-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_13978949-14273036

-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 CodingQuarry_transcript_52345-T1
Valid prediction for Augustus_model.g8681.t1
Valid prediction for CodingQuarry_transcript_52347-T1
Valid prediction for GlimmerHMM_glimmerT_13043-T1
Valid prediction for snap_scaffold_5-snap.2618-T1
Valid prediction for snap_scaffold_5-snap.2584-T1
Valid prediction for snap_scaffold_5-snap.2614-T1
Valid prediction for snap_scaffold_5-snap.2621-T1
Valid prediction for snap_scaffold_5-snap.2622-T1
Valid prediction for GlimmerHMM_glimmerT_13033-T1
Valid prediction for snap_scaffold_5-snap.2623-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g8676.t1
Valid prediction for Augustus_model.g8674.t1
Valid prediction for snap_scaffold_5-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_13045-T1
Valid prediction for Augustus_model.g8673.t1
Valid prediction for GlimmerHMM_glimmerT_13048-T1
Valid prediction for GlimmerHMM_glimmerT_13057-T1
Valid prediction for Augustus_model.g8677.t1
Valid prediction for GlimmerHMM_glimmerT_13054-T1
Valid prediction for GlimmerHMM_glimmerT_13027-T1
Valid prediction for Augustus_model.g8679.t1
Valid prediction for pasa_asmbl_45906.p1
Valid prediction for snap_scaffold_5-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_13051-T1
Valid prediction for Augustus_model.g8657.t1
Valid prediction for Augustus_model.g8684.t1
Valid prediction for snap_scaffold_5-snap.2628-T1
Valid prediction for CodingQuarry_transcript_52343-T1
Couldn't classify 72805, 72897
Sorry, prediction pasa_asmbl_45894.p1 fails validation.
(AAC)	 AT	72805-72897	GT	TGG
(CCT)	 AG	73119-73230	GT	AGG
(AGG)	 AG	73710-73891	GT	CAG
(CCC)	 AG	74690-74798	GT	CGG
(ACC)	 AG	74876-74969	GT	ACG
(GTC)	 AG	76161-76239	GT	AGG
(GCG)	 AG	76400-76498	CC	AGC
-recovered pasa_asmbl_45894.p1, terminal, 76400, 76498
-recovered pasa_asmbl_45894.p1, internal, 73119, 73230
-recovered pasa_asmbl_45894.p1, internal, 73710, 73891
-recovered pasa_asmbl_45894.p1, internal, 74690, 74798
-recovered pasa_asmbl_45894.p1, internal, 74876, 74969
-recovered pasa_asmbl_45894.p1, internal, 76161, 76239
Valid prediction for GlimmerHMM_glimmerT_13041-T1
Valid prediction for snap_scaffold_5-snap.2590-T1
Valid prediction for GlimmerHMM_glimmerT_13050-T1
Valid prediction for snap_scaffold_5-snap.2619-T1
Valid prediction for HiQ_model.g8671.t1
Valid prediction for pasa_asmbl_45898.p1
Valid prediction for snap_scaffold_5-snap.2597-T1
Valid prediction for snap_scaffold_5-snap.2596-T1
Valid prediction for Augustus_model.g8654.t1
Valid prediction for snap_scaffold_5-snap.2615-T1
Valid prediction for snap_scaffold_5-snap.2602-T1
Valid prediction for snap_scaffold_5-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_13042-T1
Valid prediction for GlimmerHMM_glimmerT_13036-T1
Valid prediction for GlimmerHMM_glimmerT_13031-T1
Valid prediction for snap_scaffold_5-snap.2620-T1
Valid prediction for Augustus_model.g8664.t1
Valid prediction for pasa_asmbl_45916.p1
Valid prediction for GlimmerHMM_glimmerT_13032-T1
Valid prediction for Augustus_model.g8672.t1
Valid prediction for Augustus_model.g8662.t1
Valid prediction for CodingQuarry_transcript_52341-T1
Valid prediction for Augustus_model.g8680.t1
Valid prediction for snap_scaffold_5-snap.2609-T1
Couldn't classify 93509, 93642
Sorry, prediction pasa_asmbl_45895.p1 fails validation.
(ATG)	 CC	90185-90295	GT	AGG
(GAT)	 AG	91961-92273	GT	TGG
(ATT)	 AG	93509-93642	CA	TGC
-recovered pasa_asmbl_45895.p1, initial, 90185, 90295
-recovered pasa_asmbl_45895.p1, internal, 91961, 92273
Valid prediction for CodingQuarry_transcript_52342-T1
Valid prediction for snap_scaffold_5-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_13025-T1
Valid prediction for Augustus_model.g8655.t1
Valid prediction for HiQ_model.g8669.t1
Valid prediction for Augustus_model.g8658.t1
Valid prediction for snap_scaffold_5-snap.2589-T1
Valid prediction for snap_scaffold_5-snap.2608-T1
Valid prediction for snap_scaffold_5-snap.2598-T1
Valid prediction for GlimmerHMM_glimmerT_13039-T1
Valid prediction for snap_scaffold_5-snap.2599-T1
Valid prediction for snap_scaffold_5-snap.2624-T1
Valid prediction for GlimmerHMM_glimmerT_13049-T1
Valid prediction for GlimmerHMM_glimmerT_13056-T1
Valid prediction for GlimmerHMM_glimmerT_13044-T1
Valid prediction for Augustus_model.g8675.t1
Valid prediction for snap_scaffold_5-snap.2588-T1
Couldn't classify 93820, 94293
Sorry, prediction pasa_asmbl_45896.p1 fails validation.
(GCT)	 AC	93820-94293	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_13026-T1
Valid prediction for Augustus_model.g8668.t1
Valid prediction for snap_scaffold_5-snap.2591-T1
Valid prediction for snap_scaffold_5-snap.2625-T1
Valid prediction for snap_scaffold_5-snap.2605-T1
Valid prediction for Augustus_model.g8656.t1
Valid prediction for GlimmerHMM_glimmerT_13029-T1
Valid prediction for GlimmerHMM_glimmerT_13052-T1
Couldn't classify 152016, 152146
Sorry, prediction pasa_asmbl_45904.p1 fails validation.
(ATC)	 TG	152016-152146	GT	CAG
(CAC)	 AG	152286-152383	GT	GGG
(GTC)	 AG	152477-152638	GT	GGG
(GTT)	 AG	152750-153002	GT	TCG
(GAG)	 AG	153156-153270	GT	AGG
(GTG)	 AG	153385-153559	GT	TGG
(GTG)	 AG	153698-153831	GT	AAG
(CCT)	 AG	154006-154137	TA	GAT
-recovered pasa_asmbl_45904.p1, terminal, 154006, 154137
-recovered pasa_asmbl_45904.p1, internal, 152286, 152383
-recovered pasa_asmbl_45904.p1, internal, 152477, 152638
-recovered pasa_asmbl_45904.p1, internal, 152750, 153002
-recovered pasa_asmbl_45904.p1, internal, 153156, 153270
-recovered pasa_asmbl_45904.p1, internal, 153385, 153559
-recovered pasa_asmbl_45904.p1, internal, 153698, 153831
Valid prediction for snap_scaffold_5-snap.2607-T1
Couldn't classify 184135, 184162
Couldn't classify 185919, 185985
Sorry, prediction pasa_asmbl_46480.p2 fails validation.
(CAC)	 GG	184135-184162	GT	AGG
(GAT)	 AG	184573-184672	GT	GGG
(AGA)	 AG	184942-185002	GT	ATG
(GAT)	 AG	185401-185492	GT	AGG
(GGA)	 AG	185919-185985	CA	ACC
-recovered pasa_asmbl_46480.p2, internal, 184573, 184672
-recovered pasa_asmbl_46480.p2, internal, 184942, 185002
-recovered pasa_asmbl_46480.p2, internal, 185401, 185492
Valid prediction for CodingQuarry_transcript_52346-T1
Valid prediction for HiQ_model.g8665.t1
Valid prediction for Augustus_model.g8661.t1
Valid prediction for GlimmerHMM_glimmerT_13047-T1
Valid prediction for snap_scaffold_5-snap.2593-T1
Valid prediction for snap_scaffold_5-snap.2617-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_13034-T1
Valid prediction for snap_scaffold_5-snap.2601-T1
Valid prediction for snap_scaffold_5-snap.2616-T1
Valid prediction for GlimmerHMM_glimmerT_13037-T1
Valid prediction for GlimmerHMM_glimmerT_13046-T1
Valid prediction for GlimmerHMM_glimmerT_13053-T1
Valid prediction for Augustus_model.g8659.t1
Valid prediction for GlimmerHMM_glimmerT_13024-T1
Valid prediction for Augustus_model.g8682.t1
Valid prediction for snap_scaffold_5-snap.2586-T1
Valid prediction for Augustus_model.g8653.t1
Valid prediction for GlimmerHMM_glimmerT_13055-T1
Valid prediction for GlimmerHMM_glimmerT_13030-T1
Valid prediction for CodingQuarry_transcript_52340-T1
Valid prediction for GlimmerHMM_glimmerT_13035-T1
Valid prediction for snap_scaffold_5-snap.2595-T1
Valid prediction for snap_scaffold_5-snap.2627-T1
Valid prediction for snap_scaffold_5-snap.2610-T1
Valid prediction for GlimmerHMM_glimmerT_13038-T1
Valid prediction for snap_scaffold_5-snap.2611-T1
Valid prediction for snap_scaffold_5-snap.2592-T1
Valid prediction for snap_scaffold_5-snap.2600-T1
Valid prediction for snap_scaffold_5-snap.2587-T1
Valid prediction for snap_scaffold_5-snap.2626-T1
Valid prediction for snap_scaffold_5-snap.2583-T1
Valid prediction for CodingQuarry_transcript_52344-T1
Valid prediction for Augustus_model.g8663.t1
Valid prediction for HiQ_model.g8683.t1
Couldn't classify 230634, 230746
Sorry, prediction pasa_asmbl_44588.p1 fails validation.
(ATC)	 GC	230634-230746	GT	AGG
(GAA)	 AG	231333-231659	GT	AAG
(AGT)	 AG	232088-232224	GT	CGG
(GTC)	 AG	232392-232505	GT	AAG
(CTC)	 AG	232872-233030	GT	GGG
(ACC)	 AG	233168-233343	GT	AGG
(GAG)	 AG	233561-233737	AA	GAA
-recovered pasa_asmbl_44588.p1, terminal, 233561, 233737
-recovered pasa_asmbl_44588.p1, internal, 231333, 231659
-recovered pasa_asmbl_44588.p1, internal, 232088, 232224
-recovered pasa_asmbl_44588.p1, internal, 232392, 232505
-recovered pasa_asmbl_44588.p1, internal, 232872, 233030
-recovered pasa_asmbl_44588.p1, internal, 233168, 233343
Valid prediction for Augustus_model.g8667.t1
Valid prediction for snap_scaffold_5-snap.2604-T1
Valid prediction for snap_scaffold_5-snap.2603-T1
Valid prediction for snap_scaffold_5-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_13028-T1
Valid prediction for Augustus_model.g8678.t1
Valid prediction for HiQ_model.g8660.t1
Valid prediction for pasa_asmbl_44589.p1
Valid prediction for GlimmerHMM_glimmerT_13040-T1
Valid prediction for pasa_asmbl_44593.p1
Valid prediction for snap_scaffold_5-snap.2606-T1
Valid prediction for GlimmerHMM_glimmerT_13023-T1
Valid prediction for Augustus_model.g8666.t1
Valid prediction for pasa_asmbl_44595.p1
Valid prediction for Augustus_model.g8670.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6470, rend_intergenic: 3777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10680, rend_intergenic: 8965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40175, rend_intergenic: 34672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114501, rend_intergenic: 112318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172739, rend_intergenic: 164866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181287, rend_intergenic: 174788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200822, rend_intergenic: 194154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 294088
-exon list size: 465


building trellis

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-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 6470, rend_intergenic: 3777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10680, rend_intergenic: 8965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40175, rend_intergenic: 34672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114501, rend_intergenic: 112318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172739, rend_intergenic: 164866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181287, rend_intergenic: 174788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200822, rend_intergenic: 194154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support