-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_8973850-9164412

-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.g19661.t1
Valid prediction for pasa_asmbl_7851.p1
Valid prediction for HiQ_model.g19679.t1
Valid prediction for GlimmerHMM_glimmerT_29756-T1
Valid prediction for GlimmerHMM_glimmerT_29765-T1
Valid prediction for snap_scaffold_12-snap.1690-T1
Valid prediction for GlimmerHMM_glimmerT_29770-T1
Valid prediction for Augustus_model.g19674.t1
Valid prediction for snap_scaffold_12-snap.1711-T1
Valid prediction for HiQ_model.g19667.t1
Valid prediction for snap_scaffold_12-snap.1689-T1
Valid prediction for CodingQuarry_transcript_10328-T1
Valid prediction for GlimmerHMM_glimmerT_29753-T1
Valid prediction for snap_scaffold_12-snap.1680-T1
Valid prediction for pasa_asmbl_8215.p1
Valid prediction for Augustus_model.g19676.t1
Valid prediction for snap_scaffold_12-snap.1694-T1
Couldn't classify 41480, 42076
Sorry, prediction pasa_asmbl_7844.p1 fails validation.
(GGG)	 CA	41480-42076	GT	CGG
(ACG)	 AG	42728-42980	GT	AGG
(GTA)	 AG	45611-45853	GT	GGG
(CTT)	 AG	47243-47347	GT	AGG
(CCT)	 AG	47928-48115	GG	AAG
-recovered pasa_asmbl_7844.p1, terminal, 47928, 48115
-recovered pasa_asmbl_7844.p1, internal, 42728, 42980
-recovered pasa_asmbl_7844.p1, internal, 45611, 45853
-recovered pasa_asmbl_7844.p1, internal, 47243, 47347
Valid prediction for snap_scaffold_12-snap.1688-T1
Valid prediction for snap_scaffold_12-snap.1707-T1
Valid prediction for GlimmerHMM_glimmerT_29774-T1
Valid prediction for snap_scaffold_12-snap.1717-T1
Couldn't classify 21750, 21767
Sorry, prediction pasa_asmbl_7842.p1 fails validation.
(CCC)	 TC	21750-21767	GT	AGG
(CTC)	 AG	23151-23263	GT	CGG
(CTA)	 AG	23395-23599	GT	AGG
(TTC)	 AG	23702-23851	GT	AGG
(CGG)	 AG	24143-24276	GT	AGG
(TTT)	 AG	24473-24581	GT	AGG
(TCC)	 AG	24775-24924	AT	AAA
-recovered pasa_asmbl_7842.p1, terminal, 24775, 24924
-recovered pasa_asmbl_7842.p1, internal, 23151, 23263
-recovered pasa_asmbl_7842.p1, internal, 23395, 23599
-recovered pasa_asmbl_7842.p1, internal, 23702, 23851
-recovered pasa_asmbl_7842.p1, internal, 24143, 24276
-recovered pasa_asmbl_7842.p1, internal, 24473, 24581
Valid prediction for Augustus_model.g19666.t1
Valid prediction for GlimmerHMM_glimmerT_29759-T1
Valid prediction for CodingQuarry_transcript_10330-T1
Valid prediction for snap_scaffold_12-snap.1709-T1
Valid prediction for snap_scaffold_12-snap.1699-T1
Valid prediction for GlimmerHMM_glimmerT_29776-T1
Valid prediction for snap_scaffold_12-snap.1698-T1
Couldn't classify 161995, 162081
Couldn't classify 163386, 163428
Sorry, prediction pasa_asmbl_7853.p1 fails validation.
(GAG)	 CG	161995-162081	GT	TTG
(CTG)	 AG	162246-162357	GT	TGG
(GGT)	 AG	162615-162768	GT	CGG
(TGT)	 AG	162894-162924	GT	CTG
(CAG)	 AG	163031-163119	GT	AAG
(CTA)	 AG	163386-163428	AC	CCA
-recovered pasa_asmbl_7853.p1, internal, 162246, 162357
-recovered pasa_asmbl_7853.p1, internal, 162615, 162768
-recovered pasa_asmbl_7853.p1, internal, 162894, 162924
-recovered pasa_asmbl_7853.p1, internal, 163031, 163119
Valid prediction for snap_scaffold_12-snap.1692-T1
Valid prediction for snap_scaffold_12-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_29751-T1
Valid prediction for GlimmerHMM_glimmerT_29760-T1
Valid prediction for snap_scaffold_12-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_29764-T1
Valid prediction for pasa_asmbl_7847.p1
Valid prediction for snap_scaffold_12-snap.1710-T1
Valid prediction for Augustus_model.g19663.t1
Valid prediction for pasa_asmbl_7843.p1
Valid prediction for snap_scaffold_12-snap.1703-T1
Valid prediction for Augustus_model.g19658.t1
Valid prediction for Augustus_model.g19662.t1
Valid prediction for GlimmerHMM_glimmerT_29755-T1
Valid prediction for Augustus_model.g19678.t1
Valid prediction for snap_scaffold_12-snap.1713-T1
Valid prediction for snap_scaffold_12-snap.1719-T1
Valid prediction for HiQ_model.g19659.t1
Valid prediction for CodingQuarry_transcript_10327-T1
Valid prediction for GlimmerHMM_glimmerT_29771-T1
Valid prediction for CodingQuarry_transcript_10326-T1
Valid prediction for snap_scaffold_12-snap.1684-T1
Valid prediction for Augustus_model.g19665.t1
Valid prediction for snap_scaffold_12-snap.1714-T1
Valid prediction for Augustus_model.g19670.t1
Valid prediction for GlimmerHMM_glimmerT_29763-T1
Valid prediction for GlimmerHMM_glimmerT_29758-T1
Valid prediction for pasa_asmbl_7855.p1
Valid prediction for GlimmerHMM_glimmerT_29772-T1
Couldn't classify 54048, 54374
Sorry, prediction pasa_asmbl_7846.p2 fails validation.
(ACC)	 GG	54048-54374	GT	AGG
(ATA)	 AG	55208-55228	AC	AGA
-recovered pasa_asmbl_7846.p2, terminal, 55208, 55228
Valid prediction for GlimmerHMM_glimmerT_29757-T1
Valid prediction for Augustus_model.g19671.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: -)Couldn't classify 4310, 4352
Sorry, prediction pasa_asmbl_8656.p1 fails validation.
(TCT)	 CT	4310-4352	GT	GGG
(ACT)	 AG	5190-5319	GT	AGG
(GCT)	 AG	5538-5718	GT	AGG
(CGT)	 AG	5806-5910	GT	AGG
(AGA)	 AG	6027-6080	GT	AGG
(AGA)	 AG	6199-6406	GT	GGG
(AGA)	 AG	6514-6700	GT	AGG
(CCC)	 AG	6937-7223	GT	AGG
(AGA)	 AG	7428-7435	CC	GAC
-recovered pasa_asmbl_8656.p1, terminal, 6514, 6700
-recovered pasa_asmbl_8656.p1, terminal, 7428, 7435
-recovered pasa_asmbl_8656.p1, internal, 5190, 5319
-recovered pasa_asmbl_8656.p1, internal, 5538, 5718
-recovered pasa_asmbl_8656.p1, internal, 5806, 5910
-recovered pasa_asmbl_8656.p1, internal, 6027, 6080
-recovered pasa_asmbl_8656.p1, internal, 6199, 6406
-recovered pasa_asmbl_8656.p1, internal, 6514, 6700
-recovered pasa_asmbl_8656.p1, internal, 6937, 7223
Valid prediction for snap_scaffold_12-snap.1712-T1
Valid prediction for snap_scaffold_12-snap.1705-T1
Valid prediction for GlimmerHMM_glimmerT_29767-T1
Valid prediction for snap_scaffold_12-snap.1706-T1
Valid prediction for Augustus_model.g19675.t1
Valid prediction for Augustus_model.g19672.t1
Valid prediction for GlimmerHMM_glimmerT_29773-T1
Couldn't classify 63583, 63837
Sorry, prediction pasa_asmbl_8651.p1 fails validation.
(GCA)	 AC	63583-63837	GT	AGG
(GCC)	 AG	65079-65226	GT	GAG
(AAC)	 AG	66861-66892	GT	AGG
(GAT)	 AG	67085-67163	GT	AGG
(GCA)	 AG	68918-68965	GT	AAG
(AGC)	 AG	69087-69169	GT	TGG
(CTG)	 AG	69275-69346	GT	TGG
(AGC)	 AG	70053-70094	GT	GAG
(AAC)	 AG	73009-73100	GC	AGG
(TTT)	 AG	73333-73504	GT	AGG
(GGC)	 AG	74949-75057	GT	AGG
(ATG)	 AG	75184-75341	GT	GGG
(GGA)	 AG	76138-76206	GT	AGG
add_exon() Sorry, pasa_asmbl_8651.p1 75184-75341-initial-1 is invalid.
-recovered pasa_asmbl_8651.p1, initial, 75184, 75341
-recovered pasa_asmbl_8651.p1, terminal, 76138, 76206
-recovered pasa_asmbl_8651.p1, internal, 65079, 65226
-recovered pasa_asmbl_8651.p1, internal, 66861, 66892
-recovered pasa_asmbl_8651.p1, internal, 67085, 67163
-recovered pasa_asmbl_8651.p1, internal, 68918, 68965
-recovered pasa_asmbl_8651.p1, internal, 69087, 69169
-recovered pasa_asmbl_8651.p1, internal, 69275, 69346
-recovered pasa_asmbl_8651.p1, internal, 70053, 70094
-recovered pasa_asmbl_8651.p1, internal, 73009, 73100
-recovered pasa_asmbl_8651.p1, internal, 73333, 73504
-recovered pasa_asmbl_8651.p1, internal, 74949, 75057
-recovered pasa_asmbl_8651.p1, internal, 75184, 75341
-recovered pasa_asmbl_8651.p1, internal, 76138, 76206
Valid prediction for GlimmerHMM_glimmerT_29775-T1
Valid prediction for snap_scaffold_12-snap.1701-T1
Valid prediction for snap_scaffold_12-snap.1716-T1
Valid prediction for snap_scaffold_12-snap.1693-T1
Valid prediction for GlimmerHMM_glimmerT_29762-T1
Valid prediction for GlimmerHMM_glimmerT_29761-T1
Valid prediction for HiQ_model.g19673.t1
Valid prediction for snap_scaffold_12-snap.1715-T1
Valid prediction for snap_scaffold_12-snap.1700-T1
Valid prediction for Augustus_model.g19664.t1
Valid prediction for snap_scaffold_12-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_29754-T1
Valid prediction for snap_scaffold_12-snap.1702-T1
Valid prediction for snap_scaffold_12-snap.1708-T1
Valid prediction for snap_scaffold_12-snap.1691-T1
Couldn't classify 118784, 119015
Sorry, prediction pasa_asmbl_8646.p1 fails validation.
(CCT)	 AC	118784-119015	GT	TGG
(GCG)	 AG	119968-120247	GT	AGG
(CAT)	 AG	120536-120687	GT	TGG
(ACA)	 AG	120974-121261	GT	GGG
(TTC)	 AG	122032-122168	GT	AGG
(AAG)	 AG	122318-122506	CC	AGC
-recovered pasa_asmbl_8646.p1, terminal, 122318, 122506
-recovered pasa_asmbl_8646.p1, internal, 119968, 120247
-recovered pasa_asmbl_8646.p1, internal, 120536, 120687
-recovered pasa_asmbl_8646.p1, internal, 120974, 121261
-recovered pasa_asmbl_8646.p1, internal, 122032, 122168
Valid prediction for CodingQuarry_transcript_10325-T1
Valid prediction for snap_scaffold_12-snap.1704-T1
Valid prediction for HiQ_model.g19660.t1
Valid prediction for GlimmerHMM_glimmerT_29752-T1
Valid prediction for snap_scaffold_12-snap.1683-T1
Valid prediction for GlimmerHMM_glimmerT_29766-T1
Valid prediction for snap_scaffold_12-snap.1686-T1
Valid prediction for Augustus_model.g19669.t1
Valid prediction for GlimmerHMM_glimmerT_29769-T1
Valid prediction for GlimmerHMM_glimmerT_29768-T1
Valid prediction for CodingQuarry_transcript_10329-T1
Valid prediction for snap_scaffold_12-snap.1696-T1
Valid prediction for pasa_asmbl_8652.p1
Valid prediction for pasa_asmbl_8638.p1
Valid prediction for HiQ_model.g19668.t1
Valid prediction for snap_scaffold_12-snap.1697-T1
Valid prediction for snap_scaffold_12-snap.1681-T1
Valid prediction for snap_scaffold_12-snap.1695-T1
Valid prediction for HiQ_model.g19677.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12805, rend_intergenic: 10126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15903, rend_intergenic: 12976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25160, rend_intergenic: 22873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49606, rend_intergenic: 48852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61670, rend_intergenic: 58241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65879, rend_intergenic: 62912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122609, rend_intergenic: 118250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141515, rend_intergenic: 139824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147269, rend_intergenic: 143614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179430, rend_intergenic: 173690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190563
-exon list size: 370


building trellis

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37.6    
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40.1    
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40.6    
40.9    
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41.4    
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97.6    
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98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 12805, rend_intergenic: 10126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15903, rend_intergenic: 12976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25160, rend_intergenic: 22873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49606, rend_intergenic: 48852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61670, rend_intergenic: 58241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65879, rend_intergenic: 62912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122609, rend_intergenic: 118250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141515, rend_intergenic: 139824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147269, rend_intergenic: 143614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179430, rend_intergenic: 173690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support