-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_10873837-11092662

-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: +)Couldn't classify 20318, 20356
Sorry, prediction pasa_asmbl_47305.p1 fails validation.
(CTC)	 GT	20318-20356	GT	TGG
(TCT)	 AG	21582-21774	GT	AAG
(AAC)	 AG	22119-22287	GT	TGG
(GTT)	 AG	22398-22533	GT	AGG
(ATG)	 AG	23504-23690	GT	AGG
(GAG)	 AG	23968-24128	GC	AGG
(ATC)	 AG	24339-24440	GT	TGG
(GGA)	 AG	24600-24695	GT	AGG
(TCA)	 AG	24908-25027	GT	TGG
(GGT)	 AG	25240-25296	AT	AGA
-recovered pasa_asmbl_47305.p1, initial, 23504, 23690
add_exon() Sorry, pasa_asmbl_47305.p1 21582-21774-terminal-3 is invalid.
-recovered pasa_asmbl_47305.p1, terminal, 21582, 21774
-recovered pasa_asmbl_47305.p1, terminal, 25240, 25296
-recovered pasa_asmbl_47305.p1, internal, 21582, 21774
-recovered pasa_asmbl_47305.p1, internal, 22119, 22287
-recovered pasa_asmbl_47305.p1, internal, 22398, 22533
-recovered pasa_asmbl_47305.p1, internal, 23504, 23690
-recovered pasa_asmbl_47305.p1, internal, 23968, 24128
-recovered pasa_asmbl_47305.p1, internal, 24339, 24440
-recovered pasa_asmbl_47305.p1, internal, 24600, 24695
-recovered pasa_asmbl_47305.p1, internal, 24908, 25027
Valid prediction for snap_scaffold_6-snap.2375-T1
Valid prediction for Augustus_model.g10299.t1
Valid prediction for snap_scaffold_6-snap.2338-T1
Valid prediction for snap_scaffold_6-snap.2368-T1
Valid prediction for GlimmerHMM_glimmerT_15453-T1
Valid prediction for snap_scaffold_6-snap.2337-T1
Valid prediction for snap_scaffold_6-snap.2356-T1
Valid prediction for HiQ_model.g10296.t1
Valid prediction for snap_scaffold_6-snap.2359-T1
Valid prediction for CodingQuarry_transcript_55219-T1
Valid prediction for Augustus_model.g10297.t1
Valid prediction for HiQ_model.g10283.t1
Valid prediction for CodingQuarry_transcript_55215-T1
Valid prediction for GlimmerHMM_glimmerT_15464-T1
Valid prediction for CodingQuarry_transcript_55216-T1
Valid prediction for snap_scaffold_6-snap.2340-T1
Valid prediction for GlimmerHMM_glimmerT_15452-T1
Valid prediction for snap_scaffold_6-snap.2334-T1
Valid prediction for snap_scaffold_6-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_15460-T1
Valid prediction for snap_scaffold_6-snap.2347-T1
Valid prediction for HiQ_model.g10285.t1
Valid prediction for snap_scaffold_6-snap.2341-T1
Valid prediction for snap_scaffold_6-snap.2369-T1
Valid prediction for snap_scaffold_6-snap.2362-T1
Valid prediction for Augustus_model.g10292.t1
Valid prediction for GlimmerHMM_glimmerT_15466-T1
Valid prediction for GlimmerHMM_glimmerT_15459-T1
Valid prediction for pasa_asmbl_47315.p1
Couldn't classify 15521, 15526
Sorry, prediction pasa_asmbl_47301.p1 fails validation.
(GAT)	 CA	15521-15526	GT	ACG
(CAA)	 AG	15814-15951	GT	AGG
(TGG)	 AG	16094-16183	GT	AGG
(GAG)	 AG	16260-16367	GT	AGG
(GCC)	 AG	16455-16788	GT	CGG
(CCA)	 AG	17128-17219	GT	AGG
(GAA)	 AG	17311-17391	GG	AAG
-recovered pasa_asmbl_47301.p1, terminal, 17311, 17391
-recovered pasa_asmbl_47301.p1, internal, 15814, 15951
-recovered pasa_asmbl_47301.p1, internal, 16094, 16183
-recovered pasa_asmbl_47301.p1, internal, 16260, 16367
-recovered pasa_asmbl_47301.p1, internal, 16455, 16788
-recovered pasa_asmbl_47301.p1, internal, 17128, 17219
Couldn't classify 165497, 165527
Sorry, prediction pasa_asmbl_47318.p1 fails validation.
(ATG)	 AG	164745-164983	GT	AGG
(TGG)	 AG	165497-165527	GC	TGG
-recovered pasa_asmbl_47318.p1, initial, 164745, 164983
-recovered pasa_asmbl_47318.p1, internal, 164745, 164983
-recovered pasa_asmbl_47318.p1, internal, 165497, 165527
Valid prediction for GlimmerHMM_glimmerT_15456-T1
Valid prediction for Augustus_model.g10302.t1
Valid prediction for GlimmerHMM_glimmerT_15449-T1
Valid prediction for GlimmerHMM_glimmerT_15480-T1
Valid prediction for snap_scaffold_6-snap.2370-T1
Valid prediction for snap_scaffold_6-snap.2353-T1
Valid prediction for snap_scaffold_6-snap.2367-T1
Valid prediction for GlimmerHMM_glimmerT_15479-T1
Valid prediction for snap_scaffold_6-snap.2363-T1
Valid prediction for Augustus_model.g10289.t1
Valid prediction for pasa_asmbl_47314.p1
Valid prediction for GlimmerHMM_glimmerT_15450-T1
Valid prediction for snap_scaffold_6-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_15467-T1
Valid prediction for GlimmerHMM_glimmerT_15474-T1
Valid prediction for GlimmerHMM_glimmerT_15475-T1
Valid prediction for snap_scaffold_6-snap.2335-T1
Valid prediction for snap_scaffold_6-snap.2354-T1
Valid prediction for Augustus_model.g10298.t1
Valid prediction for GlimmerHMM_glimmerT_15470-T1
Valid prediction for snap_scaffold_6-snap.2361-T1
Valid prediction for HiQ_model.g10287.t1
Valid prediction for Augustus_model.g10306.t1
Valid prediction for snap_scaffold_6-snap.2344-T1
Valid prediction for HiQ_model.g10291.t1
Valid prediction for HiQ_model.g10288.t1
Valid prediction for GlimmerHMM_glimmerT_15469-T1
Valid prediction for snap_scaffold_6-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_15468-T1
Valid prediction for Augustus_model.g10282.t1
Valid prediction for snap_scaffold_6-snap.2352-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.g10304.t1
Valid prediction for GlimmerHMM_glimmerT_15478-T1
Valid prediction for Augustus_model.g10290.t1
Valid prediction for GlimmerHMM_glimmerT_15448-T1
Valid prediction for HiQ_model.g10284.t1
Valid prediction for GlimmerHMM_glimmerT_15455-T1
Valid prediction for GlimmerHMM_glimmerT_15477-T1
Valid prediction for GlimmerHMM_glimmerT_15454-T1
Valid prediction for snap_scaffold_6-snap.2350-T1
Valid prediction for Augustus_model.g10286.t1
Valid prediction for snap_scaffold_6-snap.2336-T1
Valid prediction for snap_scaffold_6-snap.2342-T1
Valid prediction for GlimmerHMM_glimmerT_15472-T1
Valid prediction for snap_scaffold_6-snap.2339-T1
Valid prediction for Augustus_model.g10303.t1
Valid prediction for GlimmerHMM_glimmerT_15463-T1
Valid prediction for Augustus_model.g10305.t1
Valid prediction for Augustus_model.g10295.t1
Valid prediction for HiQ_model.g10293.t1
Valid prediction for HiQ_model.g10301.t1
Valid prediction for GlimmerHMM_glimmerT_15457-T1
Valid prediction for GlimmerHMM_glimmerT_15471-T1
Valid prediction for snap_scaffold_6-snap.2364-T1
Valid prediction for snap_scaffold_6-snap.2351-T1
Valid prediction for snap_scaffold_6-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_15473-T1
Valid prediction for snap_scaffold_6-snap.2355-T1
Valid prediction for GlimmerHMM_glimmerT_15462-T1
Valid prediction for snap_scaffold_6-snap.2345-T1
Valid prediction for GlimmerHMM_glimmerT_15461-T1
Valid prediction for GlimmerHMM_glimmerT_15476-T1
Valid prediction for snap_scaffold_6-snap.2372-T1
Valid prediction for pasa_asmbl_48725.p1
Valid prediction for Augustus_model.g10281.t1
Valid prediction for snap_scaffold_6-snap.2374-T1
Valid prediction for Augustus_model.g10294.t1
Valid prediction for GlimmerHMM_glimmerT_15451-T1
Valid prediction for snap_scaffold_6-snap.2360-T1
Valid prediction for snap_scaffold_6-snap.2348-T1
Valid prediction for snap_scaffold_6-snap.2357-T1
Valid prediction for snap_scaffold_6-snap.2333-T1
Couldn't classify 71406, 71513
Sorry, prediction pasa_asmbl_48733.p1 fails validation.
(CAG)	 TG	71406-71513	GT	ACG
(AAG)	 AG	72282-72358	GT	GGG
(GAA)	 AG	72536-72647	GT	AGG
(GTG)	 AG	72890-72966	GT	AGG
(GTG)	 AG	73253-73370	GT	AGG
(GAT)	 AG	74431-74499	GT	TGG
(CTG)	 AG	74608-74689	GT	AGG
(ACT)	 AG	74789-74916	GT	AGG
(GGC)	 AG	75596-75707	GT	TGG
(GAG)	 AG	75969-76050	GT	AAG
(TGT)	 AG	76255-76335	GT	AGG
(GTA)	 AG	76429-76542	GT	GGG
(CAC)	 AG	76751-76842	GT	TGG
(ACA)	 AG	77066-77412	GC	AAG
-recovered pasa_asmbl_48733.p1, terminal, 77066, 77412
-recovered pasa_asmbl_48733.p1, internal, 72282, 72358
-recovered pasa_asmbl_48733.p1, internal, 72536, 72647
-recovered pasa_asmbl_48733.p1, internal, 72890, 72966
-recovered pasa_asmbl_48733.p1, internal, 73253, 73370
-recovered pasa_asmbl_48733.p1, internal, 74431, 74499
-recovered pasa_asmbl_48733.p1, internal, 74608, 74689
-recovered pasa_asmbl_48733.p1, internal, 74789, 74916
-recovered pasa_asmbl_48733.p1, internal, 75596, 75707
-recovered pasa_asmbl_48733.p1, internal, 75969, 76050
-recovered pasa_asmbl_48733.p1, internal, 76255, 76335
-recovered pasa_asmbl_48733.p1, internal, 76429, 76542
-recovered pasa_asmbl_48733.p1, internal, 76751, 76842
-recovered pasa_asmbl_48733.p1, internal, 77066, 77412
Couldn't classify 188816, 188851
Sorry, prediction pasa_asmbl_48723.p1 fails validation.
(CAC)	 GC	188816-188851	GT	GAG
(ATC)	 AG	189630-189788	GT	GGG
(TTG)	 AG	190751-190850	GT	AGG
(GCT)	 AG	191323-191455	GT	GGG
(TTC)	 AG	191545-191682	GT	GGG
(ACA)	 AG	191923-192129	GT	TGG
(GTA)	 AG	192292-192412	GT	AGG
(AAA)	 AG	192569-192712	CA	AGC
-recovered pasa_asmbl_48723.p1, terminal, 192569, 192712
-recovered pasa_asmbl_48723.p1, internal, 189630, 189788
-recovered pasa_asmbl_48723.p1, internal, 190751, 190850
-recovered pasa_asmbl_48723.p1, internal, 191323, 191455
-recovered pasa_asmbl_48723.p1, internal, 191545, 191682
-recovered pasa_asmbl_48723.p1, internal, 191923, 192129
-recovered pasa_asmbl_48723.p1, internal, 192292, 192412
Valid prediction for CodingQuarry_transcript_55214-T1
Valid prediction for snap_scaffold_6-snap.2358-T1
Valid prediction for GlimmerHMM_glimmerT_15458-T1
Valid prediction for Augustus_model.g10300.t1
Valid prediction for pasa_asmbl_48721.p1
Valid prediction for pasa_asmbl_48736.p1
Couldn't classify 213802, 213904
Sorry, prediction pasa_asmbl_48720.p1 fails validation.
(AAG)	 GG	213802-213904	GT	AGG
(CCA)	 AG	214598-214669	GT	AGG
(AGT)	 AG	214935-215093	GT	AGG
(AGA)	 AG	215219-215312	GT	AGG
(TAT)	 AG	216072-216483	CA	GAC
-recovered pasa_asmbl_48720.p1, terminal, 216072, 216483
-recovered pasa_asmbl_48720.p1, internal, 214598, 214669
-recovered pasa_asmbl_48720.p1, internal, 214935, 215093
-recovered pasa_asmbl_48720.p1, internal, 215219, 215312
Valid prediction for snap_scaffold_6-snap.2343-T1
Valid prediction for GlimmerHMM_glimmerT_15465-T1
Valid prediction for snap_scaffold_6-snap.2349-T1
Valid prediction for snap_scaffold_6-snap.2365-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34210, rend_intergenic: 27155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52171, rend_intergenic: 47806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107568, rend_intergenic: 106282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108866, rend_intergenic: 108249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114815, rend_intergenic: 112449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120842, rend_intergenic: 117893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124612, rend_intergenic: 121326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198345, rend_intergenic: 196308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212668, rend_intergenic: 207928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218826
-exon list size: 425


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 34210, rend_intergenic: 27155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52171, rend_intergenic: 47806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107568, rend_intergenic: 106282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108866, rend_intergenic: 108249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114815, rend_intergenic: 112449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120842, rend_intergenic: 117893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124612, rend_intergenic: 121326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198345, rend_intergenic: 196308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212668, rend_intergenic: 207928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support