-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_2763263-2931197

-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_2-snap.647-T1
Couldn't classify 35779, 36625
Sorry, prediction pasa_asmbl_24254.p1 fails validation.
(TCA)	 TT	35779-36625	GT	GGG
(TGA)	 AG	36714-36901	GT	CAG
(GAG)	 AG	37049-37146	GT	AGG
(GCT)	 AG	37488-37648	GT	TGG
(ACA)	 AG	37742-37934	GT	GGG
(GTG)	 AG	38077-38227	GT	AGG
(GTG)	 AG	38312-38384	GT	AAG
(GGA)	 AG	38532-38629	AC	AAA
add_exon() Sorry, pasa_asmbl_24254.p1 37049-37146-terminal-2 is invalid.
-recovered pasa_asmbl_24254.p1, terminal, 37049, 37146
-recovered pasa_asmbl_24254.p1, terminal, 38532, 38629
-recovered pasa_asmbl_24254.p1, internal, 36714, 36901
-recovered pasa_asmbl_24254.p1, internal, 37049, 37146
-recovered pasa_asmbl_24254.p1, internal, 37488, 37648
-recovered pasa_asmbl_24254.p1, internal, 37742, 37934
-recovered pasa_asmbl_24254.p1, internal, 38077, 38227
-recovered pasa_asmbl_24254.p1, internal, 38312, 38384
Valid prediction for snap_scaffold_2-snap.659-T1
Valid prediction for GlimmerHMM_glimmerT_3437-T1
Valid prediction for snap_scaffold_2-snap.645-T1
Valid prediction for Augustus_model.g2293.t1
Valid prediction for GlimmerHMM_glimmerT_3431-T1
Valid prediction for snap_scaffold_2-snap.651-T1
Valid prediction for snap_scaffold_2-snap.663-T1
Valid prediction for snap_scaffold_2-snap.654-T1
Valid prediction for snap_scaffold_2-snap.653-T1
Valid prediction for snap_scaffold_2-snap.657-T1
Valid prediction for GlimmerHMM_glimmerT_3419-T1
Valid prediction for GlimmerHMM_glimmerT_3435-T1
Valid prediction for snap_scaffold_2-snap.650-T1
Valid prediction for Augustus_model.g2306.t1
Valid prediction for snap_scaffold_2-snap.669-T1
Valid prediction for snap_scaffold_2-snap.677-T1
Valid prediction for snap_scaffold_2-snap.661-T1
Valid prediction for GlimmerHMM_glimmerT_3438-T1
Valid prediction for snap_scaffold_2-snap.649-T1
Valid prediction for HiQ_model.g2291.t1
Valid prediction for snap_scaffold_2-snap.668-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g2299.t1
Valid prediction for snap_scaffold_2-snap.667-T1
Valid prediction for snap_scaffold_2-snap.671-T1
Valid prediction for Augustus_model.g2305.t1
Valid prediction for GlimmerHMM_glimmerT_3434-T1
Valid prediction for Augustus_model.g2286.t1
Valid prediction for Augustus_model.g2288.t1
Valid prediction for snap_scaffold_2-snap.675-T1
Valid prediction for GlimmerHMM_glimmerT_3421-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.678-T1
Valid prediction for snap_scaffold_2-snap.670-T1
Valid prediction for Augustus_model.g2287.t1
Valid prediction for snap_scaffold_2-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_3422-T1
Valid prediction for snap_scaffold_2-snap.644-T1
Valid prediction for pasa_asmbl_23944.p1
Valid prediction for snap_scaffold_2-snap.656-T1
Couldn't classify 109120, 109260
Couldn't classify 111171, 111251
Sorry, prediction pasa_asmbl_22924.p1 fails validation.
(CTG)	 CC	109120-109260	GT	AGG
(GAC)	 AG	109609-109703	GT	AGG
(TCA)	 AG	110900-111050	GT	AGG
(GGT)	 AG	111171-111251	TA	GAT
-recovered pasa_asmbl_22924.p1, internal, 109609, 109703
-recovered pasa_asmbl_22924.p1, internal, 110900, 111050
Couldn't classify 108619, 108852
Sorry, prediction pasa_asmbl_22925.p1 fails validation.
(ATG)	 AA	107736-107819	GT	AAG
(AAT)	 AG	108319-108366	GT	GCG
(GAG)	 AG	108619-108852	GA	AGG
-recovered pasa_asmbl_22925.p1, initial, 107736, 107819
-recovered pasa_asmbl_22925.p1, internal, 108319, 108366
Valid prediction for HiQ_model.g2302.t1
Valid prediction for snap_scaffold_2-snap.676-T1
Couldn't classify 96722, 96749
Couldn't classify 98622, 98716
Sorry, prediction pasa_asmbl_23976.p1 fails validation.
(GAA)	 CG	96722-96749	GT	ATG
(TGT)	 AG	96866-96924	GT	AGG
(GCA)	 AG	97149-97293	GT	CTG
(TGT)	 AG	98622-98716	GT	AGG
-recovered pasa_asmbl_23976.p1, internal, 96866, 96924
-recovered pasa_asmbl_23976.p1, internal, 97149, 97293
-recovered pasa_asmbl_23976.p1, internal, 98622, 98716
Valid prediction for snap_scaffold_2-snap.674-T1
Valid prediction for snap_scaffold_2-snap.652-T1
Valid prediction for Augustus_model.g2298.t1
Valid prediction for GlimmerHMM_glimmerT_3436-T1
Couldn't classify 160274, 160306
Couldn't classify 161312, 161338
Sorry, prediction pasa_asmbl_24015.p1 fails validation.
(GTC)	 CC	160274-160306	GT	AGG
(AAG)	 AG	160516-160611	GT	CGG
(CAA)	 AG	160971-161204	GT	AGG
(AGT)	 AG	161312-161338	GA	CTG
-recovered pasa_asmbl_24015.p1, internal, 160516, 160611
-recovered pasa_asmbl_24015.p1, internal, 160971, 161204
Valid prediction for Augustus_model.g2294.t1
Valid prediction for Augustus_model.g2300.t1
Valid prediction for GlimmerHMM_glimmerT_3429-T1
Valid prediction for snap_scaffold_2-snap.658-T1
Valid prediction for snap_scaffold_2-snap.660-T1
Valid prediction for GlimmerHMM_glimmerT_3425-T1
Valid prediction for GlimmerHMM_glimmerT_3433-T1
Valid prediction for snap_scaffold_2-snap.664-T1
Valid prediction for snap_scaffold_2-snap.646-T1
Valid prediction for HiQ_model.g2304.t1
Valid prediction for pasa_asmbl_22919.p1
Valid prediction for snap_scaffold_2-snap.648-T1
Couldn't classify 28597, 28923
Sorry, prediction pasa_asmbl_22947.p2 fails validation.
(ATG)	 AC	28597-28923	GG	GGG
Valid prediction for snap_scaffold_2-snap.672-T1
Valid prediction for snap_scaffold_2-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_3430-T1
Valid prediction for CodingQuarry_transcript_28483-T1
Valid prediction for snap_scaffold_2-snap.662-T1
Valid prediction for pasa_asmbl_22942.p1
Valid prediction for GlimmerHMM_glimmerT_3427-T1
Valid prediction for Augustus_model.g2303.t1
Valid prediction for pasa_asmbl_22922.p1
Valid prediction for CodingQuarry_transcript_28485-T1
Valid prediction for GlimmerHMM_glimmerT_3417-T1
Valid prediction for pasa_asmbl_22930.p1
Valid prediction for Augustus_model.g2289.t1
Valid prediction for GlimmerHMM_glimmerT_3420-T1
Valid prediction for snap_scaffold_2-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_3415-T1
Valid prediction for snap_scaffold_2-snap.673-T1
Valid prediction for GlimmerHMM_glimmerT_3416-T1
Valid prediction for GlimmerHMM_glimmerT_3426-T1
Couldn't classify 88756, 88918
Couldn't classify 93041, 93161
Sorry, prediction pasa_asmbl_24006.p1 fails validation.
(GTG)	 CT	88756-88918	GT	AGG
(AGA)	 AG	91060-91146	GT	GAG
(ATG)	 AG	91486-91546	GT	TGG
(GTT)	 AG	93041-93161	AA	GAA
-recovered pasa_asmbl_24006.p1, initial, 91486, 91546
-recovered pasa_asmbl_24006.p1, internal, 91060, 91146
-recovered pasa_asmbl_24006.p1, internal, 91486, 91546
Valid prediction for GlimmerHMM_glimmerT_3424-T1
Valid prediction for Augustus_model.g2290.t1
Valid prediction for Augustus_model.g2295.t1
Valid prediction for GlimmerHMM_glimmerT_3414-T1
Couldn't classify 77142, 77271
Couldn't classify 78243, 78306
Sorry, prediction pasa_asmbl_24009.p1 fails validation.
(GCC)	 AC	77142-77271	GT	TGG
(GAG)	 AG	77881-77998	GT	GGG
(CTA)	 AG	78243-78306	TT	CCT
-recovered pasa_asmbl_24009.p1, internal, 77881, 77998
Valid prediction for snap_scaffold_2-snap.655-T1
Valid prediction for CodingQuarry_transcript_28484-T1
Valid prediction for HiQ_model.g2292.t1
Couldn't classify 112439, 112586
Sorry, prediction pasa_asmbl_22923.p1 fails validation.
(CAG)	 CT	112439-112586	GT	CGG
(TGG)	 AG	112765-112909	GT	TTG
(CAT)	 AG	113002-113121	GT	AGG
(ACA)	 AG	115432-115540	AA	AGA
-recovered pasa_asmbl_22923.p1, terminal, 115432, 115540
-recovered pasa_asmbl_22923.p1, internal, 112765, 112909
-recovered pasa_asmbl_22923.p1, internal, 113002, 113121
Valid prediction for GlimmerHMM_glimmerT_3432-T1
Valid prediction for HiQ_model.g2301.t1
Valid prediction for GlimmerHMM_glimmerT_3418-T1
Couldn't classify 33148, 33222
Couldn't classify 34794, 34810
Sorry, prediction pasa_asmbl_23980.p1 fails validation.
(TTC)	 AC	33148-33222	GT	GGG
(GAC)	 AG	33851-34000	GT	AGG
(GCA)	 AG	34543-34648	GT	CGG
(CCA)	 AG	34794-34810	GA	AGG
-recovered pasa_asmbl_23980.p1, internal, 33851, 34000
-recovered pasa_asmbl_23980.p1, internal, 34543, 34648
Valid prediction for GlimmerHMM_glimmerT_3428-T1
Valid prediction for Augustus_model.g2296.t1
Valid prediction for GlimmerHMM_glimmerT_3423-T1
Couldn't classify 82934, 83100
Sorry, prediction pasa_asmbl_22928.p1 fails validation.
(GTG)	 AG	82934-83100	GT	GGG
(GGA)	 AG	84487-84600	GT	AGG
(ACA)	 AG	85365-85538	GT	TGG
(GTG)	 AG	85661-85790	GC	GAG
-recovered pasa_asmbl_22928.p1, terminal, 85661, 85790
-recovered pasa_asmbl_22928.p1, internal, 82934, 83100
-recovered pasa_asmbl_22928.p1, internal, 84487, 84600
-recovered pasa_asmbl_22928.p1, internal, 85365, 85538
-recovered pasa_asmbl_22928.p1, internal, 85661, 85790
Valid prediction for Augustus_model.g2297.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22189, rend_intergenic: 12828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54286, rend_intergenic: 52396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68489, rend_intergenic: 65267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86544, rend_intergenic: 82146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89672, rend_intergenic: 87690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104047, rend_intergenic: 94713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126676, rend_intergenic: 114573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149135, rend_intergenic: 143558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165914, rend_intergenic: 155193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167935
-exon list size: 477


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 22189, rend_intergenic: 12828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54286, rend_intergenic: 52396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68489, rend_intergenic: 65267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86544, rend_intergenic: 82146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89672, rend_intergenic: 87690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104047, rend_intergenic: 94713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126676, rend_intergenic: 114573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149135, rend_intergenic: 143558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165914, rend_intergenic: 155193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support