-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_4976761-5115270

-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.82207_t
Valid prediction for snap_scaffold_20-snap.1114-T1
Valid prediction for snap_scaffold_20-snap.1090-T1
Valid prediction for GeneMark_model.82199_t
Valid prediction for GeneMark_model.82223_t
Valid prediction for GeneMark_model.82200_t
Valid prediction for GlimmerHMM_glimmerT_47064-T1
Valid prediction for GeneMark_model.82204_t
Valid prediction for pasa_asmbl_25754.p1
Valid prediction for snap_scaffold_20-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_47058-T1
Valid prediction for snap_scaffold_20-snap.1083-T1
Valid prediction for Augustus_model.g31387.t1
Valid prediction for snap_scaffold_20-snap.1101-T1
Valid prediction for snap_scaffold_20-snap.1104-T1
Valid prediction for CodingQuarry_transcript_30441-T1
Valid prediction for snap_scaffold_20-snap.1103-T1
Valid prediction for GeneMark_model.82205_t
Valid prediction for HiQ_model.g31397.t1
Valid prediction for GeneMark_model.82213_t
Valid prediction for snap_scaffold_20-snap.1099-T1
Valid prediction for Augustus_model.g31392.t1
Valid prediction for snap_scaffold_20-snap.1108-T1
Valid prediction for GeneMark_model.82196_t
Valid prediction for GeneMark_model.82208_t
Valid prediction for snap_scaffold_20-snap.1100-T1
Valid prediction for snap_scaffold_20-snap.1084-T1
Valid prediction for GeneMark_model.82233_t
Couldn't classify 82117, 82437
Sorry, prediction pasa_asmbl_26675.p1 fails validation.
(CTT)	 CT	82117-82437	CC	AGC
Valid prediction for snap_scaffold_20-snap.1086-T1
Valid prediction for snap_scaffold_20-snap.1110-T1
Valid prediction for snap_scaffold_20-snap.1109-T1
Valid prediction for snap_scaffold_20-snap.1087-T1
Valid prediction for snap_scaffold_20-snap.1089-T1
Valid prediction for snap_scaffold_20-snap.1095-T1
Valid prediction for GlimmerHMM_glimmerT_47061-T1
Valid prediction for GeneMark_model.82228_t
Valid prediction for GeneMark_model.82231_t
Valid prediction for GeneMark_model.82227_t
Valid prediction for Augustus_model.g31395.t1
Valid prediction for Augustus_model.g31388.t1
Valid prediction for GeneMark_model.82229_t
Valid prediction for GeneMark_model.82201_t
Valid prediction for GeneMark_model.82211_t
Valid prediction for GeneMark_model.82219_t
Valid prediction for GlimmerHMM_glimmerT_47062-T1
Valid prediction for GlimmerHMM_glimmerT_47056-T1
Valid prediction for GeneMark_model.82203_t
Valid prediction for snap_scaffold_20-snap.1082-T1
Valid prediction for GeneMark_model.82215_t
Valid prediction for snap_scaffold_20-snap.1092-T1
Valid prediction for GeneMark_model.82217_t

-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 GlimmerHMM_glimmerT_47060-T1
Valid prediction for GeneMark_model.82230_t
Valid prediction for Augustus_model.g31391.t1
Valid prediction for GeneMark_model.82210_t
Valid prediction for snap_scaffold_20-snap.1088-T1
Valid prediction for snap_scaffold_20-snap.1102-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 109311, 109349
Couldn't classify 109979, 110806
Sorry, prediction pasa_asmbl_26671.p1 fails validation.
(CTC)	 AT	109311-109349	GT	TGG
(GGA)	 AG	109436-109555	GT	ATG
(GTT)	 AG	109979-110806	TC	GCT
-recovered pasa_asmbl_26671.p1, internal, 109436, 109555
Valid prediction for GeneMark_model.82202_t
Couldn't classify 107423, 107541
Couldn't classify 108519, 108837
Sorry, prediction pasa_asmbl_26672.p1 fails validation.
(GAG)	 CA	107423-107541	GT	AGG
(ACA)	 AG	108519-108837	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_47065-T1
Valid prediction for snap_scaffold_20-snap.1098-T1
Valid prediction for GeneMark_model.82221_t
Valid prediction for snap_scaffold_20-snap.1105-T1
Valid prediction for GlimmerHMM_glimmerT_47063-T1
Couldn't classify 111026, 111364
Sorry, prediction pasa_asmbl_26670.p1 fails validation.
(GAG)	 AG	111026-111364	AG	CCA
Valid prediction for GeneMark_model.82222_t
Valid prediction for GeneMark_model.82220_t
Valid prediction for snap_scaffold_20-snap.1106-T1
Valid prediction for snap_scaffold_20-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_47057-T1
Couldn't classify 111581, 111955
Sorry, prediction pasa_asmbl_26669.p1 fails validation.
(CCG)	 GC	111581-111955	GA	GAG
Valid prediction for GeneMark_model.82197_t
Valid prediction for Augustus_model.g31393.t1
Valid prediction for snap_scaffold_20-snap.1097-T1
Valid prediction for GeneMark_model.82224_t
Valid prediction for Augustus_model.g31396.t1
Valid prediction for GeneMark_model.82214_t
Valid prediction for snap_scaffold_20-snap.1112-T1
Valid prediction for Augustus_model.g31389.t1
Valid prediction for Augustus_model.g31390.t1
Valid prediction for GeneMark_model.82225_t
Valid prediction for GeneMark_model.82216_t
Valid prediction for snap_scaffold_20-snap.1107-T1
Valid prediction for Augustus_model.g31398.t1
Valid prediction for GeneMark_model.82195_t
Valid prediction for snap_scaffold_20-snap.1094-T1
Valid prediction for GeneMark_model.82212_t
Valid prediction for CodingQuarry_transcript_30440-T1
Valid prediction for snap_scaffold_20-snap.1093-T1
Valid prediction for GeneMark_model.82198_t
Valid prediction for GeneMark_model.82226_t
Valid prediction for GeneMark_model.82218_t
Valid prediction for snap_scaffold_20-snap.1085-T1
Valid prediction for Augustus_model.g31394.t1
Valid prediction for GeneMark_model.82232_t
Valid prediction for GeneMark_model.82206_t
Valid prediction for snap_scaffold_20-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_47059-T1
Couldn't classify 40445, 40627
Sorry, prediction pasa_asmbl_26676.p1 fails validation.
(CCC)	 TT	40445-40627	GT	AGG
(GAA)	 AG	40942-41064	GT	ACG
(GTA)	 AG	41194-41266	GT	ATG
(ATG)	 AG	41345-41502	CC	GAC
-recovered pasa_asmbl_26676.p1, terminal, 41345, 41502
-recovered pasa_asmbl_26676.p1, internal, 40942, 41064
-recovered pasa_asmbl_26676.p1, internal, 41194, 41266
Valid prediction for GeneMark_model.82234_t
Valid prediction for snap_scaffold_20-snap.1091-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14860, rend_intergenic: 10530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35562, rend_intergenic: 30973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38421, rend_intergenic: 36821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39904, rend_intergenic: 38438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51927, rend_intergenic: 49439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61893, rend_intergenic: 52705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77587, rend_intergenic: 65202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81614, rend_intergenic: 80937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87569, rend_intergenic: 85984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117664, rend_intergenic: 113104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133864, rend_intergenic: 123767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138510
-exon list size: 500


building trellis

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98.2    
98.4    
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99.6    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 14860, rend_intergenic: 10530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35562, rend_intergenic: 30973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38421, rend_intergenic: 36821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39904, rend_intergenic: 38438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51927, rend_intergenic: 49439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61893, rend_intergenic: 52705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77587, rend_intergenic: 65202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81614, rend_intergenic: 80937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87569, rend_intergenic: 85984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117664, rend_intergenic: 113104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133864, rend_intergenic: 123767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support