-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_2544500-2798838

-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 Augustus_model.g5746.t1
Valid prediction for snap_scaffold_4-snap.577-T1
Valid prediction for snap_scaffold_4-snap.580-T1
Valid prediction for snap_scaffold_4-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_8953-T1
Valid prediction for Augustus_model.g5740.t1
Valid prediction for snap_scaffold_4-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_8951-T1
Valid prediction for snap_scaffold_4-snap.593-T1
Valid prediction for snap_scaffold_4-snap.602-T1
Valid prediction for snap_scaffold_4-snap.581-T1
Valid prediction for GlimmerHMM_glimmerT_8963-T1
Couldn't classify 92096, 92208
Couldn't classify 95502, 95521
Sorry, prediction pasa_asmbl_42280.p2 fails validation.
(GAG)	 AG	92096-92208	GT	AGG
(AAA)	 AG	92617-92690	GT	AGG
(CCT)	 AG	93042-93103	GT	AGG
(AAG)	 AG	93871-93901	GT	AGG
(TCT)	 AG	95502-95521	GA	TGG
-recovered pasa_asmbl_42280.p2, internal, 92096, 92208
-recovered pasa_asmbl_42280.p2, internal, 92617, 92690
-recovered pasa_asmbl_42280.p2, internal, 93042, 93103
-recovered pasa_asmbl_42280.p2, internal, 93871, 93901
Valid prediction for GlimmerHMM_glimmerT_8942-T1
Valid prediction for snap_scaffold_4-snap.606-T1
Valid prediction for snap_scaffold_4-snap.596-T1
Valid prediction for snap_scaffold_4-snap.604-T1
Valid prediction for Augustus_model.g5741.t1
Valid prediction for Augustus_model.g5738.t1
Valid prediction for snap_scaffold_4-snap.616-T1
Valid prediction for snap_scaffold_4-snap.615-T1
Valid prediction for GlimmerHMM_glimmerT_8952-T1
Valid prediction for snap_scaffold_4-snap.578-T1
Valid prediction for snap_scaffold_4-snap.572-T1
Valid prediction for GlimmerHMM_glimmerT_8956-T1
Valid prediction for GlimmerHMM_glimmerT_8961-T1
Couldn't classify 101438, 101592
Sorry, prediction pasa_asmbl_41157.p1 fails validation.
(ATG)	 GC	99822-99944	GT	AGG
(GAG)	 AG	100107-100219	GT	AGG
(GGA)	 AG	100417-100522	GT	AGG
(AGG)	 AG	100624-100750	GT	AGG
(GCA)	 AG	101438-101592	CA	AGC
-recovered pasa_asmbl_41157.p1, initial, 99822, 99944
-recovered pasa_asmbl_41157.p1, internal, 100107, 100219
-recovered pasa_asmbl_41157.p1, internal, 100417, 100522
-recovered pasa_asmbl_41157.p1, internal, 100624, 100750
Valid prediction for GlimmerHMM_glimmerT_8950-T1
Valid prediction for GlimmerHMM_glimmerT_8959-T1
Valid prediction for snap_scaffold_4-snap.575-T1
Valid prediction for Augustus_model.g5745.t1
Valid prediction for GlimmerHMM_glimmerT_8945-T1
Valid prediction for snap_scaffold_4-snap.619-T1
Valid prediction for snap_scaffold_4-snap.613-T1
Valid prediction for GlimmerHMM_glimmerT_8958-T1
Couldn't classify 103282, 103500
Couldn't classify 104717, 105151
Sorry, prediction pasa_asmbl_41158.p1 fails validation.
(GAG)	 CG	103282-103500	GT	AGG
(CTC)	 AG	104717-105151	AG	AGA
Valid prediction for snap_scaffold_4-snap.618-T1
Valid prediction for GlimmerHMM_glimmerT_8960-T1
Valid prediction for snap_scaffold_4-snap.617-T1
Valid prediction for snap_scaffold_4-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_8947-T1
Valid prediction for snap_scaffold_4-snap.605-T1
Valid prediction for snap_scaffold_4-snap.590-T1
Valid prediction for snap_scaffold_4-snap.609-T1
Valid prediction for Augustus_model.g5742.t1
Valid prediction for Augustus_model.g5751.t1
Valid prediction for Augustus_model.g5744.t1
Valid prediction for snap_scaffold_4-snap.607-T1
Valid prediction for snap_scaffold_4-snap.574-T1
Valid prediction for snap_scaffold_4-snap.594-T1
Valid prediction for snap_scaffold_4-snap.599-T1
Valid prediction for CodingQuarry_transcript_48894-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_4-snap.600-T1
Valid prediction for Augustus_model.g5749.t1
Valid prediction for GlimmerHMM_glimmerT_8948-T1
Valid prediction for GlimmerHMM_glimmerT_8957-T1
Valid prediction for snap_scaffold_4-snap.587-T1
Valid prediction for snap_scaffold_4-snap.579-T1
Valid prediction for snap_scaffold_4-snap.595-T1
Valid prediction for Augustus_model.g5754.t1
Valid prediction for Augustus_model.g5747.t1
Valid prediction for snap_scaffold_4-snap.608-T1
Valid prediction for GlimmerHMM_glimmerT_8962-T1
Valid prediction for snap_scaffold_4-snap.610-T1
Valid prediction for snap_scaffold_4-snap.603-T1
Valid prediction for snap_scaffold_4-snap.591-T1
Valid prediction for snap_scaffold_4-snap.601-T1
Couldn't classify 21278, 21406
Couldn't classify 24411, 24544
Sorry, prediction pasa_asmbl_42405.p1 fails validation.
(TGC)	 AC	21278-21406	GT	AGG
(AAT)	 AG	23424-23649	GT	CGG
(GTC)	 AG	24411-24544	GA	CCG
-recovered pasa_asmbl_42405.p1, internal, 23424, 23649
Valid prediction for GlimmerHMM_glimmerT_8946-T1
Valid prediction for snap_scaffold_4-snap.612-T1
Valid prediction for GlimmerHMM_glimmerT_8954-T1
Valid prediction for snap_scaffold_4-snap.586-T1
Valid prediction for snap_scaffold_4-snap.592-T1
Valid prediction for Augustus_model.g5753.t1
Valid prediction for snap_scaffold_4-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_8955-T1
Valid prediction for GlimmerHMM_glimmerT_8949-T1
Valid prediction for snap_scaffold_4-snap.570-T1
Valid prediction for snap_scaffold_4-snap.573-T1
Valid prediction for HiQ_model.g5748.t1
Couldn't classify 135604, 136113
Sorry, prediction pasa_asmbl_42398.p1 fails validation.
(ATG)	 CT	135604-136113	AG	GAA
Couldn't classify 131778, 131929
Sorry, prediction pasa_asmbl_42399.p3 fails validation.
(GGC)	 TA	131778-131929	GT	AGG
(GGA)	 AG	132876-132962	GT	AGG
(GTT)	 AG	133237-133398	GT	AGG
(GTT)	 AG	133668-133722	CA	GAC
-recovered pasa_asmbl_42399.p3, terminal, 133668, 133722
-recovered pasa_asmbl_42399.p3, internal, 132876, 132962
-recovered pasa_asmbl_42399.p3, internal, 133237, 133398
Valid prediction for snap_scaffold_4-snap.571-T1
Valid prediction for snap_scaffold_4-snap.597-T1
Valid prediction for snap_scaffold_4-snap.588-T1
Valid prediction for Augustus_model.g5755.t1
Valid prediction for CodingQuarry_transcript_48895-T1
Couldn't classify 55908, 56044
Sorry, prediction pasa_asmbl_42401.p1 fails validation.
(GCT)	 TA	55908-56044	GT	AGG
(GAA)	 AG	57141-57297	GT	AGG
(GCA)	 AG	57981-58181	GT	GGG
(AGG)	 AG	59267-59442	GT	AAG
(GTG)	 AG	59580-59727	AC	AAA
-recovered pasa_asmbl_42401.p1, terminal, 59580, 59727
-recovered pasa_asmbl_42401.p1, internal, 57141, 57297
-recovered pasa_asmbl_42401.p1, internal, 57981, 58181
-recovered pasa_asmbl_42401.p1, internal, 59267, 59442
Valid prediction for snap_scaffold_4-snap.611-T1
Valid prediction for GlimmerHMM_glimmerT_8943-T1
Couldn't classify 127551, 127674
Couldn't classify 128335, 128381
Sorry, prediction pasa_asmbl_42400.p1 fails validation.
(GTC)	 CA	127551-127674	GT	AGG
(ACC)	 AG	127977-128117	GT	AGG
(ATA)	 AG	128335-128381	CC	TGC
-recovered pasa_asmbl_42400.p1, internal, 127977, 128117
Valid prediction for Augustus_model.g5752.t1
Valid prediction for snap_scaffold_4-snap.584-T1
Valid prediction for GlimmerHMM_glimmerT_8944-T1
Valid prediction for snap_scaffold_4-snap.598-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g5750.t1
Valid prediction for snap_scaffold_4-snap.576-T1
Couldn't classify 31314, 31517
Couldn't classify 39893, 40016
Sorry, prediction pasa_asmbl_42404.p1 fails validation.
(CCG)	 AG	31314-31517	GT	AGG
(GTG)	 AG	32412-32497	GT	AAG
(GGT)	 AG	33190-33356	GT	TGG
(GGG)	 AG	33656-33801	GT	AGG
(GTG)	 AG	34879-34999	GT	GGG
(CCA)	 AG	35110-35252	GT	AGG
(AGC)	 AG	38018-38155	GT	AGG
(GTG)	 AG	38544-38664	GT	AGG
(ATG)	 AG	38752-38884	GT	AGG
(TCT)	 AG	39893-40016	AG	CCA
add_exon() Sorry, pasa_asmbl_42404.p1 38752-38884-initial-1 is invalid.
-recovered pasa_asmbl_42404.p1, initial, 38752, 38884
-recovered pasa_asmbl_42404.p1, internal, 31314, 31517
-recovered pasa_asmbl_42404.p1, internal, 32412, 32497
-recovered pasa_asmbl_42404.p1, internal, 33190, 33356
-recovered pasa_asmbl_42404.p1, internal, 33656, 33801
-recovered pasa_asmbl_42404.p1, internal, 34879, 34999
-recovered pasa_asmbl_42404.p1, internal, 35110, 35252
-recovered pasa_asmbl_42404.p1, internal, 38018, 38155
-recovered pasa_asmbl_42404.p1, internal, 38544, 38664
-recovered pasa_asmbl_42404.p1, internal, 38752, 38884
Valid prediction for Augustus_model.g5743.t1
Couldn't classify 17772, 17963
Couldn't classify 18358, 18480
Sorry, prediction pasa_asmbl_42406.p1 fails validation.
(CTG)	 CC	17772-17963	GT	AGG
(GTG)	 AG	18358-18480	TG	TGT
Valid prediction for Augustus_model.g5739.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12984, rend_intergenic: 12784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15867, rend_intergenic: 13122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20618, rend_intergenic: 17177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32659, rend_intergenic: 25429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38395, rend_intergenic: 34818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47525, rend_intergenic: 39663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55351, rend_intergenic: 47525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60846, rend_intergenic: 60619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65594, rend_intergenic: 61314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66263, rend_intergenic: 65757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82259, rend_intergenic: 70860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86947, rend_intergenic: 85329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98819, rend_intergenic: 95498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108565, rend_intergenic: 99093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111788, rend_intergenic: 109748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124062, rend_intergenic: 117319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125589, rend_intergenic: 124461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131971, rend_intergenic: 127702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161010, rend_intergenic: 139758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172372, rend_intergenic: 163154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185337, rend_intergenic: 176084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254339
-exon list size: 436


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 12984, rend_intergenic: 12784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15867, rend_intergenic: 13122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20618, rend_intergenic: 17177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32659, rend_intergenic: 25429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38395, rend_intergenic: 34818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47525, rend_intergenic: 39663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55351, rend_intergenic: 47525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60846, rend_intergenic: 60619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65594, rend_intergenic: 61314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66263, rend_intergenic: 65757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82259, rend_intergenic: 70860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86947, rend_intergenic: 85329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98819, rend_intergenic: 95498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108565, rend_intergenic: 99093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111788, rend_intergenic: 109748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124062, rend_intergenic: 117319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125589, rend_intergenic: 124461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131971, rend_intergenic: 127702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161010, rend_intergenic: 139758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172372, rend_intergenic: 163154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185337, rend_intergenic: 176084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 237118 - 254339
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 238123 - 254339
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 241576 - 254339
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support