-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_14462993-14685832

-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.2774-T1
Valid prediction for pasa_asmbl_24963.p1
Valid prediction for GlimmerHMM_glimmerT_4940-T1
Valid prediction for pasa_asmbl_24957.p1
Valid prediction for GlimmerHMM_glimmerT_4938-T1
Valid prediction for CodingQuarry_transcript_28745-T1
Valid prediction for GlimmerHMM_glimmerT_4941-T1
Valid prediction for HiQ_model.g3324.t1
Valid prediction for snap_scaffold_2-snap.2770-T1
Valid prediction for pasa_asmbl_24965.p1
Valid prediction for CodingQuarry_transcript_28741-T1
Valid prediction for GlimmerHMM_glimmerT_4945-T1
Valid prediction for CodingQuarry_transcript_28740-T1
Valid prediction for snap_scaffold_2-snap.2771-T1
Valid prediction for snap_scaffold_2-snap.2759-T1
Valid prediction for GlimmerHMM_glimmerT_4923-T1
Valid prediction for GlimmerHMM_glimmerT_4924-T1
Valid prediction for GlimmerHMM_glimmerT_4933-T1
Valid prediction for GlimmerHMM_glimmerT_4931-T1
Valid prediction for snap_scaffold_2-snap.2764-T1
Valid prediction for HiQ_model.g3323.t1
Valid prediction for snap_scaffold_2-snap.2767-T1
Valid prediction for GlimmerHMM_glimmerT_4932-T1
Valid prediction for Augustus_model.g3317.t1
Valid prediction for Augustus_model.g3322.t1
Valid prediction for snap_scaffold_2-snap.2780-T1
Valid prediction for HiQ_model.g3334.t1
Valid prediction for GlimmerHMM_glimmerT_4946-T1
Valid prediction for GlimmerHMM_glimmerT_4928-T1
Valid prediction for snap_scaffold_2-snap.2757-T1
Valid prediction for GlimmerHMM_glimmerT_4926-T1
Couldn't classify 43641, 43716
Sorry, prediction pasa_asmbl_24939.p1 fails validation.
(ATG)	 GC	39168-39233	GT	AGG
(ATT)	 AG	39452-39685	GT	AGG
(TTT)	 AG	40159-40237	GT	AGG
(GAC)	 AG	40325-40504	GT	TTG
(CTG)	 AG	40637-40784	GT	AGG
(GTC)	 AG	40893-40989	GT	CGG
(AAC)	 AG	41227-41411	GT	CGG
(AGC)	 AG	42362-42515	GT	AGG
(CTT)	 AG	42615-42736	GT	GGG
(TGG)	 AG	42814-42956	GT	AGG
(AGA)	 AG	43041-43178	GT	CGG
(ACC)	 AG	43334-43439	GT	AGG
(GTT)	 AG	43641-43716	GG	CGG
-recovered pasa_asmbl_24939.p1, initial, 39168, 39233
add_exon() Sorry, pasa_asmbl_24939.p1 43334-43439-terminal-3 is invalid.
-recovered pasa_asmbl_24939.p1, terminal, 43334, 43439
-recovered pasa_asmbl_24939.p1, internal, 39452, 39685
-recovered pasa_asmbl_24939.p1, internal, 40159, 40237
-recovered pasa_asmbl_24939.p1, internal, 40325, 40504
-recovered pasa_asmbl_24939.p1, internal, 40637, 40784
-recovered pasa_asmbl_24939.p1, internal, 40893, 40989
-recovered pasa_asmbl_24939.p1, internal, 41227, 41411
-recovered pasa_asmbl_24939.p1, internal, 42362, 42515
-recovered pasa_asmbl_24939.p1, internal, 42615, 42736
-recovered pasa_asmbl_24939.p1, internal, 42814, 42956
-recovered pasa_asmbl_24939.p1, internal, 43041, 43178
-recovered pasa_asmbl_24939.p1, internal, 43334, 43439
Valid prediction for GlimmerHMM_glimmerT_4944-T1
Valid prediction for GlimmerHMM_glimmerT_4930-T1
Valid prediction for HiQ_model.g3321.t1
Valid prediction for Augustus_model.g3327.t1
Valid prediction for snap_scaffold_2-snap.2789-T1
Valid prediction for Augustus_model.g3331.t1
Valid prediction for snap_scaffold_2-snap.2786-T1
Valid prediction for snap_scaffold_2-snap.2758-T1
Valid prediction for GlimmerHMM_glimmerT_4937-T1
Valid prediction for Augustus_model.g3333.t1
Valid prediction for snap_scaffold_2-snap.2755-T1
Valid prediction for snap_scaffold_2-snap.2785-T1
Valid prediction for snap_scaffold_2-snap.2761-T1
Valid prediction for Augustus_model.g3336.t1
Valid prediction for GlimmerHMM_glimmerT_4920-T1
Valid prediction for pasa_asmbl_25339.p1
Valid prediction for snap_scaffold_2-snap.2762-T1
Valid prediction for Augustus_model.g3326.t1
Valid prediction for snap_scaffold_2-snap.2777-T1
Valid prediction for Augustus_model.g3319.t1
Valid prediction for snap_scaffold_2-snap.2760-T1
Valid prediction for snap_scaffold_2-snap.2781-T1
Valid prediction for HiQ_model.g3330.t1
Valid prediction for Augustus_model.g3320.t1
Valid prediction for snap_scaffold_2-snap.2782-T1
Valid prediction for GlimmerHMM_glimmerT_4929-T1
Couldn't classify 53164, 53579
Couldn't classify 54057, 54119
Sorry, prediction pasa_asmbl_24942.p1 fails validation.
(AGC)	 GC	53164-53579	GT	AGG
(GTA)	 AG	53694-53829	GT	AGG
(GAG)	 AG	54057-54119	AC	AGA
-recovered pasa_asmbl_24942.p1, internal, 53694, 53829
Valid prediction for Augustus_model.g3325.t1
Valid prediction for GlimmerHMM_glimmerT_4925-T1
Valid prediction for snap_scaffold_2-snap.2795-T1
Valid prediction for snap_scaffold_2-snap.2754-T1
Valid prediction for snap_scaffold_2-snap.2791-T1
Valid prediction for GlimmerHMM_glimmerT_4921-T1
Valid prediction for pasa_asmbl_24944.p1
Valid prediction for Augustus_model.g3337.t1
Valid prediction for CodingQuarry_transcript_28742-T1
Valid prediction for snap_scaffold_2-snap.2783-T1
Valid prediction for snap_scaffold_2-snap.2772-T1
Valid prediction for Augustus_model.g3338.t1
Valid prediction for snap_scaffold_2-snap.2787-T1
Valid prediction for snap_scaffold_2-snap.2776-T1
Valid prediction for GlimmerHMM_glimmerT_4939-T1
Valid prediction for snap_scaffold_2-snap.2775-T1
Valid prediction for GlimmerHMM_glimmerT_4943-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.2779-T1
Valid prediction for snap_scaffold_2-snap.2794-T1
Valid prediction for CodingQuarry_transcript_28743-T1
Valid prediction for GlimmerHMM_glimmerT_4947-T1
Valid prediction for GlimmerHMM_glimmerT_4942-T1
Couldn't classify 204307, 204442
Couldn't classify 207630, 207725
Sorry, prediction pasa_asmbl_23605.p1 fails validation.
(CTA)	 AG	204307-204442	GT	AGG
(CAG)	 AG	205186-205299	GT	AGG
(AAG)	 AG	205542-205604	GT	TTG
(TGA)	 AG	205889-205991	GT	GGG
(GCG)	 AG	206350-206511	GT	TGG
(TGA)	 AG	206778-206959	GT	CGG
(GTC)	 AG	207382-207476	GT	AGG
(TGT)	 AG	207630-207725	GG	AGG
-recovered pasa_asmbl_23605.p1, internal, 204307, 204442
-recovered pasa_asmbl_23605.p1, internal, 205186, 205299
-recovered pasa_asmbl_23605.p1, internal, 205542, 205604
-recovered pasa_asmbl_23605.p1, internal, 205889, 205991
-recovered pasa_asmbl_23605.p1, internal, 206350, 206511
-recovered pasa_asmbl_23605.p1, internal, 206778, 206959
-recovered pasa_asmbl_23605.p1, internal, 207382, 207476
Valid prediction for snap_scaffold_2-snap.2773-T1
Valid prediction for Augustus_model.g3328.t1
Valid prediction for snap_scaffold_2-snap.2753-T1
Valid prediction for pasa_asmbl_23609.p1
Valid prediction for snap_scaffold_2-snap.2766-T1
Valid prediction for CodingQuarry_transcript_28744-T1
Valid prediction for GlimmerHMM_glimmerT_4934-T1
Couldn't classify 209047, 209162
Sorry, prediction pasa_asmbl_23953.p1 fails validation.
(GAA)	 AG	209047-209162	GT	AGG
(GCT)	 AG	209453-209705	GG	GAG
-recovered pasa_asmbl_23953.p1, terminal, 209453, 209705
-recovered pasa_asmbl_23953.p1, internal, 209047, 209162
Valid prediction for snap_scaffold_2-snap.2778-T1
Valid prediction for CodingQuarry_transcript_28739-T1
Valid prediction for GlimmerHMM_glimmerT_4927-T1
Valid prediction for snap_scaffold_2-snap.2784-T1
Valid prediction for snap_scaffold_2-snap.2790-T1
Valid prediction for GlimmerHMM_glimmerT_4936-T1
Valid prediction for Augustus_model.g3318.t1
Valid prediction for pasa_asmbl_23608.p1
Valid prediction for snap_scaffold_2-snap.2768-T1
Valid prediction for GlimmerHMM_glimmerT_4935-T1
Valid prediction for snap_scaffold_2-snap.2756-T1
Valid prediction for snap_scaffold_2-snap.2765-T1
Valid prediction for snap_scaffold_2-snap.2792-T1
Valid prediction for HiQ_model.g3332.t1
Valid prediction for snap_scaffold_2-snap.2793-T1
Valid prediction for HiQ_model.g3329.t1
Valid prediction for snap_scaffold_2-snap.2763-T1
Valid prediction for snap_scaffold_2-snap.2796-T1
Valid prediction for snap_scaffold_2-snap.2788-T1
Valid prediction for GlimmerHMM_glimmerT_4922-T1
Valid prediction for Augustus_model.g3335.t1
Valid prediction for snap_scaffold_2-snap.2769-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54359, rend_intergenic: 48907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63874, rend_intergenic: 58874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70406, rend_intergenic: 65720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73487, rend_intergenic: 71828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100156, rend_intergenic: 99703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103838, rend_intergenic: 100983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153443, rend_intergenic: 151516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195439, rend_intergenic: 193688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214180, rend_intergenic: 202937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222377, rend_intergenic: 219318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222840
-exon list size: 453


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 54359, rend_intergenic: 48907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63874, rend_intergenic: 58874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70406, rend_intergenic: 65720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73487, rend_intergenic: 71828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100156, rend_intergenic: 99703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103838, rend_intergenic: 100983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153443, rend_intergenic: 151516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195439, rend_intergenic: 193688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214180, rend_intergenic: 202937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222377, rend_intergenic: 219318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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