-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_12389646-12722460

-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_3-snap.2424-T1
Valid prediction for HiQ_model.g4869.t1
Valid prediction for Augustus_model.g4860.t1
Valid prediction for snap_scaffold_3-snap.2456-T1
Valid prediction for snap_scaffold_3-snap.2438-T1
Valid prediction for snap_scaffold_3-snap.2416-T1
Valid prediction for snap_scaffold_3-snap.2457-T1
Valid prediction for CodingQuarry_transcript_46302-T1
Couldn't classify 273292, 273331
Sorry, prediction pasa_asmbl_40413.p1 fails validation.
(GAG)	 CA	273292-273331	GT	GGG
(AAC)	 AG	273408-274009	CC	AAC
-recovered pasa_asmbl_40413.p1, terminal, 273408, 274009
Valid prediction for snap_scaffold_3-snap.2421-T1
Valid prediction for Augustus_model.g4883.t1
Valid prediction for CodingQuarry_transcript_46303-T1
Valid prediction for snap_scaffold_3-snap.2450-T1
Valid prediction for Augustus_model.g4858.t1
Valid prediction for snap_scaffold_3-snap.2437-T1
Valid prediction for snap_scaffold_3-snap.2428-T1
Valid prediction for snap_scaffold_3-snap.2447-T1
Valid prediction for snap_scaffold_3-snap.2427-T1
Valid prediction for pasa_asmbl_40410.p1
Valid prediction for snap_scaffold_3-snap.2436-T1
Valid prediction for snap_scaffold_3-snap.2448-T1
Valid prediction for snap_scaffold_3-snap.2435-T1
Valid prediction for GlimmerHMM_glimmerT_7458-T1
Valid prediction for snap_scaffold_3-snap.2415-T1
Valid prediction for snap_scaffold_3-snap.2425-T1
Valid prediction for snap_scaffold_3-snap.2420-T1
Valid prediction for GlimmerHMM_glimmerT_7465-T1
Valid prediction for GlimmerHMM_glimmerT_7480-T1
Valid prediction for snap_scaffold_3-snap.2452-T1
Valid prediction for snap_scaffold_3-snap.2442-T1
Valid prediction for GlimmerHMM_glimmerT_7478-T1
Valid prediction for Augustus_model.g4855.t1
Valid prediction for snap_scaffold_3-snap.2451-T1
Valid prediction for snap_scaffold_3-snap.2453-T1
Valid prediction for snap_scaffold_3-snap.2463-T1
Valid prediction for snap_scaffold_3-snap.2413-T1
Valid prediction for GlimmerHMM_glimmerT_7462-T1
Valid prediction for GlimmerHMM_glimmerT_7456-T1
Valid prediction for Augustus_model.g4861.t1
Valid prediction for GlimmerHMM_glimmerT_7475-T1
Couldn't classify 262628, 262966
Sorry, prediction pasa_asmbl_40798.p1 fails validation.
(AGT)	 AC	262628-262966	GG	CAG
Valid prediction for snap_scaffold_3-snap.2449-T1
Valid prediction for snap_scaffold_3-snap.2443-T1
Valid prediction for GlimmerHMM_glimmerT_7486-T1
Valid prediction for snap_scaffold_3-snap.2423-T1
Valid prediction for Augustus_model.g4854.t1
Valid prediction for Augustus_model.g4884.t1
Valid prediction for Augustus_model.g4868.t1
Valid prediction for GlimmerHMM_glimmerT_7483-T1
Valid prediction for GlimmerHMM_glimmerT_7477-T1
Valid prediction for GlimmerHMM_glimmerT_7471-T1
Valid prediction for snap_scaffold_3-snap.2412-T1
Valid prediction for Augustus_model.g4877.t1
Valid prediction for GlimmerHMM_glimmerT_7466-T1
Valid prediction for Augustus_model.g4870.t1
Valid prediction for GlimmerHMM_glimmerT_7487-T1
Valid prediction for snap_scaffold_3-snap.2439-T1
Couldn't classify 105579, 106169
Sorry, prediction pasa_asmbl_40408.p1 fails validation.
(CTT)	 CC	105579-106169	GT	AGG
(ATT)	 AG	106439-106543	CT	AAC
-recovered pasa_asmbl_40408.p1, terminal, 106439, 106543
Valid prediction for snap_scaffold_3-snap.2426-T1
Valid prediction for Augustus_model.g4862.t1
Valid prediction for snap_scaffold_3-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_7474-T1
Valid prediction for GlimmerHMM_glimmerT_7481-T1
Couldn't classify 104459, 105275
Sorry, prediction pasa_asmbl_40407.p1 fails validation.
(ATG)	 TG	103769-103796	GT	GAG
(TGA)	 AG	104089-104230	GT	GTG
(TAA)	 AG	104459-105275	AC	CCA
-recovered pasa_asmbl_40407.p1, initial, 103769, 103796
-recovered pasa_asmbl_40407.p1, internal, 104089, 104230
Valid prediction for snap_scaffold_3-snap.2411-T1
Couldn't classify 268726, 268762
Couldn't classify 269236, 269690
Sorry, prediction pasa_asmbl_40412.p2 fails validation.
(TTG)	 GG	268726-268762	GT	AGG
(GGA)	 AG	269236-269690	GG	CTG
Valid prediction for Augustus_model.g4880.t1
Valid prediction for Augustus_model.g4871.t1
Valid prediction for snap_scaffold_3-snap.2445-T1
Valid prediction for Augustus_model.g4859.t1
Valid prediction for GlimmerHMM_glimmerT_7461-T1
Valid prediction for Augustus_model.g4876.t1
Valid prediction for GlimmerHMM_glimmerT_7468-T1
Valid prediction for Augustus_model.g4874.t1
Valid prediction for snap_scaffold_3-snap.2422-T1
Couldn't classify 181924, 182034
Sorry, prediction pasa_asmbl_40409.p1 fails validation.
(ATG)	 TA	180986-181059	GT	AGG
(TGC)	 AG	181302-181405	GT	CGG
(GTG)	 AG	181513-181682	GT	AGG
(GCC)	 AG	181924-182034	GG	CAG
-recovered pasa_asmbl_40409.p1, initial, 180986, 181059
-recovered pasa_asmbl_40409.p1, internal, 181302, 181405
-recovered pasa_asmbl_40409.p1, internal, 181513, 181682
Valid prediction for snap_scaffold_3-snap.2446-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_3-snap.2459-T1
Valid prediction for GlimmerHMM_glimmerT_7464-T1
Valid prediction for pasa_asmbl_39208.p1
Valid prediction for CodingQuarry_transcript_46298-T1
Valid prediction for Augustus_model.g4866.t1
Couldn't classify 91760, 91768
Sorry, prediction pasa_asmbl_39218.p1 fails validation.
(CTC)	 TG	91760-91768	GT	TGG
(GAC)	 AG	91997-92062	GT	AGG
(GCT)	 AG	92180-92320	GT	AGG
(CTG)	 AG	93079-93297	GT	ATG
(AAG)	 AG	93526-93596	GT	ATG
(GGA)	 AG	93702-93801	GT	AGG
(AAC)	 AG	94047-94229	GT	GGG
(GTG)	 AG	94591-94691	GT	TGG
(GCC)	 AG	94798-94894	GT	AGG
(GAC)	 AG	94994-95134	GA	GAG
-recovered pasa_asmbl_39218.p1, terminal, 94994, 95134
-recovered pasa_asmbl_39218.p1, internal, 91997, 92062
-recovered pasa_asmbl_39218.p1, internal, 92180, 92320
-recovered pasa_asmbl_39218.p1, internal, 93079, 93297
-recovered pasa_asmbl_39218.p1, internal, 93526, 93596
-recovered pasa_asmbl_39218.p1, internal, 93702, 93801
-recovered pasa_asmbl_39218.p1, internal, 94047, 94229
-recovered pasa_asmbl_39218.p1, internal, 94591, 94691
-recovered pasa_asmbl_39218.p1, internal, 94798, 94894
Valid prediction for snap_scaffold_3-snap.2441-T1
Couldn't classify 30829, 30855
Couldn't classify 32601, 32630
Sorry, prediction pasa_asmbl_39753.p1 fails validation.
(ACG)	 GC	30829-30855	GT	TGG
(AGC)	 AG	31544-31669	GT	TGG
(ACT)	 AG	32254-32318	GT	GGG
(GAG)	 AG	32419-32482	GT	AGG
(ACT)	 AG	32601-32630	GG	TGG
-recovered pasa_asmbl_39753.p1, internal, 31544, 31669
-recovered pasa_asmbl_39753.p1, internal, 32254, 32318
-recovered pasa_asmbl_39753.p1, internal, 32419, 32482
Valid prediction for snap_scaffold_3-snap.2433-T1
Valid prediction for snap_scaffold_3-snap.2462-T1
Valid prediction for snap_scaffold_3-snap.2460-T1
Valid prediction for snap_scaffold_3-snap.2440-T1
Valid prediction for HiQ_model.g4881.t1
Valid prediction for snap_scaffold_3-snap.2461-T1
Valid prediction for Augustus_model.g4872.t1
Valid prediction for snap_scaffold_3-snap.2455-T1
Valid prediction for snap_scaffold_3-snap.2430-T1
Valid prediction for GlimmerHMM_glimmerT_7482-T1
Valid prediction for Augustus_model.g4886.t1
Valid prediction for snap_scaffold_3-snap.2419-T1
Valid prediction for Augustus_model.g4885.t1
Valid prediction for GlimmerHMM_glimmerT_7476-T1
Valid prediction for Augustus_model.g4887.t1
Valid prediction for HiQ_model.g4856.t1
Valid prediction for CodingQuarry_transcript_46304-T1
Valid prediction for HiQ_model.g4882.t1
Valid prediction for snap_scaffold_3-snap.2429-T1
Valid prediction for pasa_asmbl_39788.p1
Valid prediction for snap_scaffold_3-snap.2432-T1
Valid prediction for GlimmerHMM_glimmerT_7467-T1
Valid prediction for snap_scaffold_3-snap.2434-T1
Valid prediction for GlimmerHMM_glimmerT_7459-T1
Valid prediction for GlimmerHMM_glimmerT_7469-T1
Valid prediction for GlimmerHMM_glimmerT_7463-T1
Valid prediction for Augustus_model.g4873.t1
Valid prediction for GlimmerHMM_glimmerT_7488-T1
Valid prediction for GlimmerHMM_glimmerT_7460-T1
Valid prediction for GlimmerHMM_glimmerT_7457-T1
Valid prediction for snap_scaffold_3-snap.2454-T1
Valid prediction for Augustus_model.g4865.t1
Valid prediction for GlimmerHMM_glimmerT_7473-T1
Valid prediction for Augustus_model.g4867.t1
Valid prediction for CodingQuarry_transcript_46299-T1
Valid prediction for Augustus_model.g4879.t1
Valid prediction for Augustus_model.g4878.t1
Valid prediction for GlimmerHMM_glimmerT_7470-T1
Valid prediction for GlimmerHMM_glimmerT_7485-T1
Valid prediction for Augustus_model.g4875.t1
Couldn't classify 48173, 48584
Couldn't classify 48863, 49026
Sorry, prediction pasa_asmbl_39225.p1 fails validation.
(AAG)	 AA	48173-48584	GT	GGG
(GAG)	 AG	48863-49026	GG	GGG
Valid prediction for pasa_asmbl_39221.p1
Valid prediction for HiQ_model.g4864.t1
Valid prediction for CodingQuarry_transcript_46300-T1
Valid prediction for GlimmerHMM_glimmerT_7479-T1
Valid prediction for snap_scaffold_3-snap.2431-T1
Valid prediction for Augustus_model.g4863.t1
Valid prediction for snap_scaffold_3-snap.2444-T1
Valid prediction for CodingQuarry_transcript_46301-T1
Couldn't classify 328457, 328876
Sorry, prediction pasa_asmbl_40398.p1 fails validation.
(ATG)	 CA	328457-328876	TG	CCT
Couldn't classify 13624, 13840
Sorry, prediction pasa_asmbl_39228.p1 fails validation.
(AGT)	 TC	13624-13840	GT	AGG
(ACA)	 AG	15126-15309	GT	AAG
(GGG)	 AG	15666-15857	GT	AAG
(CGT)	 AG	16462-16620	GT	TGG
(GTC)	 AG	16776-16934	GT	TGG
(GCA)	 AG	17367-17475	GT	AGG
(GCG)	 AG	17911-18020	GT	AGG
(ACA)	 AG	18149-18302	TT	GAT
-recovered pasa_asmbl_39228.p1, terminal, 18149, 18302
-recovered pasa_asmbl_39228.p1, internal, 15126, 15309
-recovered pasa_asmbl_39228.p1, internal, 15666, 15857
-recovered pasa_asmbl_39228.p1, internal, 16462, 16620
-recovered pasa_asmbl_39228.p1, internal, 16776, 16934
-recovered pasa_asmbl_39228.p1, internal, 17367, 17475
-recovered pasa_asmbl_39228.p1, internal, 17911, 18020
Valid prediction for GlimmerHMM_glimmerT_7484-T1
Valid prediction for pasa_asmbl_39216.p1
Valid prediction for HiQ_model.g4857.t1
Valid prediction for GlimmerHMM_glimmerT_7472-T1
Valid prediction for snap_scaffold_3-snap.2458-T1
Valid prediction for snap_scaffold_3-snap.2418-T1
Valid prediction for snap_scaffold_3-snap.2414-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25331, rend_intergenic: 22653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68095, rend_intergenic: 63861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148319, rend_intergenic: 145913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 330212, rend_intergenic: 321219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 332815
-exon list size: 498


building trellis

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-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 25331, rend_intergenic: 22653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68095, rend_intergenic: 63861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148319, rend_intergenic: 145913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 330212, rend_intergenic: 321219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support