-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_17600295-17785972

-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 GlimmerHMM_glimmerT_2351-T1
Valid prediction for snap_scaffold_1-snap.3222-T1
Valid prediction for snap_scaffold_1-snap.3237-T1
Valid prediction for GlimmerHMM_glimmerT_2347-T1
Valid prediction for snap_scaffold_1-snap.3213-T1
Valid prediction for Augustus_model.g1738.t1
Valid prediction for snap_scaffold_1-snap.3239-T1
Valid prediction for GlimmerHMM_glimmerT_2364-T1
Valid prediction for snap_scaffold_1-snap.3190-T1
Valid prediction for snap_scaffold_1-snap.3229-T1
Valid prediction for Augustus_model.g1737.t1
Valid prediction for snap_scaffold_1-snap.3188-T1
Valid prediction for snap_scaffold_1-snap.3215-T1
Valid prediction for Augustus_model.g1741.t1
Valid prediction for GlimmerHMM_glimmerT_2369-T1
Valid prediction for GlimmerHMM_glimmerT_2358-T1
Valid prediction for Augustus_model.g1742.t1
Couldn't classify 127774, 127838
Sorry, prediction pasa_asmbl_2532.p1 fails validation.
(GCT)	 GC	127774-127838	GT	AGG
(TCG)	 AG	127943-127996	GT	AGG
(GCA)	 AG	128276-128393	GT	AAG
(GTG)	 AG	128625-128783	GT	TGG
(GCG)	 AG	128906-129043	GT	GGG
(ATA)	 AG	129266-129331	GT	CGG
(TTT)	 AG	129434-129638	GT	GGG
(GTA)	 AG	129803-129889	GT	AGG
(CTG)	 AG	130046-130178	GT	AAG
(CGA)	 AG	130328-130433	GT	AGG
(GGC)	 AG	130542-130620	GT	TGG
(GCA)	 AG	130798-130901	TC	GAT
-recovered pasa_asmbl_2532.p1, terminal, 130798, 130901
-recovered pasa_asmbl_2532.p1, internal, 127943, 127996
-recovered pasa_asmbl_2532.p1, internal, 128276, 128393
-recovered pasa_asmbl_2532.p1, internal, 128625, 128783
-recovered pasa_asmbl_2532.p1, internal, 128906, 129043
-recovered pasa_asmbl_2532.p1, internal, 129266, 129331
-recovered pasa_asmbl_2532.p1, internal, 129434, 129638
-recovered pasa_asmbl_2532.p1, internal, 129803, 129889
-recovered pasa_asmbl_2532.p1, internal, 130046, 130178
-recovered pasa_asmbl_2532.p1, internal, 130328, 130433
-recovered pasa_asmbl_2532.p1, internal, 130542, 130620
Valid prediction for GlimmerHMM_glimmerT_2355-T1
Valid prediction for snap_scaffold_1-snap.3191-T1
Valid prediction for HiQ_model.g1734.t1
Valid prediction for GlimmerHMM_glimmerT_2367-T1
Valid prediction for snap_scaffold_1-snap.3225-T1
Valid prediction for snap_scaffold_1-snap.3198-T1
Valid prediction for snap_scaffold_1-snap.3206-T1
Valid prediction for Augustus_model.g1730.t1
Valid prediction for pasa_asmbl_2525.p1
Valid prediction for snap_scaffold_1-snap.3205-T1
Valid prediction for Augustus_model.g1736.t1
Valid prediction for GlimmerHMM_glimmerT_2353-T1
Valid prediction for CodingQuarry_transcript_2977-T1
Valid prediction for snap_scaffold_1-snap.3231-T1
Valid prediction for snap_scaffold_1-snap.3220-T1
Valid prediction for snap_scaffold_1-snap.3203-T1
Valid prediction for snap_scaffold_1-snap.3196-T1
Valid prediction for snap_scaffold_1-snap.3227-T1
Valid prediction for GlimmerHMM_glimmerT_2366-T1
Valid prediction for GlimmerHMM_glimmerT_2373-T1
Valid prediction for snap_scaffold_1-snap.3194-T1
Valid prediction for snap_scaffold_1-snap.3212-T1
Valid prediction for snap_scaffold_1-snap.3200-T1
Valid prediction for GlimmerHMM_glimmerT_2374-T1
Valid prediction for GlimmerHMM_glimmerT_2356-T1
Valid prediction for snap_scaffold_1-snap.3197-T1
Valid prediction for Augustus_model.g1739.t1
Valid prediction for Augustus_model.g1740.t1
Valid prediction for snap_scaffold_1-snap.3217-T1
Valid prediction for GlimmerHMM_glimmerT_2357-T1
Valid prediction for snap_scaffold_1-snap.3210-T1
Valid prediction for GlimmerHMM_glimmerT_2368-T1
Valid prediction for GlimmerHMM_glimmerT_2372-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 GlimmerHMM_glimmerT_2362-T1
Valid prediction for snap_scaffold_1-snap.3192-T1
Valid prediction for snap_scaffold_1-snap.3238-T1
Valid prediction for snap_scaffold_1-snap.3207-T1
Couldn't classify 165779, 165984
Couldn't classify 166344, 166524
Sorry, prediction pasa_asmbl_1047.p2 fails validation.
(GGG)	 TA	165779-165984	GT	AAG
(CCT)	 AG	166344-166524	AG	ACA
Valid prediction for GlimmerHMM_glimmerT_2350-T1
Valid prediction for snap_scaffold_1-snap.3202-T1
Valid prediction for GlimmerHMM_glimmerT_2370-T1
Valid prediction for GlimmerHMM_glimmerT_2352-T1
Valid prediction for Augustus_model.g1729.t1
Valid prediction for GlimmerHMM_glimmerT_2348-T1
Valid prediction for snap_scaffold_1-snap.3209-T1
Valid prediction for snap_scaffold_1-snap.3226-T1
Valid prediction for snap_scaffold_1-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_2361-T1
Valid prediction for HiQ_model.g1726.t1
Valid prediction for snap_scaffold_1-snap.3201-T1
Valid prediction for HiQ_model.g1733.t1
Valid prediction for Augustus_model.g1728.t1
Valid prediction for snap_scaffold_1-snap.3195-T1
Valid prediction for GlimmerHMM_glimmerT_2363-T1
Couldn't classify 116270, 116602
Sorry, prediction pasa_asmbl_1054.p1 fails validation.
(TGC)	 TT	116270-116602	CC	AAC
Couldn't classify 134039, 134082
Couldn't classify 135310, 135845
Sorry, prediction pasa_asmbl_1052.p1 fails validation.
(AAG)	 GG	134039-134082	GT	AGG
(GTT)	 AG	134490-134668	GT	AGG
(AGC)	 AG	135043-135192	GT	AGG
(ACC)	 AG	135310-135845	CC	GCC
-recovered pasa_asmbl_1052.p1, internal, 134490, 134668
-recovered pasa_asmbl_1052.p1, internal, 135043, 135192
Valid prediction for snap_scaffold_1-snap.3235-T1
Valid prediction for GlimmerHMM_glimmerT_2375-T1
Valid prediction for snap_scaffold_1-snap.3236-T1
Valid prediction for snap_scaffold_1-snap.3189-T1
Valid prediction for snap_scaffold_1-snap.3230-T1
Couldn't classify 115969, 116049
Sorry, prediction pasa_asmbl_1055.p1 fails validation.
(ATG)	 AA	112454-112511	GT	TGG
(ACG)	 AG	113471-113656	GT	AGG
(AGG)	 AG	114252-114332	GT	AGG
(GCA)	 AG	114865-115051	GT	AGG
(GGA)	 AG	115325-115426	GT	CAG
(GGC)	 AG	115709-115850	GT	TGG
(ATC)	 AG	115969-116049	CA	CCC
-recovered pasa_asmbl_1055.p1, initial, 112454, 112511
-recovered pasa_asmbl_1055.p1, internal, 113471, 113656
-recovered pasa_asmbl_1055.p1, internal, 114252, 114332
-recovered pasa_asmbl_1055.p1, internal, 114865, 115051
-recovered pasa_asmbl_1055.p1, internal, 115325, 115426
-recovered pasa_asmbl_1055.p1, internal, 115709, 115850
Valid prediction for pasa_asmbl_1044.p1
Valid prediction for Augustus_model.g1744.t1
Valid prediction for GlimmerHMM_glimmerT_2359-T1
Valid prediction for GlimmerHMM_glimmerT_2371-T1
Valid prediction for CodingQuarry_transcript_2973-T1
Valid prediction for snap_scaffold_1-snap.3208-T1
Valid prediction for pasa_asmbl_1060.p1
Valid prediction for snap_scaffold_1-snap.3216-T1
Valid prediction for GlimmerHMM_glimmerT_2354-T1
Valid prediction for snap_scaffold_1-snap.3218-T1
Valid prediction for snap_scaffold_1-snap.3232-T1
Valid prediction for snap_scaffold_1-snap.3211-T1
Valid prediction for Augustus_model.g1745.t1
Valid prediction for Augustus_model.g1743.t1
Valid prediction for snap_scaffold_1-snap.3214-T1
Couldn't classify 170863, 171558
Sorry, prediction pasa_asmbl_1046.p1 fails validation.
(CAG)	 TG	170863-171558	CC	AGC
Valid prediction for Augustus_model.g1731.t1
Valid prediction for snap_scaffold_1-snap.3199-T1
Valid prediction for CodingQuarry_transcript_2978-T1
Valid prediction for GlimmerHMM_glimmerT_2360-T1
Valid prediction for GlimmerHMM_glimmerT_2349-T1
Valid prediction for Augustus_model.g1732.t1
Valid prediction for snap_scaffold_1-snap.3221-T1
Valid prediction for snap_scaffold_1-snap.3219-T1
Couldn't classify 105988, 106027
Sorry, prediction pasa_asmbl_1058.p1 fails validation.
(GGT)	 TA	105988-106027	GT	GGG
(CGG)	 AG	106430-106574	GT	AAG
(GCT)	 AG	106918-107014	GT	AGG
(ATC)	 AG	107420-107618	GT	CGG
(GTA)	 AG	107969-108087	GT	AGG
(TTG)	 AG	108343-108516	GT	AGG
(GTC)	 AG	108969-109129	GT	AAG
(GGA)	 AG	109421-109532	GT	CTG
(CTC)	 AG	109667-109846	GT	AGG
(GCG)	 AG	109954-110052	GT	AGG
(GGC)	 AG	110322-110465	GT	AGG
(GGG)	 AG	110700-110780	GA	GAG
-recovered pasa_asmbl_1058.p1, terminal, 110700, 110780
-recovered pasa_asmbl_1058.p1, internal, 106430, 106574
-recovered pasa_asmbl_1058.p1, internal, 106918, 107014
-recovered pasa_asmbl_1058.p1, internal, 107420, 107618
-recovered pasa_asmbl_1058.p1, internal, 107969, 108087
-recovered pasa_asmbl_1058.p1, internal, 108343, 108516
-recovered pasa_asmbl_1058.p1, internal, 108969, 109129
-recovered pasa_asmbl_1058.p1, internal, 109421, 109532
-recovered pasa_asmbl_1058.p1, internal, 109667, 109846
-recovered pasa_asmbl_1058.p1, internal, 109954, 110052
-recovered pasa_asmbl_1058.p1, internal, 110322, 110465
Valid prediction for HiQ_model.g1735.t1
Valid prediction for snap_scaffold_1-snap.3234-T1
Valid prediction for snap_scaffold_1-snap.3224-T1
Valid prediction for snap_scaffold_1-snap.3193-T1
Valid prediction for GlimmerHMM_glimmerT_2376-T1
Couldn't classify 135942, 136289
Sorry, prediction pasa_asmbl_1051.p1 fails validation.
(GGG)	 TA	135942-136289	AA	TCA
Valid prediction for Augustus_model.g1727.t1
Valid prediction for GlimmerHMM_glimmerT_2365-T1
Valid prediction for snap_scaffold_1-snap.3233-T1
Valid prediction for GlimmerHMM_glimmerT_2377-T1
Valid prediction for snap_scaffold_1-snap.3204-T1
Valid prediction for snap_scaffold_1-snap.3228-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8379, rend_intergenic: 4596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17970, rend_intergenic: 14121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21342, rend_intergenic: 19501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21782, rend_intergenic: 21576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37263, rend_intergenic: 24363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48469, rend_intergenic: 41518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52662, rend_intergenic: 50434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53132, rend_intergenic: 52691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64720, rend_intergenic: 53490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85476, rend_intergenic: 81896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101367, rend_intergenic: 97956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108926, rend_intergenic: 103512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116738, rend_intergenic: 112002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121517, rend_intergenic: 119637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123126, rend_intergenic: 121772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130372, rend_intergenic: 127474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141161, rend_intergenic: 139712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143346, rend_intergenic: 141579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147238, rend_intergenic: 143448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174876, rend_intergenic: 147458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181656, rend_intergenic: 178260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185678
-exon list size: 463


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 8379, rend_intergenic: 4596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17970, rend_intergenic: 14121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21342, rend_intergenic: 19501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21782, rend_intergenic: 21576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37263, rend_intergenic: 24363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48469, rend_intergenic: 41518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52662, rend_intergenic: 50434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53132, rend_intergenic: 52691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64720, rend_intergenic: 53490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85476, rend_intergenic: 81896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101367, rend_intergenic: 97956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108926, rend_intergenic: 103512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116738, rend_intergenic: 112002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121517, rend_intergenic: 119637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123126, rend_intergenic: 121772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130372, rend_intergenic: 127474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141161, rend_intergenic: 139712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143346, rend_intergenic: 141579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147238, rend_intergenic: 143448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174876, rend_intergenic: 147458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181656, rend_intergenic: 178260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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