-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_5339401-5497226

-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 GeneMark_model.99533_t
Valid prediction for snap_scaffold_26-snap.1237-T1
Valid prediction for GeneMark_model.99523_t
Valid prediction for GeneMark_model.99532_t
Valid prediction for snap_scaffold_26-snap.1206-T1
Valid prediction for Augustus_model.g37986.t1
Valid prediction for GeneMark_model.99548_t
Valid prediction for GlimmerHMM_glimmerT_57019-T1
Valid prediction for Augustus_model.g37979.t1
Valid prediction for GlimmerHMM_glimmerT_57020-T1
Valid prediction for GlimmerHMM_glimmerT_57011-T1
Valid prediction for GlimmerHMM_glimmerT_57021-T1
Valid prediction for GeneMark_model.99519_t
Valid prediction for GlimmerHMM_glimmerT_57026-T1
Valid prediction for snap_scaffold_26-snap.1219-T1
Valid prediction for Augustus_model.g37965.t1
Couldn't classify 141563, 141674
Sorry, prediction pasa_asmbl_35522.p1 fails validation.
(TGC)	 CA	141563-141674	GT	GGG
(GTT)	 AG	142153-142233	GT	AGG
(AAT)	 AG	142902-142958	GT	AGG
(CCA)	 AG	143228-143290	GT	AGG
(GCT)	 AG	143396-143550	GT	GGG
(GGT)	 AG	143822-143863	GA	GAG
-recovered pasa_asmbl_35522.p1, terminal, 143822, 143863
-recovered pasa_asmbl_35522.p1, internal, 142153, 142233
-recovered pasa_asmbl_35522.p1, internal, 142902, 142958
-recovered pasa_asmbl_35522.p1, internal, 143228, 143290
-recovered pasa_asmbl_35522.p1, internal, 143396, 143550
Valid prediction for GlimmerHMM_glimmerT_57027-T1
Couldn't classify 23197, 23280
Sorry, prediction pasa_asmbl_35509.p1 fails validation.
(GAG)	 AA	23197-23280	GT	AGG
(AAA)	 AG	23372-23461	GT	CGG
(TAT)	 AG	23575-23678	GT	CTG
(GCC)	 AG	23762-23839	GT	TGG
(GTA)	 AG	24386-24548	GC	AGG
(GAG)	 AG	24655-24726	GT	CAG
(ATC)	 AG	24822-24944	GT	AGG
(GAG)	 AG	25083-25199	GT	AGG
(GGT)	 AG	25335-25445	GG	GAG
-recovered pasa_asmbl_35509.p1, terminal, 25335, 25445
-recovered pasa_asmbl_35509.p1, internal, 23372, 23461
-recovered pasa_asmbl_35509.p1, internal, 23575, 23678
-recovered pasa_asmbl_35509.p1, internal, 23762, 23839
-recovered pasa_asmbl_35509.p1, internal, 24386, 24548
-recovered pasa_asmbl_35509.p1, internal, 24655, 24726
-recovered pasa_asmbl_35509.p1, internal, 24822, 24944
-recovered pasa_asmbl_35509.p1, internal, 25083, 25199
Valid prediction for GlimmerHMM_glimmerT_57010-T1
Valid prediction for HiQ_model.g37988.t1
Valid prediction for HiQ_model.g37973.t1
Valid prediction for GlimmerHMM_glimmerT_57015-T1
Valid prediction for Augustus_model.g37990.t1
Valid prediction for CodingQuarry_transcript_40255-T1
Valid prediction for GeneMark_model.99552_t
Couldn't classify 61346, 61419
Sorry, prediction pasa_asmbl_35512.p1 fails validation.
(GAT)	 CT	61346-61419	GT	AGG
(GTT)	 AG	61496-61605	GT	TGG
(GGC)	 AG	61735-61966	GT	AAG
(GGA)	 AG	62281-62347	GT	AGG
(GCC)	 AG	62459-62560	GT	CGG
(CAT)	 AG	62696-62886	GT	TAG
(TCA)	 AG	63270-63351	GT	TGG
(AGC)	 AG	63457-63549	GT	CGG
(TAC)	 AG	63656-63837	GT	AGG
(CAC)	 AG	64139-64274	GT	AGG
(GGC)	 AG	64464-64538	GT	TGG
(CTG)	 AG	64671-64792	GC	AGG
(GAA)	 AG	64889-64996	GT	AGG
(GGT)	 AG	65139-65286	GT	AGG
(CTG)	 AG	65497-65659	GT	AGG
(CTC)	 AG	65760-65968	CA	GAC
-recovered pasa_asmbl_35512.p1, terminal, 65760, 65968
-recovered pasa_asmbl_35512.p1, internal, 61496, 61605
-recovered pasa_asmbl_35512.p1, internal, 61735, 61966
-recovered pasa_asmbl_35512.p1, internal, 62281, 62347
-recovered pasa_asmbl_35512.p1, internal, 62459, 62560
-recovered pasa_asmbl_35512.p1, internal, 62696, 62886
-recovered pasa_asmbl_35512.p1, internal, 63270, 63351
-recovered pasa_asmbl_35512.p1, internal, 63457, 63549
-recovered pasa_asmbl_35512.p1, internal, 63656, 63837
-recovered pasa_asmbl_35512.p1, internal, 64139, 64274
-recovered pasa_asmbl_35512.p1, internal, 64464, 64538
-recovered pasa_asmbl_35512.p1, internal, 64671, 64792
-recovered pasa_asmbl_35512.p1, internal, 64889, 64996
-recovered pasa_asmbl_35512.p1, internal, 65139, 65286
-recovered pasa_asmbl_35512.p1, internal, 65497, 65659
Valid prediction for HiQ_model.g37987.t1
Valid prediction for snap_scaffold_26-snap.1221-T1
Valid prediction for HiQ_model.g37981.t1
Valid prediction for GlimmerHMM_glimmerT_57002-T1
Valid prediction for Augustus_model.g37976.t1
Valid prediction for snap_scaffold_26-snap.1209-T1
Valid prediction for Augustus_model.g37985.t1
Valid prediction for snap_scaffold_26-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_57008-T1
Valid prediction for GeneMark_model.99540_t
Valid prediction for HiQ_model.g37967.t1
Valid prediction for GeneMark_model.99546_t
Valid prediction for GlimmerHMM_glimmerT_57023-T1
Valid prediction for Augustus_model.g37982.t1
Valid prediction for Augustus_model.g37984.t1
Valid prediction for GeneMark_model.99529_t
Valid prediction for CodingQuarry_transcript_40250-T1
Valid prediction for pasa_asmbl_35526.p1
Valid prediction for GlimmerHMM_glimmerT_57000-T1
Valid prediction for Augustus_model.g37980.t1
Valid prediction for CodingQuarry_transcript_40253-T1
Valid prediction for GeneMark_model.99539_t
Couldn't classify 116939, 117080
Sorry, prediction pasa_asmbl_35517.p1 fails validation.
(TGT)	 CA	116939-117080	GT	AGG
(GTG)	 AG	117304-117334	GT	CGG
(CGT)	 AG	117455-117553	GT	AGG
(TTG)	 AG	117665-117729	GT	AGG
(AGC)	 AG	117822-117915	GT	AGG
(TGA)	 AG	118048-118468	AA	AAA
add_exon() Sorry, pasa_asmbl_35517.p1 117455-117553-terminal-1 is invalid.
-recovered pasa_asmbl_35517.p1, terminal, 117455, 117553
-recovered pasa_asmbl_35517.p1, terminal, 118048, 118468
-recovered pasa_asmbl_35517.p1, internal, 117304, 117334
-recovered pasa_asmbl_35517.p1, internal, 117455, 117553
-recovered pasa_asmbl_35517.p1, internal, 117665, 117729
-recovered pasa_asmbl_35517.p1, internal, 117822, 117915
Valid prediction for snap_scaffold_26-snap.1220-T1
Couldn't classify 46996, 47223
Sorry, prediction pasa_asmbl_35887.p1 fails validation.
(CAG)	 TC	46996-47223	GT	CGG
(CCT)	 AG	47341-47484	GT	AGG
(GTG)	 AG	48141-48227	GT	AAG
(CAA)	 AG	48682-48951	GT	AGG
(GGC)	 AG	49126-49946	GT	TGG
(GTG)	 AG	50125-50288	GT	AGG
(GTC)	 AG	50475-50636	GT	AGG
(GTC)	 AG	50826-51044	GT	AGG
(TGT)	 AG	51184-51365	TT	AGT
-recovered pasa_asmbl_35887.p1, terminal, 51184, 51365
-recovered pasa_asmbl_35887.p1, internal, 47341, 47484
-recovered pasa_asmbl_35887.p1, internal, 48141, 48227
-recovered pasa_asmbl_35887.p1, internal, 48682, 48951
-recovered pasa_asmbl_35887.p1, internal, 49126, 49946
-recovered pasa_asmbl_35887.p1, internal, 50125, 50288
-recovered pasa_asmbl_35887.p1, internal, 50475, 50636
-recovered pasa_asmbl_35887.p1, internal, 50826, 51044
Valid prediction for GeneMark_model.99521_t
Valid prediction for GeneMark_model.99527_t
Valid prediction for GeneMark_model.99537_t
Valid prediction for snap_scaffold_26-snap.1235-T1
Valid prediction for snap_scaffold_26-snap.1205-T1
Valid prediction for snap_scaffold_26-snap.1229-T1
Valid prediction for Augustus_model.g37971.t1
Valid prediction for GeneMark_model.99549_t
Valid prediction for GlimmerHMM_glimmerT_57024-T1
Couldn't classify 8600, 9847
Sorry, prediction pasa_asmbl_35507.p1 fails validation.
(TGT)	 TG	8600-9847	GG	GAG
Valid prediction for pasa_asmbl_35516.p1
Valid prediction for snap_scaffold_26-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_57016-T1
Valid prediction for pasa_asmbl_35525.p2
Valid prediction for GlimmerHMM_glimmerT_57004-T1
Valid prediction for snap_scaffold_26-snap.1231-T1
Valid prediction for snap_scaffold_26-snap.1214-T1
Valid prediction for GlimmerHMM_glimmerT_57006-T1
Valid prediction for GlimmerHMM_glimmerT_57003-T1
Valid prediction for snap_scaffold_26-snap.1224-T1
Valid prediction for GeneMark_model.99543_t
Valid prediction for snap_scaffold_26-snap.1211-T1
Valid prediction for snap_scaffold_26-snap.1227-T1
Valid prediction for CodingQuarry_transcript_40251-T1
Valid prediction for Augustus_model.g37975.t1
Valid prediction for snap_scaffold_26-snap.1234-T1
Valid prediction for CodingQuarry_transcript_40254-T1
Valid prediction for GeneMark_model.99535_t
Valid prediction for GlimmerHMM_glimmerT_57025-T1
Valid prediction for snap_scaffold_26-snap.1241-T1
Valid prediction for CodingQuarry_transcript_40256-T1
Valid prediction for snap_scaffold_26-snap.1216-T1
Valid prediction for snap_scaffold_26-snap.1239-T1
Valid prediction for snap_scaffold_26-snap.1225-T1
Valid prediction for Augustus_model.g37978.t1
Valid prediction for GeneMark_model.99550_t
Valid prediction for GlimmerHMM_glimmerT_57012-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 GeneMark_model.99545_t
Valid prediction for Augustus_model.g37974.t1
Valid prediction for Augustus_model.g37977.t1
Valid prediction for snap_scaffold_26-snap.1213-T1
Valid prediction for GlimmerHMM_glimmerT_57009-T1
Valid prediction for Augustus_model.g37969.t1
Valid prediction for Augustus_model.g37989.t1
Valid prediction for GeneMark_model.99536_t
Valid prediction for GeneMark_model.99531_t
Valid prediction for GeneMark_model.99547_t
Valid prediction for GeneMark_model.99526_t
Valid prediction for GlimmerHMM_glimmerT_57018-T1
Valid prediction for GeneMark_model.99524_t
Valid prediction for snap_scaffold_26-snap.1207-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_34882.p1
Valid prediction for snap_scaffold_26-snap.1217-T1
Valid prediction for GeneMark_model.99520_t
Valid prediction for Augustus_model.g37991.t1
Valid prediction for GlimmerHMM_glimmerT_57007-T1
Valid prediction for snap_scaffold_26-snap.1232-T1
Valid prediction for Augustus_model.g37968.t1
Valid prediction for GeneMark_model.99534_t
Valid prediction for GlimmerHMM_glimmerT_56999-T1
Valid prediction for snap_scaffold_26-snap.1240-T1
Valid prediction for Augustus_model.g37983.t1
Valid prediction for snap_scaffold_26-snap.1212-T1
Valid prediction for snap_scaffold_26-snap.1233-T1
Valid prediction for snap_scaffold_26-snap.1208-T1
Valid prediction for Augustus_model.g37972.t1
Valid prediction for HiQ_model.g37970.t1
Valid prediction for GlimmerHMM_glimmerT_57005-T1
Valid prediction for GlimmerHMM_glimmerT_57001-T1
Valid prediction for Augustus_model.g37966.t1
Valid prediction for snap_scaffold_26-snap.1236-T1
Valid prediction for snap_scaffold_26-snap.1238-T1
Valid prediction for snap_scaffold_26-snap.1222-T1
Valid prediction for snap_scaffold_26-snap.1215-T1
Valid prediction for GeneMark_model.99528_t
Valid prediction for snap_scaffold_26-snap.1218-T1
Valid prediction for snap_scaffold_26-snap.1223-T1
Valid prediction for GlimmerHMM_glimmerT_57022-T1
Valid prediction for GeneMark_model.99538_t
Valid prediction for GeneMark_model.99530_t
Valid prediction for snap_scaffold_26-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_57014-T1
Valid prediction for GeneMark_model.99544_t
Valid prediction for GlimmerHMM_glimmerT_57013-T1
Valid prediction for GlimmerHMM_glimmerT_57017-T1
Valid prediction for GeneMark_model.99518_t
Valid prediction for GeneMark_model.99542_t
Valid prediction for snap_scaffold_26-snap.1210-T1
Valid prediction for GeneMark_model.99551_t
Valid prediction for GlimmerHMM_glimmerT_56998-T1
Valid prediction for snap_scaffold_26-snap.1230-T1
Valid prediction for snap_scaffold_26-snap.1204-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9847, rend_intergenic: 9430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33022, rend_intergenic: 26789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96891, rend_intergenic: 94398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122904, rend_intergenic: 122453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139957, rend_intergenic: 137278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157826
-exon list size: 495


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 9847, rend_intergenic: 9430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33022, rend_intergenic: 26789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96891, rend_intergenic: 94398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122904, rend_intergenic: 122453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139957, rend_intergenic: 137278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support