-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_8770836-8971949

-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: +)Couldn't classify 120070, 120118
Couldn't classify 125784, 125849
Sorry, prediction pasa_asmbl_16448.p1 fails validation.
(TTT)	 GT	120070-120118	GT	AGG
(TTC)	 AG	120365-120425	GT	ACG
(ATT)	 AG	120632-120671	GT	ATG
(TTC)	 AG	121311-121434	GT	AGG
(GTA)	 AG	122236-122281	GT	CTG
(GCT)	 AG	123835-123915	GT	GGG
(ACC)	 AG	124962-125061	GT	AGG
(GAG)	 AG	125337-125414	GT	AGG
(TCA)	 AG	125784-125849	GG	ATG
-recovered pasa_asmbl_16448.p1, internal, 120365, 120425
-recovered pasa_asmbl_16448.p1, internal, 120632, 120671
-recovered pasa_asmbl_16448.p1, internal, 121311, 121434
-recovered pasa_asmbl_16448.p1, internal, 122236, 122281
-recovered pasa_asmbl_16448.p1, internal, 123835, 123915
-recovered pasa_asmbl_16448.p1, internal, 124962, 125061
-recovered pasa_asmbl_16448.p1, internal, 125337, 125414
Valid prediction for snap_scaffold_16-snap.1648-T1
Valid prediction for GlimmerHMM_glimmerT_38745-T1
Valid prediction for snap_scaffold_16-snap.1624-T1
Valid prediction for snap_scaffold_16-snap.1616-T1
Valid prediction for snap_scaffold_16-snap.1629-T1
Valid prediction for snap_scaffold_16-snap.1623-T1
Valid prediction for Augustus_model.g25873.t1
Valid prediction for snap_scaffold_16-snap.1621-T1
Valid prediction for GlimmerHMM_glimmerT_38737-T1
Valid prediction for GlimmerHMM_glimmerT_38751-T1
Valid prediction for Augustus_model.g25881.t1
Valid prediction for snap_scaffold_16-snap.1647-T1
Couldn't classify 131115, 131214
Sorry, prediction pasa_asmbl_16451.p1 fails validation.
(GAG)	 CA	131115-131214	GT	CGG
(GCA)	 AG	131816-131873	GT	AGG
(ATT)	 AG	132124-132177	GT	AGG
(GGA)	 AG	134387-134443	GT	GGG
(TGA)	 AG	137299-137428	GT	AGG
(GCC)	 AG	138275-138343	GT	TGG
(TCG)	 AG	139268-139552	AC	AAA
-recovered pasa_asmbl_16451.p1, terminal, 139268, 139552
-recovered pasa_asmbl_16451.p1, internal, 131816, 131873
-recovered pasa_asmbl_16451.p1, internal, 132124, 132177
-recovered pasa_asmbl_16451.p1, internal, 134387, 134443
-recovered pasa_asmbl_16451.p1, internal, 137299, 137428
-recovered pasa_asmbl_16451.p1, internal, 138275, 138343
Valid prediction for snap_scaffold_16-snap.1640-T1
Valid prediction for snap_scaffold_16-snap.1634-T1
Valid prediction for snap_scaffold_16-snap.1649-T1
Valid prediction for GlimmerHMM_glimmerT_38742-T1
Valid prediction for GlimmerHMM_glimmerT_38732-T1
Valid prediction for GlimmerHMM_glimmerT_38750-T1
Valid prediction for Augustus_model.g25875.t1
Valid prediction for snap_scaffold_16-snap.1641-T1
Valid prediction for snap_scaffold_16-snap.1636-T1
Valid prediction for Augustus_model.g25872.t1
Valid prediction for Augustus_model.g25880.t1
Valid prediction for GlimmerHMM_glimmerT_38729-T1
Valid prediction for Augustus_model.g25864.t1
Valid prediction for GlimmerHMM_glimmerT_38738-T1
Valid prediction for snap_scaffold_16-snap.1630-T1
Valid prediction for Augustus_model.g25869.t1
Valid prediction for Augustus_model.g25874.t1
Valid prediction for snap_scaffold_16-snap.1627-T1
Valid prediction for Augustus_model.g25877.t1
Valid prediction for GlimmerHMM_glimmerT_38740-T1
Valid prediction for GlimmerHMM_glimmerT_38744-T1
Valid prediction for GlimmerHMM_glimmerT_38754-T1
Valid prediction for snap_scaffold_16-snap.1626-T1
Valid prediction for GlimmerHMM_glimmerT_38749-T1
Valid prediction for Augustus_model.g25870.t1
Valid prediction for GlimmerHMM_glimmerT_38735-T1
Valid prediction for snap_scaffold_16-snap.1644-T1
Valid prediction for Augustus_model.g25878.t1
Valid prediction for Augustus_model.g25865.t1
Couldn't classify 115956, 116048
Sorry, prediction pasa_asmbl_16447.p1 fails validation.
(GGG)	 CA	115956-116048	GT	AGG
(TAT)	 AG	116234-116351	GT	AGG
(AGA)	 AG	116528-116639	GT	CAG
(GTA)	 AG	117212-117338	GG	GAG
-recovered pasa_asmbl_16447.p1, terminal, 117212, 117338
-recovered pasa_asmbl_16447.p1, internal, 116234, 116351
-recovered pasa_asmbl_16447.p1, internal, 116528, 116639
Valid prediction for snap_scaffold_16-snap.1620-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_16-snap.1650-T1
Valid prediction for snap_scaffold_16-snap.1653-T1
Valid prediction for snap_scaffold_16-snap.1642-T1
Valid prediction for pasa_asmbl_17260.p1
Valid prediction for snap_scaffold_16-snap.1615-T1
Valid prediction for GlimmerHMM_glimmerT_38752-T1
Valid prediction for GlimmerHMM_glimmerT_38731-T1
Valid prediction for Augustus_model.g25866.t1
Valid prediction for snap_scaffold_16-snap.1638-T1
Valid prediction for snap_scaffold_16-snap.1628-T1
Valid prediction for Augustus_model.g25871.t1
Valid prediction for snap_scaffold_16-snap.1631-T1
Valid prediction for snap_scaffold_16-snap.1643-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38747-T1
Valid prediction for snap_scaffold_16-snap.1637-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1633-T1
Valid prediction for snap_scaffold_16-snap.1625-T1
Valid prediction for Augustus_model.g25879.t1
Valid prediction for GlimmerHMM_glimmerT_38734-T1
Valid prediction for snap_scaffold_16-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_38743-T1
Valid prediction for snap_scaffold_16-snap.1617-T1
Valid prediction for snap_scaffold_16-snap.1632-T1
Valid prediction for GlimmerHMM_glimmerT_38746-T1
Valid prediction for GlimmerHMM_glimmerT_38741-T1
Valid prediction for snap_scaffold_16-snap.1646-T1
Valid prediction for HiQ_model.g25876.t1
Valid prediction for snap_scaffold_16-snap.1619-T1
Valid prediction for snap_scaffold_16-snap.1645-T1
Valid prediction for snap_scaffold_16-snap.1618-T1
Valid prediction for snap_scaffold_16-snap.1651-T1
Valid prediction for snap_scaffold_16-snap.1622-T1
Valid prediction for GlimmerHMM_glimmerT_38755-T1
Valid prediction for Augustus_model.g25867.t1
Valid prediction for snap_scaffold_16-snap.1635-T1
Valid prediction for GlimmerHMM_glimmerT_38748-T1
Valid prediction for GlimmerHMM_glimmerT_38733-T1
Valid prediction for GlimmerHMM_glimmerT_38756-T1
Valid prediction for snap_scaffold_16-snap.1639-T1
Valid prediction for GlimmerHMM_glimmerT_38753-T1
Valid prediction for GlimmerHMM_glimmerT_38730-T1
Valid prediction for Augustus_model.g25868.t1
Valid prediction for snap_scaffold_16-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_38739-T1
Valid prediction for GlimmerHMM_glimmerT_38736-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18276, rend_intergenic: 13671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31053, rend_intergenic: 21779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33907, rend_intergenic: 31597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40263, rend_intergenic: 38323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45801, rend_intergenic: 40277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58153, rend_intergenic: 50304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74090, rend_intergenic: 61379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77935, rend_intergenic: 74491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86685, rend_intergenic: 79312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89412, rend_intergenic: 88348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94297, rend_intergenic: 90755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139552, rend_intergenic: 131700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151911, rend_intergenic: 144161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201114
-exon list size: 355


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 18276, rend_intergenic: 13671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31053, rend_intergenic: 21779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33907, rend_intergenic: 31597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40263, rend_intergenic: 38323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45801, rend_intergenic: 40277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58153, rend_intergenic: 50304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74090, rend_intergenic: 61379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77935, rend_intergenic: 74491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86685, rend_intergenic: 79312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89412, rend_intergenic: 88348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94297, rend_intergenic: 90755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139552, rend_intergenic: 131700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151911, rend_intergenic: 144161  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 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11535
-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

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support