-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_16130794-16371532

-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_1-snap.2839-T1
Valid prediction for snap_scaffold_1-snap.2829-T1
Valid prediction for snap_scaffold_1-snap.2837-T1
Valid prediction for snap_scaffold_1-snap.2842-T1
Valid prediction for Augustus_model.g1589.t1
Valid prediction for snap_scaffold_1-snap.2851-T1
Valid prediction for snap_scaffold_1-snap.2869-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g1587.t1
Valid prediction for snap_scaffold_1-snap.2857-T1
Valid prediction for snap_scaffold_1-snap.2846-T1
Valid prediction for snap_scaffold_1-snap.2824-T1
Valid prediction for snap_scaffold_1-snap.2835-T1
Valid prediction for snap_scaffold_1-snap.2853-T1
Valid prediction for snap_scaffold_1-snap.2843-T1
Valid prediction for GlimmerHMM_glimmerT_2135-T1
Valid prediction for snap_scaffold_1-snap.2867-T1
Valid prediction for Augustus_model.g1584.t1
Valid prediction for GlimmerHMM_glimmerT_2147-T1
Valid prediction for pasa_asmbl_2467.p1
Valid prediction for snap_scaffold_1-snap.2832-T1
Valid prediction for Augustus_model.g1582.t1
Couldn't classify 191820, 191976
Couldn't classify 192096, 192433
Sorry, prediction pasa_asmbl_2475.p1 fails validation.
(GGG)	 AG	191820-191976	GT	GGG
(CTC)	 AG	192096-192433	CA	ACC
-recovered pasa_asmbl_2475.p1, internal, 191820, 191976
Valid prediction for GlimmerHMM_glimmerT_2138-T1
Valid prediction for HiQ_model.g1585.t1
Valid prediction for snap_scaffold_1-snap.2827-T1
Valid prediction for snap_scaffold_1-snap.2854-T1
Valid prediction for Augustus_model.g1588.t1
Couldn't classify 192640, 192651
Couldn't classify 194479, 194599
Sorry, prediction pasa_asmbl_2476.p1 fails validation.
(CCT)	 AA	192640-192651	GT	AGG
(AAT)	 AG	192814-192999	GT	AGG
(TGG)	 AG	193318-193479	GT	AGG
(CTT)	 AG	194276-194376	GT	GAG
(GCA)	 AG	194479-194599	GT	TGG
-recovered pasa_asmbl_2476.p1, internal, 192814, 192999
-recovered pasa_asmbl_2476.p1, internal, 193318, 193479
-recovered pasa_asmbl_2476.p1, internal, 194276, 194376
-recovered pasa_asmbl_2476.p1, internal, 194479, 194599
Valid prediction for CodingQuarry_transcript_2953-T1
Valid prediction for GlimmerHMM_glimmerT_2141-T1
Valid prediction for GlimmerHMM_glimmerT_2129-T1
Valid prediction for snap_scaffold_1-snap.2822-T1
Valid prediction for GlimmerHMM_glimmerT_2124-T1
Valid prediction for GlimmerHMM_glimmerT_2154-T1
Valid prediction for GlimmerHMM_glimmerT_2143-T1
Valid prediction for snap_scaffold_1-snap.2856-T1
Valid prediction for snap_scaffold_1-snap.2865-T1
Couldn't classify 77015, 77491
Sorry, prediction pasa_asmbl_2465.p1 fails validation.
(TCT)	 TG	77015-77491	AC	ACA
Valid prediction for Augustus_model.g1595.t1
Valid prediction for GlimmerHMM_glimmerT_2149-T1
Valid prediction for snap_scaffold_1-snap.2845-T1
Valid prediction for GlimmerHMM_glimmerT_2134-T1
Valid prediction for GlimmerHMM_glimmerT_2137-T1
Valid prediction for snap_scaffold_1-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_2136-T1
Valid prediction for snap_scaffold_1-snap.2848-T1
Valid prediction for GlimmerHMM_glimmerT_2145-T1
Valid prediction for GlimmerHMM_glimmerT_2119-T1
Valid prediction for Augustus_model.g1597.t1
Valid prediction for snap_scaffold_1-snap.2871-T1
Valid prediction for snap_scaffold_1-snap.2847-T1
Valid prediction for GlimmerHMM_glimmerT_2130-T1
Valid prediction for snap_scaffold_1-snap.2870-T1
Valid prediction for GlimmerHMM_glimmerT_2121-T1
Valid prediction for Augustus_model.g1586.t1
Valid prediction for Augustus_model.g1591.t1
Valid prediction for snap_scaffold_1-snap.2862-T1
Valid prediction for snap_scaffold_1-snap.2859-T1
Valid prediction for GlimmerHMM_glimmerT_2126-T1
Valid prediction for CodingQuarry_transcript_2954-T1
Valid prediction for CodingQuarry_transcript_2955-T1
Valid prediction for snap_scaffold_1-snap.2850-T1
Valid prediction for GlimmerHMM_glimmerT_2131-T1
Valid prediction for snap_scaffold_1-snap.2864-T1
Valid prediction for GlimmerHMM_glimmerT_2132-T1
Valid prediction for GlimmerHMM_glimmerT_2128-T1
Valid prediction for snap_scaffold_1-snap.2875-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_2150-T1
Valid prediction for pasa_asmbl_985.p1
Valid prediction for GlimmerHMM_glimmerT_2151-T1
Valid prediction for Augustus_model.g1592.t1
Valid prediction for snap_scaffold_1-snap.2863-T1
Valid prediction for Augustus_model.g1598.t1
Valid prediction for snap_scaffold_1-snap.2861-T1
Valid prediction for Augustus_model.g1593.t1
Valid prediction for snap_scaffold_1-snap.2833-T1
Valid prediction for snap_scaffold_1-snap.2873-T1
Valid prediction for snap_scaffold_1-snap.2826-T1
Couldn't classify 221959, 222009
Sorry, prediction Augustus_model.g1579.t1 fails validation.
(CTC)	 AG	221959-222009	GT	GGG
(GCC)	 AG	223217-223334	AG	GAA
-recovered Augustus_model.g1579.t1, terminal, 223217, 223334
-recovered Augustus_model.g1579.t1, internal, 221959, 222009
Valid prediction for GlimmerHMM_glimmerT_2155-T1
Valid prediction for snap_scaffold_1-snap.2838-T1
Valid prediction for pasa_asmbl_983.p1
Valid prediction for snap_scaffold_1-snap.2844-T1
Valid prediction for GlimmerHMM_glimmerT_2153-T1
Valid prediction for snap_scaffold_1-snap.2823-T1
Valid prediction for snap_scaffold_1-snap.2872-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.2830-T1
Valid prediction for Augustus_model.g1578.t1
Valid prediction for HiQ_model.g1599.t1
Valid prediction for GlimmerHMM_glimmerT_2122-T1
Valid prediction for snap_scaffold_1-snap.2860-T1
Valid prediction for snap_scaffold_1-snap.2849-T1
Valid prediction for GlimmerHMM_glimmerT_2120-T1
Valid prediction for snap_scaffold_1-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_2146-T1
Valid prediction for Augustus_model.g1580.t1
Valid prediction for GlimmerHMM_glimmerT_2123-T1
Valid prediction for HiQ_model.g1596.t1
Valid prediction for snap_scaffold_1-snap.2825-T1
Couldn't classify 17181, 17282
Sorry, prediction pasa_asmbl_986.p1 fails validation.
(TAT)	 AG	17181-17282	GT	AGG
(TGG)	 AG	17420-17521	GT	AGG
(CCC)	 AG	17788-17949	GT	AGG
(ATC)	 AG	18140-18237	GT	AGG
(CGT)	 AG	18430-18565	GT	AGG
(ATC)	 AG	19228-19350	GT	AGG
(ACC)	 AG	21082-21183	GT	AGG
(GTC)	 AG	21882-21935	GG	GAG
-recovered pasa_asmbl_986.p1, terminal, 21882, 21935
-recovered pasa_asmbl_986.p1, internal, 17181, 17282
-recovered pasa_asmbl_986.p1, internal, 17420, 17521
-recovered pasa_asmbl_986.p1, internal, 17788, 17949
-recovered pasa_asmbl_986.p1, internal, 18140, 18237
-recovered pasa_asmbl_986.p1, internal, 18430, 18565
-recovered pasa_asmbl_986.p1, internal, 19228, 19350
-recovered pasa_asmbl_986.p1, internal, 21082, 21183
Valid prediction for snap_scaffold_1-snap.2840-T1
Valid prediction for snap_scaffold_1-snap.2874-T1
Valid prediction for GlimmerHMM_glimmerT_2148-T1
Valid prediction for snap_scaffold_1-snap.2852-T1
Valid prediction for GlimmerHMM_glimmerT_2142-T1
Valid prediction for snap_scaffold_1-snap.2868-T1
Couldn't classify 74877, 74981
Sorry, prediction pasa_asmbl_977.p2 fails validation.
(GTC)	 CA	74877-74981	GT	TGG
(TGG)	 AG	76600-76680	GT	CGG
(CAC)	 AG	77096-77275	GT	GGG
(GAA)	 AG	78540-78704	AG	AGA
-recovered pasa_asmbl_977.p2, terminal, 78540, 78704
-recovered pasa_asmbl_977.p2, internal, 76600, 76680
-recovered pasa_asmbl_977.p2, internal, 77096, 77275
Couldn't classify 15556, 15710
Couldn't classify 16513, 16626
Sorry, prediction pasa_asmbl_1371.p1 fails validation.
(CCA)	 CC	15556-15710	GT	CAG
(CAC)	 AG	16098-16140	GT	GGG
(ATC)	 AG	16513-16626	CC	GAC
-recovered pasa_asmbl_1371.p1, internal, 16098, 16140
Valid prediction for snap_scaffold_1-snap.2831-T1
Valid prediction for GlimmerHMM_glimmerT_2125-T1
Valid prediction for GlimmerHMM_glimmerT_2139-T1
Valid prediction for Augustus_model.g1583.t1
Valid prediction for GlimmerHMM_glimmerT_2144-T1
Valid prediction for snap_scaffold_1-snap.2834-T1
Valid prediction for Augustus_model.g1590.t1
Valid prediction for snap_scaffold_1-snap.2841-T1
Valid prediction for GlimmerHMM_glimmerT_2127-T1
Valid prediction for Augustus_model.g1594.t1
Valid prediction for GlimmerHMM_glimmerT_2152-T1
Valid prediction for GlimmerHMM_glimmerT_2140-T1
Valid prediction for Augustus_model.g1600.t1
Valid prediction for snap_scaffold_1-snap.2836-T1
Valid prediction for Augustus_model.g1581.t1
Valid prediction for snap_scaffold_1-snap.2855-T1
Valid prediction for snap_scaffold_1-snap.2828-T1
Valid prediction for GlimmerHMM_glimmerT_2133-T1
Valid prediction for snap_scaffold_1-snap.2866-T1
Valid prediction for snap_scaffold_1-snap.2858-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6357, rend_intergenic: 4218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9628, rend_intergenic: 6556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15024, rend_intergenic: 10433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23668, rend_intergenic: 15334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25297, rend_intergenic: 23754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34163, rend_intergenic: 26315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44385, rend_intergenic: 34373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49786, rend_intergenic: 47725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53399, rend_intergenic: 50243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56435, rend_intergenic: 54248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56974, rend_intergenic: 56462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59656, rend_intergenic: 57613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61329, rend_intergenic: 60642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64530, rend_intergenic: 61827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70888, rend_intergenic: 65074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86956, rend_intergenic: 82823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116637, rend_intergenic: 113174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141358, rend_intergenic: 123862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146142, rend_intergenic: 142270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156851, rend_intergenic: 155582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164817, rend_intergenic: 162085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170986, rend_intergenic: 166361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197245, rend_intergenic: 188994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206644, rend_intergenic: 202714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237048, rend_intergenic: 235018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240739
-exon list size: 494


building trellis

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-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 6357, rend_intergenic: 4218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9628, rend_intergenic: 6556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15024, rend_intergenic: 10433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23668, rend_intergenic: 15334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25297, rend_intergenic: 23754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34163, rend_intergenic: 26315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44385, rend_intergenic: 34373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49786, rend_intergenic: 47725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53399, rend_intergenic: 50243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56435, rend_intergenic: 54248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56974, rend_intergenic: 56462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59656, rend_intergenic: 57613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61329, rend_intergenic: 60642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64530, rend_intergenic: 61827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70888, rend_intergenic: 65074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86956, rend_intergenic: 82823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116637, rend_intergenic: 113174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141358, rend_intergenic: 123862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146142, rend_intergenic: 142270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156851, rend_intergenic: 155582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164817, rend_intergenic: 162085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170986, rend_intergenic: 166361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197245, rend_intergenic: 188994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206644, rend_intergenic: 202714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237048, rend_intergenic: 235018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support