-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_17755451-17942703

-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_4-snap.3641-T1
Valid prediction for snap_scaffold_4-snap.3666-T1
Valid prediction for snap_scaffold_4-snap.3674-T1
Valid prediction for snap_scaffold_4-snap.3664-T1
Valid prediction for snap_scaffold_4-snap.3671-T1
Valid prediction for GlimmerHMM_glimmerT_11060-T1
Valid prediction for GlimmerHMM_glimmerT_11058-T1
Valid prediction for GlimmerHMM_glimmerT_11045-T1
Valid prediction for GlimmerHMM_glimmerT_11063-T1
Valid prediction for snap_scaffold_4-snap.3653-T1
Valid prediction for Augustus_model.g7266.t1
Valid prediction for snap_scaffold_4-snap.3672-T1
Valid prediction for GlimmerHMM_glimmerT_11062-T1
Valid prediction for snap_scaffold_4-snap.3678-T1
Couldn't classify 50785, 50998
Sorry, prediction pasa_asmbl_42074.p2 fails validation.
(ATG)	 AT	50563-50657	GT	AGG
(TCG)	 AG	50785-50998	CT	GTC
-recovered pasa_asmbl_42074.p2, initial, 50563, 50657
Valid prediction for GlimmerHMM_glimmerT_11048-T1
Valid prediction for snap_scaffold_4-snap.3645-T1
Valid prediction for snap_scaffold_4-snap.3662-T1
Valid prediction for snap_scaffold_4-snap.3670-T1
Valid prediction for snap_scaffold_4-snap.3644-T1
Valid prediction for snap_scaffold_4-snap.3647-T1
Valid prediction for snap_scaffold_4-snap.3657-T1
Valid prediction for snap_scaffold_4-snap.3658-T1
Valid prediction for snap_scaffold_4-snap.3667-T1
Valid prediction for snap_scaffold_4-snap.3655-T1
Valid prediction for Augustus_model.g7249.t1
Valid prediction for Augustus_model.g7250.t1
Valid prediction for snap_scaffold_4-snap.3673-T1
Couldn't classify 49569, 49675
Sorry, prediction pasa_asmbl_42072.p1 fails validation.
(ATG)	 TG	44808-44836	GT	GGG
(TCG)	 AG	45262-45439	GT	AGG
(ATT)	 AG	45940-46068	GT	AGG
(ATC)	 AG	46759-46838	GT	GGG
(GGA)	 AG	47204-47256	GT	CAG
(GAG)	 AG	47573-47748	GT	GGG
(ATG)	 AG	47863-48074	GT	AGG
(TCA)	 AG	48437-48497	GT	CAG
(GTC)	 AG	48783-48840	GT	AGG
(GCT)	 AG	49569-49675	CA	CCC
-recovered pasa_asmbl_42072.p1, initial, 44808, 44836
-recovered pasa_asmbl_42072.p1, initial, 47863, 48074
-recovered pasa_asmbl_42072.p1, internal, 45262, 45439
-recovered pasa_asmbl_42072.p1, internal, 45940, 46068
-recovered pasa_asmbl_42072.p1, internal, 46759, 46838
-recovered pasa_asmbl_42072.p1, internal, 47204, 47256
-recovered pasa_asmbl_42072.p1, internal, 47573, 47748
-recovered pasa_asmbl_42072.p1, internal, 47863, 48074
-recovered pasa_asmbl_42072.p1, internal, 48437, 48497
-recovered pasa_asmbl_42072.p1, internal, 48783, 48840
Valid prediction for snap_scaffold_4-snap.3660-T1
Valid prediction for HiQ_model.g7252.t1
Valid prediction for CodingQuarry_transcript_49349-T1
Valid prediction for snap_scaffold_4-snap.3663-T1
Valid prediction for GlimmerHMM_glimmerT_11049-T1
Valid prediction for snap_scaffold_4-snap.3650-T1
Valid prediction for CodingQuarry_transcript_49350-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 Augustus_model.g7264.t1
Couldn't classify 75062, 75090
Sorry, prediction pasa_asmbl_43318.p1 fails validation.
(GCC)	 GA	75062-75090	GT	AGG
(GTC)	 AG	75438-75504	GT	AGG
(GTG)	 AG	75775-75889	GT	AGG
(GAA)	 AG	76415-76521	AT	AAA
add_exon() Sorry, pasa_asmbl_43318.p1 75775-75889-terminal-3 is invalid.
-recovered pasa_asmbl_43318.p1, terminal, 75775, 75889
-recovered pasa_asmbl_43318.p1, terminal, 76415, 76521
-recovered pasa_asmbl_43318.p1, internal, 75438, 75504
-recovered pasa_asmbl_43318.p1, internal, 75775, 75889
Valid prediction for snap_scaffold_4-snap.3656-T1
Valid prediction for snap_scaffold_4-snap.3677-T1
Valid prediction for GlimmerHMM_glimmerT_11051-T1
Valid prediction for GlimmerHMM_glimmerT_11053-T1
Valid prediction for snap_scaffold_4-snap.3668-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11064-T1
Valid prediction for snap_scaffold_4-snap.3652-T1
Valid prediction for GlimmerHMM_glimmerT_11056-T1
Valid prediction for snap_scaffold_4-snap.3665-T1
Valid prediction for Augustus_model.g7260.t1
Couldn't classify 36390, 36473
Sorry, prediction pasa_asmbl_43523.p1 fails validation.
(GAG)	 CA	36390-36473	GT	AGG
(ACT)	 AG	36664-36743	GT	AGG
(GGC)	 AG	37144-37243	GT	GGG
(AGA)	 AG	37651-37833	CC	GAC
-recovered pasa_asmbl_43523.p1, terminal, 37651, 37833
-recovered pasa_asmbl_43523.p1, internal, 36664, 36743
-recovered pasa_asmbl_43523.p1, internal, 37144, 37243
Couldn't classify 4988, 5053
Couldn't classify 7045, 7093
Sorry, prediction pasa_asmbl_43604.p1 fails validation.
(GAG)	 GG	4988-5053	GT	TGG
(GAT)	 AG	5274-5403	GT	GGG
(GTG)	 AG	6130-6250	GT	GAG
(AGT)	 AG	7045-7093	CA	CCC
add_exon() Sorry, pasa_asmbl_43604.p1 6130-6250-terminal-3 is invalid.
-recovered pasa_asmbl_43604.p1, terminal, 6130, 6250
-recovered pasa_asmbl_43604.p1, internal, 5274, 5403
-recovered pasa_asmbl_43604.p1, internal, 6130, 6250
Valid prediction for GlimmerHMM_glimmerT_11046-T1
Valid prediction for snap_scaffold_4-snap.3642-T1
Valid prediction for CodingQuarry_transcript_49351-T1
Valid prediction for Augustus_model.g7265.t1
Valid prediction for Augustus_model.g7267.t1
Valid prediction for GlimmerHMM_glimmerT_11050-T1
Valid prediction for GlimmerHMM_glimmerT_11057-T1
Valid prediction for GlimmerHMM_glimmerT_11065-T1
Valid prediction for snap_scaffold_4-snap.3646-T1
Valid prediction for snap_scaffold_4-snap.3651-T1
Valid prediction for snap_scaffold_4-snap.3643-T1
Valid prediction for snap_scaffold_4-snap.3675-T1
Valid prediction for snap_scaffold_4-snap.3654-T1
Valid prediction for Augustus_model.g7257.t1
Valid prediction for GlimmerHMM_glimmerT_11047-T1
Valid prediction for snap_scaffold_4-snap.3676-T1
Valid prediction for snap_scaffold_4-snap.3679-T1
Valid prediction for Augustus_model.g7248.t1
Couldn't classify 2730, 2771
Sorry, prediction pasa_asmbl_43330.p1 fails validation.
(ATG)	 GG	1648-1850	GT	CAG
(GTC)	 AG	2245-2414	GT	CCG
(TGG)	 AG	2582-2625	GT	CAG
(TTT)	 AG	2730-2771	GT	ACG
-recovered pasa_asmbl_43330.p1, initial, 1648, 1850
-recovered pasa_asmbl_43330.p1, internal, 2245, 2414
-recovered pasa_asmbl_43330.p1, internal, 2582, 2625
-recovered pasa_asmbl_43330.p1, internal, 2730, 2771
Couldn't classify 35150, 35244
Sorry, prediction pasa_asmbl_43325.p1 fails validation.
(ATG)	 TC	30215-30280	GT	CTG
(CGG)	 AG	32445-32532	GT	ATG
(ATG)	 AG	33309-33375	GT	AGG
(GGG)	 AG	33743-33859	GT	CAG
(ACT)	 AG	34802-34968	GT	CTG
(TTC)	 AG	35150-35244	GT	AGG
-recovered pasa_asmbl_43325.p1, initial, 30215, 30280
add_exon() Sorry, pasa_asmbl_43325.p1 33309-33375-initial-1 is invalid.
-recovered pasa_asmbl_43325.p1, initial, 33309, 33375
-recovered pasa_asmbl_43325.p1, internal, 32445, 32532
-recovered pasa_asmbl_43325.p1, internal, 33309, 33375
-recovered pasa_asmbl_43325.p1, internal, 33743, 33859
-recovered pasa_asmbl_43325.p1, internal, 34802, 34968
-recovered pasa_asmbl_43325.p1, internal, 35150, 35244
Valid prediction for snap_scaffold_4-snap.3661-T1
Valid prediction for Augustus_model.g7253.t1
Valid prediction for Augustus_model.g7251.t1
Valid prediction for Augustus_model.g7263.t1
Valid prediction for snap_scaffold_4-snap.3649-T1
Valid prediction for snap_scaffold_4-snap.3659-T1
Valid prediction for GlimmerHMM_glimmerT_11043-T1
Valid prediction for Augustus_model.g7255.t1
Valid prediction for GlimmerHMM_glimmerT_11059-T1
Valid prediction for GlimmerHMM_glimmerT_11054-T1
Valid prediction for Augustus_model.g7262.t1
Valid prediction for GlimmerHMM_glimmerT_11052-T1
Valid prediction for Augustus_model.g7261.t1
Valid prediction for GlimmerHMM_glimmerT_11061-T1
Valid prediction for GlimmerHMM_glimmerT_11044-T1
Valid prediction for Augustus_model.g7259.t1
Valid prediction for GlimmerHMM_glimmerT_11055-T1
Couldn't classify 58475, 58605
Couldn't classify 59607, 59702
Sorry, prediction pasa_asmbl_43319.p1 fails validation.
(GGC)	 TG	58475-58605	GT	AGG
(GTT)	 AG	59054-59132	GT	GGG
(ACC)	 AG	59607-59702	GA	GGG
-recovered pasa_asmbl_43319.p1, internal, 59054, 59132
Valid prediction for Augustus_model.g7258.t1
Valid prediction for Augustus_model.g7254.t1
Couldn't classify 12863, 12965
Sorry, prediction pasa_asmbl_43329.p1 fails validation.
(GAG)	 AG	12863-12965	GT	GGG
(GGG)	 AG	13157-13398	GT	ACG
(CAT)	 AG	13511-13599	GT	AAG
(GAG)	 AG	13762-13879	AG	AAA
-recovered pasa_asmbl_43329.p1, terminal, 13762, 13879
-recovered pasa_asmbl_43329.p1, internal, 12863, 12965
-recovered pasa_asmbl_43329.p1, internal, 13157, 13398
-recovered pasa_asmbl_43329.p1, internal, 13511, 13599
Valid prediction for Augustus_model.g7256.t1
Valid prediction for snap_scaffold_4-snap.3648-T1
Valid prediction for snap_scaffold_4-snap.3669-T1
Valid prediction for GlimmerHMM_glimmerT_11066-T1
Valid prediction for GlimmerHMM_glimmerT_11042-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11437, rend_intergenic: 6476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39737, rend_intergenic: 35223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42586, rend_intergenic: 40080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47414, rend_intergenic: 45233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52874, rend_intergenic: 49058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69432, rend_intergenic: 63321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78246, rend_intergenic: 72021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90119, rend_intergenic: 78367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91930, rend_intergenic: 90819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96727, rend_intergenic: 94078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96850, rend_intergenic: 96769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106713, rend_intergenic: 96914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116813, rend_intergenic: 109701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125235, rend_intergenic: 118537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136634, rend_intergenic: 127052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164991, rend_intergenic: 142787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182081, rend_intergenic: 172743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182929, rend_intergenic: 182343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185731, rend_intergenic: 182988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187253
-exon list size: 431


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11437, rend_intergenic: 6476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39737, rend_intergenic: 35223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42586, rend_intergenic: 40080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47414, rend_intergenic: 45233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52874, rend_intergenic: 49058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69432, rend_intergenic: 63321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78246, rend_intergenic: 72021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90119, rend_intergenic: 78367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91930, rend_intergenic: 90819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96727, rend_intergenic: 94078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96850, rend_intergenic: 96769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106713, rend_intergenic: 96914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116813, rend_intergenic: 109701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125235, rend_intergenic: 118537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136634, rend_intergenic: 127052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164991, rend_intergenic: 142787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182081, rend_intergenic: 172743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182929, rend_intergenic: 182343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185731, rend_intergenic: 182988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support