-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_669984-887052

-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.121_t
Valid prediction for Augustus_model.g84.t1
Valid prediction for Augustus_model.g83.t1
Couldn't classify 180812, 180978
Sorry, prediction pasa_asmbl_1425.p1 fails validation.
(GGG)	 CC	180812-180978	GT	ATG
(GTA)	 AG	181407-181581	GT	AGG
(GCA)	 AG	183353-183500	GT	GGG
(TGT)	 AG	183578-183719	GT	ATG
(CAT)	 AG	184208-184292	GT	TGG
(ATT)	 AG	184537-184668	GT	CCG
(GGA)	 AG	184838-184996	GT	TTG
(GTA)	 AG	185105-185230	GT	TGG
(ATC)	 AG	185424-185540	AG	GAA
-recovered pasa_asmbl_1425.p1, terminal, 185424, 185540
-recovered pasa_asmbl_1425.p1, internal, 181407, 181581
-recovered pasa_asmbl_1425.p1, internal, 183353, 183500
-recovered pasa_asmbl_1425.p1, internal, 183578, 183719
-recovered pasa_asmbl_1425.p1, internal, 184208, 184292
-recovered pasa_asmbl_1425.p1, internal, 184537, 184668
-recovered pasa_asmbl_1425.p1, internal, 184838, 184996
-recovered pasa_asmbl_1425.p1, internal, 185105, 185230
Valid prediction for snap_scaffold_1-snap.136-T1
Valid prediction for Augustus_model.g81.t1
Valid prediction for GlimmerHMM_glimmerT_109-T1
Valid prediction for snap_scaffold_1-snap.141-T1
Valid prediction for GeneMark_model.108_t
Valid prediction for GlimmerHMM_glimmerT_101-T1
Valid prediction for snap_scaffold_1-snap.145-T1
Valid prediction for Augustus_model.g82.t1
Couldn't classify 122208, 122340
Couldn't classify 123033, 123148
Sorry, prediction pasa_asmbl_2694.p1 fails validation.
(AAG)	 CC	122208-122340	GT	CGG
(GTG)	 AG	122725-122850	GT	TGG
(GCA)	 AG	123033-123148	GT	AGG
-recovered pasa_asmbl_2694.p1, internal, 122725, 122850
-recovered pasa_asmbl_2694.p1, internal, 123033, 123148
Valid prediction for HiQ_model.g90.t1
Valid prediction for snap_scaffold_1-snap.134-T1
Valid prediction for GeneMark_model.112_t
Valid prediction for GlimmerHMM_glimmerT_111-T1
Valid prediction for GeneMark_model.105_t
Valid prediction for snap_scaffold_1-snap.135-T1
Valid prediction for CodingQuarry_transcript_2505-T1
Valid prediction for snap_scaffold_1-snap.147-T1
Valid prediction for Augustus_model.g80.t1
Valid prediction for GlimmerHMM_glimmerT_115-T1
Valid prediction for GlimmerHMM_glimmerT_99-T1
Valid prediction for GeneMark_model.113_t
Valid prediction for snap_scaffold_1-snap.156-T1
Valid prediction for GeneMark_model.97_t
Valid prediction for HiQ_model.g92.t1
Valid prediction for snap_scaffold_1-snap.131-T1
Valid prediction for GeneMark_model.119_t
Valid prediction for Augustus_model.g89.t1
Valid prediction for GeneMark_model.104_t
Valid prediction for GeneMark_model.99_t
Valid prediction for GlimmerHMM_glimmerT_112-T1
Valid prediction for snap_scaffold_1-snap.144-T1
Valid prediction for GeneMark_model.100_t
Valid prediction for snap_scaffold_1-snap.146-T1
Valid prediction for snap_scaffold_1-snap.143-T1
Valid prediction for snap_scaffold_1-snap.148-T1
Valid prediction for GlimmerHMM_glimmerT_97-T1
Valid prediction for GeneMark_model.101_t
Valid prediction for GlimmerHMM_glimmerT_100-T1
Valid prediction for GlimmerHMM_glimmerT_104-T1
Valid prediction for Augustus_model.g85.t1
Valid prediction for snap_scaffold_1-snap.157-T1
Valid prediction for GlimmerHMM_glimmerT_106-T1
Valid prediction for Augustus_model.g79.t1
Valid prediction for pasa_asmbl_1429.p1
Valid prediction for snap_scaffold_1-snap.150-T1
Couldn't classify 128972, 129155
Couldn't classify 130328, 130417
Sorry, prediction pasa_asmbl_1408.p1 fails validation.
(GCT)	 CA	128972-129155	GT	TGG
(GTC)	 AG	129693-129907	GT	AGG
(AAA)	 AG	130328-130417	AC	GCA
-recovered pasa_asmbl_1408.p1, internal, 129693, 129907
Valid prediction for GeneMark_model.116_t
Valid prediction for snap_scaffold_1-snap.159-T1
Valid prediction for Augustus_model.g87.t1
Valid prediction for GlimmerHMM_glimmerT_96-T1
Valid prediction for GeneMark_model.115_t
Valid prediction for snap_scaffold_1-snap.137-T1
Valid prediction for GlimmerHMM_glimmerT_107-T1
Valid prediction for snap_scaffold_1-snap.138-T1
Couldn't classify 147646, 147703
Couldn't classify 150248, 150406
Sorry, prediction pasa_asmbl_1410.p2 fails validation.
(AAC)	 AG	147646-147703	GT	TGG
(GCG)	 AG	148033-148244	GT	AGG
(ATC)	 AG	148926-149033	GT	AGG
(CTT)	 AG	150248-150406	GG	GAG
-recovered pasa_asmbl_1410.p2, internal, 147646, 147703
-recovered pasa_asmbl_1410.p2, internal, 148033, 148244
-recovered pasa_asmbl_1410.p2, internal, 148926, 149033
Valid prediction for GeneMark_model.110_t
Valid prediction for Augustus_model.g86.t1
Valid prediction for GeneMark_model.125_t
Valid prediction for snap_scaffold_1-snap.153-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 Augustus_model.g91.t1
Valid prediction for snap_scaffold_1-snap.154-T1
Couldn't classify 41212, 41235
Couldn't classify 43972, 44049
Sorry, prediction pasa_asmbl_1261.p1 fails validation.
(GGA)	 AA	41212-41235	GT	TGG
(ATG)	 AG	43537-43740	GT	AGG
(ATT)	 AG	43972-44049	GG	GGG
-recovered pasa_asmbl_1261.p1, initial, 43537, 43740
-recovered pasa_asmbl_1261.p1, internal, 43537, 43740
Valid prediction for GeneMark_model.117_t
Valid prediction for snap_scaffold_1-snap.149-T1
Valid prediction for GeneMark_model.120_t
Valid prediction for snap_scaffold_1-snap.139-T1
Valid prediction for snap_scaffold_1-snap.128-T1
Valid prediction for CodingQuarry_transcript_2504-T1
Valid prediction for GlimmerHMM_glimmerT_113-T1
Valid prediction for Augustus_model.g77.t1
Valid prediction for GeneMark_model.122_t
Valid prediction for GeneMark_model.103_t
Valid prediction for GeneMark_model.107_t
Valid prediction for GeneMark_model.98_t
Valid prediction for snap_scaffold_1-snap.152-T1
Valid prediction for GeneMark_model.126_t
Valid prediction for snap_scaffold_1-snap.133-T1
Valid prediction for GeneMark_model.95_t
Valid prediction for GeneMark_model.106_t
Valid prediction for GlimmerHMM_glimmerT_108-T1
Valid prediction for GeneMark_model.96_t
Couldn't classify 16701, 16737
Sorry, prediction pasa_asmbl_29.p1 fails validation.
(CTG)	 AA	16701-16737	GT	CAG
(CCT)	 AG	17475-17717	GC	AGG
(GTT)	 AG	17869-17957	GG	GAG
-recovered pasa_asmbl_29.p1, terminal, 17869, 17957
-recovered pasa_asmbl_29.p1, internal, 17475, 17717
Valid prediction for snap_scaffold_1-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_114-T1
Couldn't classify 10641, 10679
Couldn't classify 13808, 13861
Sorry, prediction pasa_asmbl_30.p1 fails validation.
(GGA)	 AG	10641-10679	GT	AGG
(CTG)	 AG	10829-10941	GT	AGG
(TGA)	 AG	11915-11984	GT	TGG
(CCC)	 AG	12072-12149	GT	AGG
(ATC)	 AG	12816-12956	GT	AAG
(ATC)	 AG	13808-13861	GT	GGG
-recovered pasa_asmbl_30.p1, internal, 10641, 10679
-recovered pasa_asmbl_30.p1, internal, 10829, 10941
-recovered pasa_asmbl_30.p1, internal, 11915, 11984
-recovered pasa_asmbl_30.p1, internal, 12072, 12149
-recovered pasa_asmbl_30.p1, internal, 12816, 12956
-recovered pasa_asmbl_30.p1, internal, 13808, 13861
Valid prediction for GeneMark_model.124_t
Valid prediction for snap_scaffold_1-snap.130-T1
Valid prediction for GeneMark_model.123_t
Valid prediction for snap_scaffold_1-snap.127-T1
Valid prediction for GlimmerHMM_glimmerT_103-T1
Valid prediction for GeneMark_model.109_t
Valid prediction for snap_scaffold_1-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_95-T1
Valid prediction for GlimmerHMM_glimmerT_105-T1
Valid prediction for pasa_asmbl_26.p1
Valid prediction for snap_scaffold_1-snap.132-T1
Valid prediction for CodingQuarry_transcript_2503-T1
Valid prediction for snap_scaffold_1-snap.129-T1
Valid prediction for Augustus_model.g78.t1
Valid prediction for GlimmerHMM_glimmerT_102-T1
Valid prediction for GeneMark_model.114_t
Valid prediction for GlimmerHMM_glimmerT_110-T1
Valid prediction for GlimmerHMM_glimmerT_98-T1
Valid prediction for snap_scaffold_1-snap.155-T1
Valid prediction for snap_scaffold_1-snap.140-T1
Valid prediction for GeneMark_model.111_t
Valid prediction for snap_scaffold_1-snap.142-T1
Valid prediction for Augustus_model.g93.t1
Valid prediction for Augustus_model.g88.t1
Valid prediction for GlimmerHMM_glimmerT_94-T1
Valid prediction for GlimmerHMM_glimmerT_116-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25459, rend_intergenic: 21504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53764, rend_intergenic: 50461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72106, rend_intergenic: 69926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96843, rend_intergenic: 87171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104719, rend_intergenic: 99306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150705, rend_intergenic: 148029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159749, rend_intergenic: 154412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207133, rend_intergenic: 201154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217069
-exon list size: 452


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 25459, rend_intergenic: 21504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53764, rend_intergenic: 50461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72106, rend_intergenic: 69926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96843, rend_intergenic: 87171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104719, rend_intergenic: 99306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150705, rend_intergenic: 148029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159749, rend_intergenic: 154412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207133, rend_intergenic: 201154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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