-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_3774924-4078787

-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_5-snap.783-T1
Valid prediction for snap_scaffold_5-snap.753-T1
Couldn't classify 85604, 85894
Sorry, prediction pasa_asmbl_45250.p1 fails validation.
(ACC)	 TC	85604-85894	GT	AGG
(AGC)	 AG	85995-86267	GT	AGG
(GGA)	 AG	86361-87179	GG	GAG
-recovered pasa_asmbl_45250.p1, terminal, 86361, 87179
-recovered pasa_asmbl_45250.p1, internal, 85995, 86267
Valid prediction for GlimmerHMM_glimmerT_11733-T1
Valid prediction for snap_scaffold_5-snap.776-T1
Valid prediction for pasa_asmbl_45241.p1
Valid prediction for GlimmerHMM_glimmerT_11723-T1
Valid prediction for GlimmerHMM_glimmerT_11735-T1
Valid prediction for snap_scaffold_5-snap.766-T1
Valid prediction for HiQ_model.g7672.t1
Valid prediction for GlimmerHMM_glimmerT_11741-T1
Valid prediction for CodingQuarry_transcript_52010-T1
Valid prediction for Augustus_model.g7667.t1
Valid prediction for GlimmerHMM_glimmerT_11726-T1
Couldn't classify 229683, 229827
Couldn't classify 230515, 230596
Sorry, prediction pasa_asmbl_45261.p1 fails validation.
(TGC)	 TG	229683-229827	GT	TGG
(GAA)	 AG	230130-230168	GT	ACG
(AGA)	 AG	230287-230359	GT	AGG
(CTT)	 AG	230515-230596	GG	CAG
-recovered pasa_asmbl_45261.p1, internal, 230130, 230168
-recovered pasa_asmbl_45261.p1, internal, 230287, 230359
Valid prediction for GlimmerHMM_glimmerT_11724-T1
Valid prediction for GlimmerHMM_glimmerT_11734-T1
Valid prediction for Augustus_model.g7664.t1
Valid prediction for CodingQuarry_transcript_52014-T1
Valid prediction for GlimmerHMM_glimmerT_11752-T1
Valid prediction for snap_scaffold_5-snap.773-T1
Valid prediction for CodingQuarry_transcript_52007-T1
Valid prediction for snap_scaffold_5-snap.755-T1
Valid prediction for Augustus_model.g7657.t1
Valid prediction for Augustus_model.g7662.t1
Valid prediction for GlimmerHMM_glimmerT_11728-T1
Valid prediction for Augustus_model.g7660.t1
Couldn't classify 14835, 14896
Couldn't classify 15242, 15590
Sorry, prediction pasa_asmbl_45242.p1 fails validation.
(CTA)	 CG	14835-14896	GT	AGG
(TGC)	 AG	15242-15590	CC	CGC
Valid prediction for pasa_asmbl_45262.p1
Valid prediction for snap_scaffold_5-snap.760-T1
Valid prediction for GlimmerHMM_glimmerT_11744-T1
Couldn't classify 84566, 85273
Sorry, prediction pasa_asmbl_45249.p1 fails validation.
(TCT)	 CA	84566-85273	AA	TGA
Valid prediction for Augustus_model.g7677.t1
Valid prediction for snap_scaffold_5-snap.734-T1
Valid prediction for Augustus_model.g7665.t1
Valid prediction for snap_scaffold_5-snap.738-T1
Couldn't classify 68822, 68974
Sorry, prediction pasa_asmbl_45246.p1 fails validation.
(TTT)	 TG	68822-68974	GT	AGG
(TTC)	 AG	69506-69640	GT	AAG
(GTC)	 AG	69808-69939	CC	GAC
-recovered pasa_asmbl_45246.p1, terminal, 69808, 69939
-recovered pasa_asmbl_45246.p1, internal, 69506, 69640
Valid prediction for HiQ_model.g7669.t1
Valid prediction for HiQ_model.g7678.t1
Valid prediction for HiQ_model.g7666.t1
Couldn't classify 90084, 90440
Sorry, prediction pasa_asmbl_45252.p1 fails validation.
(GAG)	 GG	90084-90440	CT	GAC
Valid prediction for snap_scaffold_5-snap.765-T1
Valid prediction for snap_scaffold_5-snap.745-T1
Valid prediction for pasa_asmbl_45253.p1
Valid prediction for snap_scaffold_5-snap.742-T1
Valid prediction for Augustus_model.g7661.t1
Couldn't classify 88760, 89002
Couldn't classify 89751, 90026
Sorry, prediction pasa_asmbl_45251.p1 fails validation.
(GGA)	 TG	88760-89002	GT	CGG
(TGT)	 AG	89194-89373	GT	ATG
(AAT)	 AG	89751-90026	GT	ATG
-recovered pasa_asmbl_45251.p1, internal, 89194, 89373
-recovered pasa_asmbl_45251.p1, internal, 89751, 90026
Valid prediction for snap_scaffold_5-snap.750-T1
Valid prediction for GlimmerHMM_glimmerT_11740-T1
Valid prediction for pasa_asmbl_45264.p1
Valid prediction for CodingQuarry_transcript_52011-T1
Valid prediction for CodingQuarry_transcript_52009-T1
Valid prediction for GlimmerHMM_glimmerT_11731-T1
Valid prediction for snap_scaffold_5-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_11727-T1
Valid prediction for GlimmerHMM_glimmerT_11748-T1
Valid prediction for snap_scaffold_5-snap.740-T1
Valid prediction for snap_scaffold_5-snap.751-T1
Valid prediction for Augustus_model.g7668.t1
Valid prediction for snap_scaffold_5-snap.752-T1
Valid prediction for GlimmerHMM_glimmerT_11732-T1
Valid prediction for Augustus_model.g7680.t1
Valid prediction for GlimmerHMM_glimmerT_11729-T1
Valid prediction for snap_scaffold_5-snap.775-T1
Valid prediction for CodingQuarry_transcript_52006-T1
Valid prediction for snap_scaffold_5-snap.739-T1
Valid prediction for snap_scaffold_5-snap.749-T1
Valid prediction for GlimmerHMM_glimmerT_11730-T1
Valid prediction for snap_scaffold_5-snap.756-T1
Valid prediction for HiQ_model.g7658.t1
Valid prediction for snap_scaffold_5-snap.784-T1
Valid prediction for snap_scaffold_5-snap.779-T1
Valid prediction for pasa_asmbl_45247.p1
Valid prediction for snap_scaffold_5-snap.746-T1
Valid prediction for pasa_asmbl_46469.p1
Valid prediction for snap_scaffold_5-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_11749-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_5-snap.735-T1
Valid prediction for Augustus_model.g7673.t1
Valid prediction for snap_scaffold_5-snap.774-T1
Valid prediction for snap_scaffold_5-snap.780-T1
Valid prediction for GlimmerHMM_glimmerT_11742-T1
Valid prediction for snap_scaffold_5-snap.754-T1
Valid prediction for snap_scaffold_5-snap.785-T1
Valid prediction for snap_scaffold_5-snap.761-T1
Valid prediction for snap_scaffold_5-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_11751-T1
Valid prediction for pasa_asmbl_43937.p1
Valid prediction for snap_scaffold_5-snap.763-T1
Valid prediction for snap_scaffold_5-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_11746-T1
Valid prediction for snap_scaffold_5-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_11725-T1
Valid prediction for snap_scaffold_5-snap.771-T1
Couldn't classify 139778, 139862
Couldn't classify 142806, 142871
Sorry, prediction pasa_asmbl_43934.p1 fails validation.
(GTA)	 AG	139778-139862	GT	TGG
(CAA)	 AG	140006-140112	GT	AGG
(GCC)	 AG	140396-140473	GT	AGG
(ACC)	 AG	140787-140844	GT	TGG
(TGA)	 AG	141104-141155	GT	AAG
(GGG)	 AG	141478-141537	GT	GTG
(GGG)	 AG	141763-141856	GT	ACG
(TTC)	 AG	142566-142613	GT	GGG
(ATT)	 AG	142806-142871	GG	GTG
-recovered pasa_asmbl_43934.p1, internal, 139778, 139862
-recovered pasa_asmbl_43934.p1, internal, 140006, 140112
-recovered pasa_asmbl_43934.p1, internal, 140396, 140473
-recovered pasa_asmbl_43934.p1, internal, 140787, 140844
-recovered pasa_asmbl_43934.p1, internal, 141104, 141155
-recovered pasa_asmbl_43934.p1, internal, 141478, 141537
-recovered pasa_asmbl_43934.p1, internal, 141763, 141856
-recovered pasa_asmbl_43934.p1, internal, 142566, 142613
Valid prediction for snap_scaffold_5-snap.781-T1
Valid prediction for snap_scaffold_5-snap.764-T1
Valid prediction for Augustus_model.g7676.t1
Valid prediction for snap_scaffold_5-snap.737-T1
Valid prediction for Augustus_model.g7681.t1
Valid prediction for Augustus_model.g7663.t1
Valid prediction for snap_scaffold_5-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_11736-T1
Valid prediction for snap_scaffold_5-snap.777-T1
Valid prediction for snap_scaffold_5-snap.743-T1
Valid prediction for Augustus_model.g7659.t1
Valid prediction for snap_scaffold_5-snap.768-T1
Valid prediction for GlimmerHMM_glimmerT_11747-T1
Valid prediction for snap_scaffold_5-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_11753-T1
Valid prediction for Augustus_model.g7671.t1
Valid prediction for GlimmerHMM_glimmerT_11738-T1
Valid prediction for snap_scaffold_5-snap.741-T1
Valid prediction for snap_scaffold_5-snap.758-T1
Couldn't classify 156926, 157010
Sorry, prediction pasa_asmbl_43931.p2 fails validation.
(TTC)	 GC	156926-157010	GT	AGG
(GGT)	 AG	157130-157434	GA	GAG
-recovered pasa_asmbl_43931.p2, terminal, 157130, 157434
Valid prediction for Augustus_model.g7675.t1
Valid prediction for snap_scaffold_5-snap.767-T1
Valid prediction for GlimmerHMM_glimmerT_11745-T1
Valid prediction for GlimmerHMM_glimmerT_11750-T1
Valid prediction for Augustus_model.g7679.t1
Valid prediction for snap_scaffold_5-snap.759-T1
Valid prediction for pasa_asmbl_44976.p1
Valid prediction for GlimmerHMM_glimmerT_11739-T1
Valid prediction for snap_scaffold_5-snap.736-T1
Valid prediction for HiQ_model.g7674.t1
Valid prediction for snap_scaffold_5-snap.778-T1
Valid prediction for GlimmerHMM_glimmerT_11743-T1
Valid prediction for snap_scaffold_5-snap.762-T1
Couldn't classify 114492, 114851
Sorry, prediction pasa_asmbl_43936.p1 fails validation.
(GGA)	 CG	114492-114851	GA	AGG
Valid prediction for snap_scaffold_5-snap.769-T1
Valid prediction for Augustus_model.g7670.t1
Valid prediction for Augustus_model.g7682.t1
Valid prediction for GlimmerHMM_glimmerT_11737-T1
Valid prediction for CodingQuarry_transcript_52013-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39722, rend_intergenic: 36201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53422, rend_intergenic: 40987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118592, rend_intergenic: 114932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142170, rend_intergenic: 140278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174568, rend_intergenic: 172364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236103, rend_intergenic: 227295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294993, rend_intergenic: 287933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 303864
-exon list size: 488


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 39722, rend_intergenic: 36201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53422, rend_intergenic: 40987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118592, rend_intergenic: 114932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142170, rend_intergenic: 140278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174568, rend_intergenic: 172364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236103, rend_intergenic: 227295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294993, rend_intergenic: 287933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support