-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_8248678-8437697

-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 GlimmerHMM_glimmerT_9965-T1
Valid prediction for Augustus_model.g6530.t1
Valid prediction for snap_scaffold_4-snap.1746-T1
Valid prediction for Augustus_model.g6523.t1
Valid prediction for GeneMark_model.16177_t
Valid prediction for snap_scaffold_4-snap.1737-T1
Valid prediction for GeneMark_model.16189_t
Valid prediction for snap_scaffold_4-snap.1753-T1
Valid prediction for GeneMark_model.16187_t
Valid prediction for Augustus_model.g6525.t1
Valid prediction for GeneMark_model.16198_t
Valid prediction for GeneMark_model.16178_t
Valid prediction for snap_scaffold_4-snap.1744-T1
Valid prediction for HiQ_model.g6534.t1
Valid prediction for snap_scaffold_4-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_9975-T1
Valid prediction for GlimmerHMM_glimmerT_9961-T1
Valid prediction for snap_scaffold_4-snap.1741-T1
Couldn't classify 129992, 130125
Couldn't classify 131218, 131343
Sorry, prediction pasa_asmbl_42889.p1 fails validation.
(GGA)	 GG	129992-130125	GT	GGG
(TGA)	 AG	130301-130430	GT	AGG
(GGT)	 AG	131218-131343	CA	TCC
-recovered pasa_asmbl_42889.p1, internal, 130301, 130430
Couldn't classify 13826, 14131
Sorry, prediction pasa_asmbl_42878.p1 fails validation.
(TCT)	 CC	13826-14131	GT	AGG
(GGC)	 AG	14446-14730	GT	CGG
(AGG)	 AG	15024-15443	AA	AGA
-recovered pasa_asmbl_42878.p1, terminal, 15024, 15443
-recovered pasa_asmbl_42878.p1, internal, 14446, 14730
Valid prediction for GeneMark_model.16193_t
Couldn't classify 37577, 37722
Couldn't classify 38409, 38500
Sorry, prediction pasa_asmbl_43537.p1 fails validation.
(TAC)	 CG	37577-37722	GT	CAG
(GAC)	 AG	37877-37977	GT	AAG
(TCT)	 AG	38409-38500	AT	AGA
-recovered pasa_asmbl_43537.p1, internal, 37877, 37977
Valid prediction for GlimmerHMM_glimmerT_9956-T1
Valid prediction for snap_scaffold_4-snap.1742-T1
Valid prediction for GeneMark_model.16173_t
Valid prediction for GlimmerHMM_glimmerT_9974-T1
Valid prediction for snap_scaffold_4-snap.1736-T1
Valid prediction for snap_scaffold_4-snap.1751-T1
Valid prediction for GeneMark_model.16195_t
Valid prediction for snap_scaffold_4-snap.1739-T1
Couldn't classify 11307, 11366
Couldn't classify 13650, 13720
Sorry, prediction pasa_asmbl_42877.p1 fails validation.
(CCC)	 CC	11307-11366	GT	AAG
(TTG)	 AG	11516-11565	GT	AAG
(CAT)	 AG	12428-12663	GT	AGG
(GTC)	 AG	13650-13720	CA	TCC
-recovered pasa_asmbl_42877.p1, internal, 11516, 11565
-recovered pasa_asmbl_42877.p1, internal, 12428, 12663
Valid prediction for GeneMark_model.16182_t
Valid prediction for GlimmerHMM_glimmerT_9971-T1
Valid prediction for GlimmerHMM_glimmerT_9968-T1
Valid prediction for snap_scaffold_4-snap.1756-T1
Valid prediction for GlimmerHMM_glimmerT_9958-T1
Valid prediction for CodingQuarry_transcript_48966-T1
Valid prediction for GeneMark_model.16201_t
Valid prediction for Augustus_model.g6529.t1
Valid prediction for Augustus_model.g6524.t1
Valid prediction for pasa_asmbl_42892.p1
Valid prediction for GlimmerHMM_glimmerT_9969-T1
Valid prediction for GlimmerHMM_glimmerT_9960-T1
Valid prediction for GlimmerHMM_glimmerT_9967-T1
Couldn't classify 42647, 42700
Couldn't classify 43633, 43675
Sorry, prediction pasa_asmbl_42883.p1 fails validation.
(GTG)	 AG	42647-42700	GT	AGG
(AGC)	 AG	42887-42991	GT	AGG
(GTG)	 AG	43316-43491	GT	AGG
(CCT)	 AG	43633-43675	GC	GAG
-recovered pasa_asmbl_42883.p1, internal, 42647, 42700
-recovered pasa_asmbl_42883.p1, internal, 42887, 42991
-recovered pasa_asmbl_42883.p1, internal, 43316, 43491
-recovered pasa_asmbl_42883.p1, internal, 43633, 43675
Valid prediction for GlimmerHMM_glimmerT_9959-T1
Valid prediction for Augustus_model.g6526.t1
Valid prediction for GeneMark_model.16184_t
Couldn't classify 44403, 44642
Couldn't classify 44999, 45058
Sorry, prediction pasa_asmbl_42884.p1 fails validation.
(GGT)	 AG	44403-44642	GT	AGG
(TCG)	 AG	44999-45058	CA	ACC
-recovered pasa_asmbl_42884.p1, internal, 44403, 44642
Valid prediction for GlimmerHMM_glimmerT_9957-T1
Valid prediction for snap_scaffold_4-snap.1740-T1
Valid prediction for GeneMark_model.16171_t
Couldn't classify 134510, 134537
Couldn't classify 135307, 135417
Sorry, prediction pasa_asmbl_43533.p2 fails validation.
(GTG)	 AG	134510-134537	GT	GGG
(GGA)	 AG	134747-134949	GT	AGG
(GAA)	 AG	135307-135417	GT	AGG
-recovered pasa_asmbl_43533.p2, internal, 134510, 134537
-recovered pasa_asmbl_43533.p2, internal, 134747, 134949
-recovered pasa_asmbl_43533.p2, internal, 135307, 135417
Couldn't classify 41709, 41932
Couldn't classify 42415, 42529
Sorry, prediction pasa_asmbl_42882.p1 fails validation.
(AAG)	 CG	41709-41932	GT	CGG
(GCC)	 AG	42415-42529	AC	CCA
Valid prediction for GeneMark_model.16180_t
Valid prediction for HiQ_model.g6522.t1
Valid prediction for snap_scaffold_4-snap.1758-T1
Valid prediction for GeneMark_model.16176_t
Valid prediction for Augustus_model.g6531.t1
Valid prediction for GlimmerHMM_glimmerT_9964-T1
Valid prediction for snap_scaffold_4-snap.1738-T1
Couldn't classify 40378, 40584
Couldn't classify 41435, 41589
Sorry, prediction pasa_asmbl_42881.p1 fails validation.
(GAG)	 AG	40378-40584	GT	AGG
(GTG)	 AG	40753-40881	GT	AAG
(GCC)	 AG	41160-41304	GT	AGG
(ACA)	 AG	41435-41589	AG	ACA
-recovered pasa_asmbl_42881.p1, internal, 40378, 40584
-recovered pasa_asmbl_42881.p1, internal, 40753, 40881
-recovered pasa_asmbl_42881.p1, internal, 41160, 41304
Valid prediction for CodingQuarry_transcript_48969-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 188, 229
Sorry, prediction pasa_asmbl_41515.p1 fails validation.
(GGT)	 GA	188-229	GT	AGG
(CTT)	 AG	495-1484	TG	GAT
-recovered pasa_asmbl_41515.p1, terminal, 495, 1484
Valid prediction for snap_scaffold_4-snap.1757-T1
Valid prediction for GeneMark_model.16186_t
Valid prediction for GeneMark_model.16179_t
Valid prediction for GlimmerHMM_glimmerT_9972-T1
Valid prediction for GlimmerHMM_glimmerT_9970-T1
Valid prediction for snap_scaffold_4-snap.1749-T1
Valid prediction for GeneMark_model.16181_t
Valid prediction for GlimmerHMM_glimmerT_9979-T1
Valid prediction for snap_scaffold_4-snap.1745-T1
Valid prediction for CodingQuarry_transcript_48968-T1
Valid prediction for GeneMark_model.16194_t
Valid prediction for GlimmerHMM_glimmerT_9976-T1
Valid prediction for GeneMark_model.16206_t
Valid prediction for snap_scaffold_4-snap.1752-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1761-T1
Valid prediction for snap_scaffold_4-snap.1763-T1
Valid prediction for GeneMark_model.16188_t
Valid prediction for Augustus_model.g6528.t1
Couldn't classify 45447, 45617
Sorry, prediction pasa_asmbl_41510.p1 fails validation.
(AGC)	 CC	45447-45617	GT	GGG
(ACG)	 AG	45811-45921	GT	TTG
(TAC)	 AG	46515-46571	GT	TGG
(GTG)	 AG	46676-46813	GT	GGG
(GCC)	 AG	47252-47365	GT	AAG
(CAG)	 AG	47497-47580	GT	AGG
(ACT)	 AG	47960-48049	GG	GAG
-recovered pasa_asmbl_41510.p1, terminal, 47960, 48049
-recovered pasa_asmbl_41510.p1, internal, 45811, 45921
-recovered pasa_asmbl_41510.p1, internal, 46515, 46571
-recovered pasa_asmbl_41510.p1, internal, 46676, 46813
-recovered pasa_asmbl_41510.p1, internal, 47252, 47365
-recovered pasa_asmbl_41510.p1, internal, 47497, 47580
Valid prediction for GeneMark_model.16200_t
Valid prediction for HiQ_model.g6536.t1
Valid prediction for GeneMark_model.16192_t
Valid prediction for GeneMark_model.16172_t
Valid prediction for Augustus_model.g6527.t1
Valid prediction for Augustus_model.g6535.t1
Valid prediction for GeneMark_model.16183_t
Valid prediction for HiQ_model.g6532.t1
Valid prediction for CodingQuarry_transcript_48970-T1
Valid prediction for snap_scaffold_4-snap.1755-T1
Valid prediction for GeneMark_model.16196_t
Valid prediction for snap_scaffold_4-snap.1750-T1
Valid prediction for Augustus_model.g6533.t1
Valid prediction for GlimmerHMM_glimmerT_9978-T1
Valid prediction for GeneMark_model.16190_t
Valid prediction for pasa_asmbl_41513.p1
Valid prediction for GeneMark_model.16174_t
Valid prediction for snap_scaffold_4-snap.1754-T1
Valid prediction for snap_scaffold_4-snap.1764-T1
Valid prediction for snap_scaffold_4-snap.1760-T1
Valid prediction for GeneMark_model.16191_t
Valid prediction for GeneMark_model.16175_t
Valid prediction for Augustus_model.g6537.t1
Valid prediction for GeneMark_model.16199_t
Valid prediction for GlimmerHMM_glimmerT_9963-T1
Valid prediction for snap_scaffold_4-snap.1748-T1
Valid prediction for GeneMark_model.16185_t
Valid prediction for snap_scaffold_4-snap.1759-T1
Couldn't classify 88431, 88554
Couldn't classify 92743, 92815
Sorry, prediction pasa_asmbl_41508.p1 fails validation.
(CAG)	 CC	88431-88554	GT	AGG
(GCG)	 AG	89284-89405	GT	AGG
(GAG)	 AG	89766-89858	GT	AGG
(AGA)	 AG	90362-90420	GT	AGG
(GCT)	 AG	90607-90725	GT	GCG
(CAA)	 AG	90941-91124	GT	AGG
(AAA)	 AG	92044-92126	GT	AAG
(GTG)	 AG	92588-92636	GT	AGG
(TGA)	 AG	92743-92815	AT	TGA
-recovered pasa_asmbl_41508.p1, terminal, 90941, 91124
-recovered pasa_asmbl_41508.p1, internal, 89284, 89405
-recovered pasa_asmbl_41508.p1, internal, 89766, 89858
-recovered pasa_asmbl_41508.p1, internal, 90362, 90420
-recovered pasa_asmbl_41508.p1, internal, 90607, 90725
-recovered pasa_asmbl_41508.p1, internal, 90941, 91124
-recovered pasa_asmbl_41508.p1, internal, 92044, 92126
-recovered pasa_asmbl_41508.p1, internal, 92588, 92636
Valid prediction for GlimmerHMM_glimmerT_9962-T1
Valid prediction for GlimmerHMM_glimmerT_9966-T1
Valid prediction for snap_scaffold_4-snap.1743-T1
Valid prediction for GlimmerHMM_glimmerT_9973-T1
Valid prediction for GlimmerHMM_glimmerT_9977-T1
Valid prediction for Augustus_model.g6538.t1
Valid prediction for GeneMark_model.16202_t
Valid prediction for snap_scaffold_4-snap.1747-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 62696, rend_intergenic: 61234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132944, rend_intergenic: 126266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186317, rend_intergenic: 184620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189020
-exon list size: 500


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 62696, rend_intergenic: 61234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132944, rend_intergenic: 126266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186317, rend_intergenic: 184620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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