-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_2055775-2256035

-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_16-snap.357-T1
Valid prediction for snap_scaffold_16-snap.346-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.339-T1
Valid prediction for Augustus_model.g25995.t1
Valid prediction for pasa_asmbl_16911.p1
Valid prediction for GeneMark_model.66248_t
Valid prediction for snap_scaffold_16-snap.350-T1
Valid prediction for GeneMark_model.66234_t
Valid prediction for GlimmerHMM_glimmerT_38741-T1
Valid prediction for GeneMark_model.66230_t
Valid prediction for GeneMark_model.66236_t
Valid prediction for GeneMark_model.66243_t
Valid prediction for snap_scaffold_16-snap.354-T1
Valid prediction for GeneMark_model.66214_t
Valid prediction for GeneMark_model.66212_t
Valid prediction for snap_scaffold_16-snap.363-T1
Valid prediction for snap_scaffold_16-snap.352-T1
Valid prediction for GlimmerHMM_glimmerT_38742-T1
Valid prediction for Augustus_model.g25999.t1
Valid prediction for HiQ_model.g25991.t1
Valid prediction for GeneMark_model.66246_t
Valid prediction for snap_scaffold_16-snap.366-T1
Valid prediction for Augustus_model.g25996.t1
Valid prediction for GlimmerHMM_glimmerT_38725-T1
Valid prediction for Augustus_model.g25997.t1
Valid prediction for GeneMark_model.66232_t
Valid prediction for GeneMark_model.66229_t
Valid prediction for GeneMark_model.66226_t
Valid prediction for GlimmerHMM_glimmerT_38727-T1
Valid prediction for snap_scaffold_16-snap.338-T1
Valid prediction for snap_scaffold_16-snap.337-T1
Valid prediction for GeneMark_model.66215_t
Valid prediction for GlimmerHMM_glimmerT_38746-T1
Valid prediction for Augustus_model.g25984.t1
Valid prediction for GeneMark_model.66242_t
Valid prediction for snap_scaffold_16-snap.361-T1
Valid prediction for Augustus_model.g25988.t1
Valid prediction for snap_scaffold_16-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_38739-T1
Valid prediction for GeneMark_model.66207_t
Valid prediction for HiQ_model.g25994.t1
Valid prediction for GlimmerHMM_glimmerT_38736-T1
Valid prediction for snap_scaffold_16-snap.342-T1
Valid prediction for GeneMark_model.66250_t
Valid prediction for snap_scaffold_16-snap.362-T1
Valid prediction for GlimmerHMM_glimmerT_38745-T1
Valid prediction for snap_scaffold_16-snap.359-T1
Valid prediction for snap_scaffold_16-snap.368-T1
Valid prediction for GeneMark_model.66222_t
Valid prediction for GlimmerHMM_glimmerT_38722-T1
Valid prediction for snap_scaffold_16-snap.365-T1
Valid prediction for pasa_asmbl_16912.p2
Valid prediction for Augustus_model.g25978.t1
Valid prediction for GeneMark_model.66244_t
Valid prediction for Augustus_model.g25992.t1
Valid prediction for GlimmerHMM_glimmerT_38733-T1
Valid prediction for snap_scaffold_16-snap.358-T1
Valid prediction for snap_scaffold_16-snap.370-T1
Couldn't classify 110317, 110367
Sorry, prediction pasa_asmbl_16900.p1 fails validation.
(GCC)	 AG	110317-110367	GT	CGG
(GAC)	 AG	111516-111596	GT	AGG
(AAA)	 AG	111808-111938	GT	AGG
(GAT)	 AG	114040-114154	GT	AGG
(GAG)	 AG	114598-114622	GT	AGG
(ATC)	 AG	114814-114930	GT	AGG
(CCA)	 AG	115307-116659	GT	AGG
(CTT)	 AG	118014-118054	CC	AAC
-recovered pasa_asmbl_16900.p1, terminal, 118014, 118054
-recovered pasa_asmbl_16900.p1, internal, 110317, 110367
-recovered pasa_asmbl_16900.p1, internal, 111516, 111596
-recovered pasa_asmbl_16900.p1, internal, 111808, 111938
-recovered pasa_asmbl_16900.p1, internal, 114040, 114154
-recovered pasa_asmbl_16900.p1, internal, 114598, 114622
-recovered pasa_asmbl_16900.p1, internal, 114814, 114930
-recovered pasa_asmbl_16900.p1, internal, 115307, 116659
Valid prediction for GlimmerHMM_glimmerT_38723-T1
Couldn't classify 15515, 15713
Couldn't classify 20300, 20437
Sorry, prediction pasa_asmbl_16897.p1 fails validation.
(GAG)	 AG	15515-15713	GT	GGG
(AGT)	 AG	16060-16262	GT	AGG
(GCT)	 AG	16420-16506	GT	CAG
(AGT)	 AG	18312-18398	GT	AGG
(CTG)	 AG	20300-20437	GA	TGG
-recovered pasa_asmbl_16897.p1, internal, 15515, 15713
-recovered pasa_asmbl_16897.p1, internal, 16060, 16262
-recovered pasa_asmbl_16897.p1, internal, 16420, 16506
-recovered pasa_asmbl_16897.p1, internal, 18312, 18398
Valid prediction for snap_scaffold_16-snap.344-T1
Valid prediction for GlimmerHMM_glimmerT_38735-T1
Valid prediction for GeneMark_model.66224_t
Valid prediction for GeneMark_model.66210_t
Valid prediction for GlimmerHMM_glimmerT_38731-T1
Valid prediction for CodingQuarry_transcript_19866-T1
Valid prediction for GeneMark_model.66238_t
Valid prediction for snap_scaffold_16-snap.343-T1
Valid prediction for CodingQuarry_transcript_19869-T1
Valid prediction for GeneMark_model.66211_t
Valid prediction for GeneMark_model.66228_t
Valid prediction for GlimmerHMM_glimmerT_38740-T1
Valid prediction for CodingQuarry_transcript_19868-T1
Valid prediction for Augustus_model.g25980.t1
Valid prediction for GeneMark_model.66241_t
Valid prediction for GeneMark_model.66239_t
Valid prediction for GlimmerHMM_glimmerT_38732-T1
Valid prediction for snap_scaffold_16-snap.351-T1
Valid prediction for Augustus_model.g25979.t1
Valid prediction for GlimmerHMM_glimmerT_38734-T1
Valid prediction for snap_scaffold_16-snap.345-T1
Valid prediction for GlimmerHMM_glimmerT_38724-T1
Valid prediction for GeneMark_model.66209_t
Valid prediction for snap_scaffold_16-snap.349-T1
Valid prediction for Augustus_model.g25982.t1
Valid prediction for snap_scaffold_16-snap.367-T1
Valid prediction for GeneMark_model.66218_t
Valid prediction for GeneMark_model.66220_t
Valid prediction for Augustus_model.g25989.t1
Valid prediction for Augustus_model.g25981.t1
Valid prediction for snap_scaffold_16-snap.356-T1
Valid prediction for snap_scaffold_16-snap.355-T1
Valid prediction for Augustus_model.g25990.t1
Valid prediction for GlimmerHMM_glimmerT_38721-T1
Valid prediction for snap_scaffold_16-snap.336-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_16-snap.374-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38720-T1
Valid prediction for GeneMark_model.66245_t
Valid prediction for snap_scaffold_16-snap.340-T1
Valid prediction for GeneMark_model.66237_t
Valid prediction for snap_scaffold_16-snap.348-T1
Valid prediction for GeneMark_model.66225_t
Valid prediction for GlimmerHMM_glimmerT_38730-T1
Valid prediction for snap_scaffold_16-snap.341-T1
Valid prediction for GlimmerHMM_glimmerT_38729-T1
Valid prediction for GlimmerHMM_glimmerT_38726-T1
Valid prediction for Augustus_model.g25986.t1
Valid prediction for GeneMark_model.66235_t
Valid prediction for snap_scaffold_16-snap.347-T1
Valid prediction for GeneMark_model.66223_t
Valid prediction for GeneMark_model.66233_t
Valid prediction for snap_scaffold_16-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_38744-T1
Valid prediction for GeneMark_model.66249_t
Valid prediction for snap_scaffold_16-snap.369-T1
Valid prediction for Augustus_model.g26000.t1
Valid prediction for snap_scaffold_16-snap.353-T1
Valid prediction for HiQ_model.g25993.t1
Valid prediction for Augustus_model.g25983.t1
Valid prediction for snap_scaffold_16-snap.371-T1
Valid prediction for Augustus_model.g25985.t1
Valid prediction for GeneMark_model.66208_t
Valid prediction for GeneMark_model.66240_t
Valid prediction for pasa_asmbl_16129.p1
Valid prediction for GeneMark_model.66231_t
Valid prediction for CodingQuarry_transcript_19867-T1
Valid prediction for snap_scaffold_16-snap.364-T1
Valid prediction for snap_scaffold_16-snap.372-T1
Valid prediction for GeneMark_model.66217_t
Valid prediction for Augustus_model.g25998.t1
Valid prediction for GeneMark_model.66227_t
Valid prediction for GlimmerHMM_glimmerT_38737-T1
Valid prediction for GlimmerHMM_glimmerT_38738-T1
Valid prediction for GeneMark_model.66213_t
Valid prediction for GlimmerHMM_glimmerT_38743-T1
Valid prediction for Augustus_model.g25987.t1
Valid prediction for GeneMark_model.66221_t
Valid prediction for GeneMark_model.66219_t
Valid prediction for GeneMark_model.66216_t
Valid prediction for GlimmerHMM_glimmerT_38728-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25717, rend_intergenic: 21905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53981, rend_intergenic: 50603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104898, rend_intergenic: 95033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120812, rend_intergenic: 118300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200261
-exon list size: 645


building trellis

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99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 25717, rend_intergenic: 21905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53981, rend_intergenic: 50603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104898, rend_intergenic: 95033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120812, rend_intergenic: 118300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support