 AG	18686-18794	GT	GGG
(GAA)	 AG	19100-19173	CG	GAC
-recovered pasa_asmbl_23903.p1, terminal, 19100, 19173
-recovered pasa_asmbl_23903.p1, internal, 16235, 16376
-recovered pasa_asmbl_23903.p1, internal, 16484, 16667
-recovered pasa_asmbl_23903.p1, internal, 16840, 16939
-recovered pasa_asmbl_23903.p1, internal, 17102, 17220
-recovered pasa_asmbl_23903.p1, internal, 17408, 17445
-recovered pasa_asmbl_23903.p1, internal, 17532, 17644
-recovered pasa_asmbl_23903.p1, internal, 17779, 17927
-recovered pasa_asmbl_23903.p1, internal, 18050, 18144
-recovered pasa_asmbl_23903.p1, internal, 18411, 18489
-recovered pasa_asmbl_23903.p1, internal, 18686, 18794
Valid prediction for snap_scaffold_2-snap.3995-T1
Valid prediction for GlimmerHMM_glimmerT_5795-T1
Valid prediction for snap_scaffold_2-snap.3998-T1
Valid prediction for snap_scaffold_2-snap.3985-T1
Valid prediction for snap_scaffold_2-snap.3978-T1
Valid prediction for snap_scaffold_2-snap.3972-T1
Couldn't classify 117991, 118088
Couldn't classify 122536, 123029
Sorry, prediction pasa_asmbl_23895.p1 fails validation.
(CAG)	 CC	117991-118088	GT	AGG
(ATC)	 AG	118837-119056	GT	AGG
(CTC)	 AG	119383-119547	GT	GGG
(GTG)	 AG	119652-119790	GT	TGG
(TAG)	 AG	122536-123029	CT	GGC
-recovered pasa_asmbl_23895.p1, internal, 118837, 119056
-recovered pasa_asmbl_23895.p1, internal, 119383, 119547
-recovered pasa_asmbl_23895.p1, internal, 119652, 119790
Valid prediction for snap_scaffold_2-snap.3997-T1
Valid prediction for snap_scaffold_2-snap.3970-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10200, rend_intergenic: 5362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14129, rend_intergenic: 10966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21484, rend_intergenic: 15421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39992, rend_intergenic: 36784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51607, rend_intergenic: 40035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75617, rend_intergenic: 69257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89206, rend_intergenic: 78512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91347, rend_intergenic: 90380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112752, rend_intergenic: 91450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120055, rend_intergenic: 115802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125688, rend_intergenic: 123984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139606, rend_intergenic: 132894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149648, rend_intergenic: 140025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192867
-exon list size: 447


building trellis

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-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 10200, rend_intergenic: 5362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14129, rend_intergenic: 10966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21484, rend_intergenic: 15421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39992, rend_intergenic: 36784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51607, rend_intergenic: 40035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75617, rend_intergenic: 69257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89206, rend_intergenic: 78512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91347, rend_intergenic: 90380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112752, rend_intergenic: 91450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120055, rend_intergenic: 115802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125688, rend_intergenic: 123984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139606, rend_intergenic: 132894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149648, rend_intergenic: 140025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support