-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_1-190124

-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_24-snap.6-T1
Valid prediction for snap_scaffold_24-snap.8-T1
Valid prediction for snap_scaffold_24-snap.35-T1
Valid prediction for snap_scaffold_24-snap.29-T1
Valid prediction for snap_scaffold_24-snap.19-T1
Valid prediction for snap_scaffold_24-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_51829-T1
Valid prediction for GlimmerHMM_glimmerT_51836-T1
Valid prediction for GlimmerHMM_glimmerT_51832-T1
Valid prediction for GlimmerHMM_glimmerT_51822-T1
Valid prediction for snap_scaffold_24-snap.3-T1
Valid prediction for Augustus_model.g34576.t1
Valid prediction for snap_scaffold_24-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_51827-T1
Valid prediction for GlimmerHMM_glimmerT_51816-T1
Valid prediction for snap_scaffold_24-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_51835-T1
Valid prediction for snap_scaffold_24-snap.16-T1
Valid prediction for snap_scaffold_24-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_51834-T1
Valid prediction for snap_scaffold_24-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_51831-T1
Valid prediction for Augustus_model.g34578.t1
Valid prediction for GlimmerHMM_glimmerT_51825-T1
Valid prediction for snap_scaffold_24-snap.18-T1
Valid prediction for GlimmerHMM_glimmerT_51826-T1
Valid prediction for snap_scaffold_24-snap.32-T1
Valid prediction for snap_scaffold_24-snap.37-T1
Valid prediction for snap_scaffold_24-snap.24-T1
Valid prediction for snap_scaffold_24-snap.5-T1
Valid prediction for snap_scaffold_24-snap.17-T1
Valid prediction for snap_scaffold_24-snap.20-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: -)Couldn't classify 117474, 117578
Sorry, prediction pasa_asmbl_32692.p1 fails validation.
(AAT)	 CA	117474-117578	GT	AGG
(TAC)	 AG	118284-118333	GT	AGG
(CAA)	 AG	118554-118632	GT	TGG
(GCA)	 AG	118739-118891	GT	CGG
(GGG)	 AG	118973-118988	GT	AGG
(GGT)	 AG	119145-119175	GT	AGG
(GAG)	 AG	119413-119575	GT	AGG
(ATC)	 AG	120290-120472	TG	GAT
-recovered pasa_asmbl_32692.p1, terminal, 120290, 120472
-recovered pasa_asmbl_32692.p1, internal, 118284, 118333
-recovered pasa_asmbl_32692.p1, internal, 118554, 118632
-recovered pasa_asmbl_32692.p1, internal, 118739, 118891
-recovered pasa_asmbl_32692.p1, internal, 118973, 118988
-recovered pasa_asmbl_32692.p1, internal, 119145, 119175
-recovered pasa_asmbl_32692.p1, internal, 119413, 119575
Valid prediction for snap_scaffold_24-snap.9-T1
Valid prediction for snap_scaffold_24-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_51820-T1
Valid prediction for Augustus_model.g34580.t1
Valid prediction for Augustus_model.g34577.t1
Valid prediction for GlimmerHMM_glimmerT_51838-T1
Valid prediction for snap_scaffold_24-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_51819-T1
Valid prediction for snap_scaffold_24-snap.22-T1
Valid prediction for snap_scaffold_24-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_51814-T1
Valid prediction for Augustus_model.g34569.t1
Valid prediction for Augustus_model.g34574.t1
Couldn't classify 178737, 178990
Couldn't classify 180288, 180427
Sorry, prediction pasa_asmbl_32680.p1 fails validation.
(AAA)	 AC	178737-178990	GT	GGG
(ATC)	 AG	179767-179870	GT	GGG
(ATG)	 AG	180288-180427	GG	ATG
-recovered pasa_asmbl_32680.p1, internal, 179767, 179870
Valid prediction for snap_scaffold_24-snap.7-T1
Couldn't classify 187328, 187345
Sorry, prediction pasa_asmbl_32678.p1 fails validation.
(GAG)	 AT	187328-187345	GT	GGG
(GTG)	 AG	187493-187823	GT	AGG
(CCT)	 AG	188037-188162	GT	GGG
(ATC)	 AG	188625-188803	AG	GAA
-recovered pasa_asmbl_32678.p1, terminal, 188625, 188803
-recovered pasa_asmbl_32678.p1, internal, 187493, 187823
-recovered pasa_asmbl_32678.p1, internal, 188037, 188162
Valid prediction for snap_scaffold_24-snap.38-T1
Valid prediction for snap_scaffold_24-snap.39-T1
Valid prediction for GlimmerHMM_glimmerT_51821-T1
Couldn't classify 99141, 99427
Couldn't classify 100732, 100809
Sorry, prediction pasa_asmbl_33283.p1 fails validation.
(GCC)	 AG	99141-99427	GT	CCG
(GAC)	 AG	100438-100504	GT	AGG
(GTC)	 AG	100732-100809	CC	CCC
-recovered pasa_asmbl_33283.p1, internal, 99141, 99427
-recovered pasa_asmbl_33283.p1, internal, 100438, 100504
Couldn't classify 187087, 187227
Sorry, prediction pasa_asmbl_32679.p1 fails validation.
(ATG)	 AG	185486-185488	GT	TGG
(GAT)	 AG	185727-185795	GT	AGG
(TTT)	 AG	185926-185973	GT	AGG
(GCC)	 AG	186125-186406	GT	AGG
(GAG)	 AG	187087-187227	AC	AGA
-recovered pasa_asmbl_32679.p1, initial, 185486, 185488
-recovered pasa_asmbl_32679.p1, internal, 185486, 185488
-recovered pasa_asmbl_32679.p1, internal, 185727, 185795
-recovered pasa_asmbl_32679.p1, internal, 185926, 185973
-recovered pasa_asmbl_32679.p1, internal, 186125, 186406
Valid prediction for GlimmerHMM_glimmerT_51811-T1
Valid prediction for Augustus_model.g34571.t1
Valid prediction for snap_scaffold_24-snap.25-T1
Valid prediction for GlimmerHMM_glimmerT_51810-T1
Couldn't classify 157451, 157774
Sorry, prediction pasa_asmbl_32685.p1 fails validation.
(ACA)	 CC	157451-157774	GC	GAG
Valid prediction for snap_scaffold_24-snap.10-T1
Valid prediction for snap_scaffold_24-snap.36-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 27170, 27487
Sorry, prediction pasa_asmbl_32700.p1 fails validation.
(TCC)	 AC	27170-27487	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_51824-T1
Valid prediction for GlimmerHMM_glimmerT_51837-T1
Valid prediction for pasa_asmbl_32686.p1
Valid prediction for snap_scaffold_24-snap.30-T1
Valid prediction for Augustus_model.g34581.t1
Valid prediction for GlimmerHMM_glimmerT_51812-T1
Valid prediction for GlimmerHMM_glimmerT_51818-T1
Valid prediction for GlimmerHMM_glimmerT_51828-T1
Valid prediction for GlimmerHMM_glimmerT_51815-T1
Valid prediction for snap_scaffold_24-snap.15-T1
Couldn't classify 24820, 24876
Sorry, prediction pasa_asmbl_32697.p1 fails validation.
(CGG)	 GA	24820-24876	GT	GGG
(GAG)	 AG	25733-25782	GT	AGG
(GGT)	 AG	27746-27884	GT	AGG
(GGT)	 AG	28825-28980	TG	GAT
-recovered pasa_asmbl_32697.p1, terminal, 28825, 28980
-recovered pasa_asmbl_32697.p1, internal, 25733, 25782
-recovered pasa_asmbl_32697.p1, internal, 27746, 27884
Valid prediction for Augustus_model.g34575.t1
Couldn't classify 101674, 101817
Couldn't classify 105983, 106012
Sorry, prediction pasa_asmbl_32695.p1 fails validation.
(CAG)	 CC	101674-101817	GT	AAG
(GTG)	 AG	102696-102803	GT	CTG
(AAG)	 AG	102957-103127	GT	AGG
(CCT)	 AG	103294-103335	GT	GTG
(TTG)	 AG	103444-103555	GT	CTG
(ATT)	 AG	103697-103770	GT	AGG
(AGT)	 AG	103858-104050	GT	TGG
(GCC)	 AG	104233-104361	GT	GGG
(AGC)	 AG	104452-104557	GT	AGG
(GGT)	 AG	104960-105091	GT	ACG
(CTG)	 AG	105337-105460	GT	CGG
(CAC)	 AG	105983-106012	CC	CCC
-recovered pasa_asmbl_32695.p1, internal, 102696, 102803
-recovered pasa_asmbl_32695.p1, internal, 102957, 103127
-recovered pasa_asmbl_32695.p1, internal, 103294, 103335
-recovered pasa_asmbl_32695.p1, internal, 103444, 103555
-recovered pasa_asmbl_32695.p1, internal, 103697, 103770
-recovered pasa_asmbl_32695.p1, internal, 103858, 104050
-recovered pasa_asmbl_32695.p1, internal, 104233, 104361
-recovered pasa_asmbl_32695.p1, internal, 104452, 104557
-recovered pasa_asmbl_32695.p1, internal, 104960, 105091
-recovered pasa_asmbl_32695.p1, internal, 105337, 105460
Valid prediction for snap_scaffold_24-snap.40-T1
Valid prediction for HiQ_model.g34570.t1
Valid prediction for Augustus_model.g34572.t1
Valid prediction for snap_scaffold_24-snap.12-T1
Valid prediction for snap_scaffold_24-snap.4-T1
Valid prediction for snap_scaffold_24-snap.14-T1
Couldn't classify 139575, 140057
Sorry, prediction pasa_asmbl_32689.p1 fails validation.
(ATG)	 TG	139575-140057	AC	CTA
Valid prediction for GlimmerHMM_glimmerT_51839-T1
Valid prediction for Augustus_model.g34573.t1
Couldn't classify 97255, 97296
Couldn't classify 98153, 98804
Sorry, prediction pasa_asmbl_32696.p1 fails validation.
(AAG)	 GG	97255-97296	GT	AGG
(CGT)	 AG	97401-97561	GT	AGG
(ATG)	 AG	98153-98804	GG	CCG
-recovered pasa_asmbl_32696.p1, internal, 97401, 97561
Valid prediction for GlimmerHMM_glimmerT_51817-T1
Valid prediction for GlimmerHMM_glimmerT_51813-T1
Valid prediction for snap_scaffold_24-snap.21-T1
Valid prediction for snap_scaffold_24-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_51833-T1
Valid prediction for snap_scaffold_24-snap.28-T1
Valid prediction for GlimmerHMM_glimmerT_51823-T1
Valid prediction for CodingQuarry_transcript_37207-T1
Valid prediction for GlimmerHMM_glimmerT_51830-T1
Valid prediction for HiQ_model.g34579.t1
Valid prediction for snap_scaffold_24-snap.31-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14479, rend_intergenic: 1880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28985, rend_intergenic: 18559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51314, rend_intergenic: 32351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57585, rend_intergenic: 51681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59232, rend_intergenic: 58235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69059, rend_intergenic: 64587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106601, rend_intergenic: 82349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125826, rend_intergenic: 120100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135242, rend_intergenic: 130425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144327, rend_intergenic: 142100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156912, rend_intergenic: 155775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161145, rend_intergenic: 160525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166593, rend_intergenic: 161145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173430, rend_intergenic: 171175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190124
-exon list size: 475


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 14479, rend_intergenic: 1880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28985, rend_intergenic: 18559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51314, rend_intergenic: 32351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57585, rend_intergenic: 51681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59232, rend_intergenic: 58235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69059, rend_intergenic: 64587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106601, rend_intergenic: 82349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125826, rend_intergenic: 120100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135242, rend_intergenic: 130425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144327, rend_intergenic: 142100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156912, rend_intergenic: 155775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161145, rend_intergenic: 160525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166593, rend_intergenic: 161145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173430, rend_intergenic: 171175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support