-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_1137359-1427341

-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_8-snap.219-T1
Couldn't classify 226015, 226227
Couldn't classify 226530, 226646
Sorry, prediction pasa_asmbl_52693.p2 fails validation.
(CAG)	 GG	226015-226227	GT	AGG
(GTG)	 AG	226530-226646	GT	GCG
-recovered pasa_asmbl_52693.p2, internal, 226530, 226646
Valid prediction for Augustus_model.g12837.t1
Valid prediction for GlimmerHMM_glimmerT_19255-T1
Valid prediction for Augustus_model.g12831.t1
Valid prediction for snap_scaffold_8-snap.215-T1
Valid prediction for pasa_asmbl_52690.p1
Valid prediction for GlimmerHMM_glimmerT_19242-T1
Valid prediction for GlimmerHMM_glimmerT_19241-T1
Valid prediction for GlimmerHMM_glimmerT_19234-T1
Valid prediction for snap_scaffold_8-snap.241-T1
Valid prediction for GlimmerHMM_glimmerT_19231-T1
Valid prediction for CodingQuarry_transcript_59593-T1
Valid prediction for snap_scaffold_8-snap.251-T1
Valid prediction for snap_scaffold_8-snap.252-T1
Couldn't classify 118630, 118808
Sorry, prediction pasa_asmbl_52685.p1 fails validation.
(ATG)	 TG	116698-116918	GT	GGG
(TAA)	 AG	118093-118286	GT	AGG
(CCA)	 AG	118630-118808	GT	TGG
-recovered pasa_asmbl_52685.p1, initial, 116698, 116918
add_exon() Sorry, pasa_asmbl_52685.p1 118093-118286-terminal-2 is invalid.
-recovered pasa_asmbl_52685.p1, terminal, 118093, 118286
-recovered pasa_asmbl_52685.p1, internal, 118093, 118286
-recovered pasa_asmbl_52685.p1, internal, 118630, 118808
Valid prediction for Augustus_model.g12846.t1
Valid prediction for GlimmerHMM_glimmerT_19228-T1
Valid prediction for snap_scaffold_8-snap.223-T1
Valid prediction for snap_scaffold_8-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_19251-T1
Valid prediction for snap_scaffold_8-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_19230-T1
Valid prediction for Augustus_model.g12842.t1
Valid prediction for snap_scaffold_8-snap.222-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g12845.t1
Valid prediction for Augustus_model.g12833.t1
Valid prediction for snap_scaffold_8-snap.239-T1
Valid prediction for snap_scaffold_8-snap.224-T1
Valid prediction for Augustus_model.g12844.t1
Valid prediction for GlimmerHMM_glimmerT_19237-T1
Valid prediction for HiQ_model.g12836.t1
Valid prediction for snap_scaffold_8-snap.258-T1
Valid prediction for snap_scaffold_8-snap.247-T1
Valid prediction for snap_scaffold_8-snap.245-T1
Valid prediction for Augustus_model.g12843.t1
Couldn't classify 242665, 243105
Sorry, prediction pasa_asmbl_52696.p1 fails validation.
(GGC)	 AG	242665-243105	AG	ACA
Couldn't classify 285100, 285950
Couldn't classify 286366, 286483
Sorry, prediction pasa_asmbl_52700.p1 fails validation.
(GGG)	 GA	285100-285950	GT	AGG
(ACC)	 AG	286366-286483	AG	GAA
Valid prediction for snap_scaffold_8-snap.218-T1
Valid prediction for snap_scaffold_8-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_19248-T1
Valid prediction for snap_scaffold_8-snap.226-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g12841.t1
Valid prediction for GlimmerHMM_glimmerT_19246-T1
Valid prediction for snap_scaffold_8-snap.254-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.214-T1
Valid prediction for GlimmerHMM_glimmerT_19232-T1
Couldn't classify 284656, 284955
Sorry, prediction pasa_asmbl_52699.p1 fails validation.
(GGT)	 CA	284656-284955	GG	GAG
Valid prediction for snap_scaffold_8-snap.248-T1
Couldn't classify 224484, 224930
Sorry, prediction pasa_asmbl_52692.p1 fails validation.
(TCG)	 AC	224484-224930	GG	TGG
Valid prediction for snap_scaffold_8-snap.231-T1
Valid prediction for snap_scaffold_8-snap.234-T1
Couldn't classify 250085, 250210
Sorry, prediction pasa_asmbl_52697.p1 fails validation.
(ATC)	 AG	250085-250210	GT	AGG
(ATT)	 AG	250736-250814	GT	AGG
(GTC)	 AG	251133-251338	TG	GAT
-recovered pasa_asmbl_52697.p1, terminal, 251133, 251338
-recovered pasa_asmbl_52697.p1, internal, 250085, 250210
-recovered pasa_asmbl_52697.p1, internal, 250736, 250814
Couldn't classify 229497, 229515
Couldn't classify 231977, 232114
Sorry, prediction pasa_asmbl_52694.p1 fails validation.
(GAG)	 AG	229497-229515	GT	AGG
(ACT)	 AG	229815-229940	GT	CGG
(ATG)	 AG	230164-230261	GT	AGG
(ACA)	 AG	230937-231083	GT	TGG
(GAG)	 AG	231462-231557	GT	AGG
(ATC)	 AG	231977-232114	TA	GAT
add_exon() Sorry, pasa_asmbl_52694.p1 230164-230261-initial-1 is invalid.
-recovered pasa_asmbl_52694.p1, initial, 230164, 230261
-recovered pasa_asmbl_52694.p1, internal, 229497, 229515
-recovered pasa_asmbl_52694.p1, internal, 229815, 229940
-recovered pasa_asmbl_52694.p1, internal, 230164, 230261
-recovered pasa_asmbl_52694.p1, internal, 230937, 231083
-recovered pasa_asmbl_52694.p1, internal, 231462, 231557
Valid prediction for snap_scaffold_8-snap.232-T1
Valid prediction for snap_scaffold_8-snap.221-T1
Valid prediction for snap_scaffold_8-snap.256-T1
Valid prediction for snap_scaffold_8-snap.236-T1
Valid prediction for snap_scaffold_8-snap.238-T1
Valid prediction for Augustus_model.g12848.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_8-snap.244-T1
Valid prediction for snap_scaffold_8-snap.216-T1
Valid prediction for snap_scaffold_8-snap.217-T1
Valid prediction for snap_scaffold_8-snap.250-T1
Valid prediction for GlimmerHMM_glimmerT_19250-T1
Valid prediction for Augustus_model.g12835.t1
Valid prediction for Augustus_model.g12832.t1
Valid prediction for snap_scaffold_8-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_19233-T1
Valid prediction for snap_scaffold_8-snap.235-T1
Valid prediction for GlimmerHMM_glimmerT_19245-T1
Valid prediction for GlimmerHMM_glimmerT_19238-T1
Valid prediction for GlimmerHMM_glimmerT_19229-T1
Valid prediction for GlimmerHMM_glimmerT_19253-T1
Valid prediction for snap_scaffold_8-snap.225-T1
Valid prediction for snap_scaffold_8-snap.227-T1
Valid prediction for Augustus_model.g12847.t1
Valid prediction for snap_scaffold_8-snap.259-T1
Valid prediction for snap_scaffold_8-snap.249-T1
Valid prediction for snap_scaffold_8-snap.213-T1
Valid prediction for CodingQuarry_transcript_59594-T1
Couldn't classify 32489, 32591
Sorry, prediction pasa_asmbl_52616.p1 fails validation.
(GAT)	 AG	32489-32591	GT	CGG
(AGG)	 AG	32906-32975	GT	GGG
(AGA)	 AG	33288-33525	CC	AGC
-recovered pasa_asmbl_52616.p1, terminal, 33288, 33525
-recovered pasa_asmbl_52616.p1, internal, 32489, 32591
-recovered pasa_asmbl_52616.p1, internal, 32906, 32975
Valid prediction for GlimmerHMM_glimmerT_19252-T1
Valid prediction for Augustus_model.g12834.t1
Valid prediction for GlimmerHMM_glimmerT_19254-T1
Valid prediction for GlimmerHMM_glimmerT_19235-T1
Valid prediction for snap_scaffold_8-snap.240-T1
Valid prediction for GlimmerHMM_glimmerT_19239-T1
Valid prediction for GlimmerHMM_glimmerT_19249-T1
Valid prediction for Augustus_model.g12838.t1
Valid prediction for GlimmerHMM_glimmerT_19243-T1
Valid prediction for snap_scaffold_8-snap.228-T1
Valid prediction for Augustus_model.g12840.t1
Valid prediction for GlimmerHMM_glimmerT_19240-T1
Valid prediction for Augustus_model.g12839.t1
Valid prediction for GlimmerHMM_glimmerT_19244-T1
Valid prediction for snap_scaffold_8-snap.255-T1
Valid prediction for snap_scaffold_8-snap.257-T1
Valid prediction for snap_scaffold_8-snap.237-T1
Valid prediction for snap_scaffold_8-snap.233-T1
Valid prediction for GlimmerHMM_glimmerT_19247-T1
Valid prediction for snap_scaffold_8-snap.230-T1
Valid prediction for GlimmerHMM_glimmerT_19236-T1
Valid prediction for snap_scaffold_8-snap.220-T1
Valid prediction for snap_scaffold_8-snap.246-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7305, rend_intergenic: 1878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50992, rend_intergenic: 8559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61810, rend_intergenic: 51029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64363, rend_intergenic: 62491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68898, rend_intergenic: 64612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75802, rend_intergenic: 74267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109366, rend_intergenic: 107442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123905, rend_intergenic: 118592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130828, rend_intergenic: 124942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133854, rend_intergenic: 131560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144283, rend_intergenic: 139387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154796, rend_intergenic: 146380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181536, rend_intergenic: 156915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184964, rend_intergenic: 181567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188848, rend_intergenic: 185806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206825, rend_intergenic: 200183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225665, rend_intergenic: 220167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234579, rend_intergenic: 225801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251338, rend_intergenic: 241577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 269857, rend_intergenic: 256242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 285954, rend_intergenic: 278519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 77021, rend_intergenic: 77018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 289983
-exon list size: 448


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 7305, rend_intergenic: 1878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50992, rend_intergenic: 8559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61810, rend_intergenic: 51029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64363, rend_intergenic: 62491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68898, rend_intergenic: 64612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75802, rend_intergenic: 74267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109366, rend_intergenic: 107442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123905, rend_intergenic: 118592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130828, rend_intergenic: 124942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133854, rend_intergenic: 131560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144283, rend_intergenic: 139387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154796, rend_intergenic: 146380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181536, rend_intergenic: 156915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184964, rend_intergenic: 181567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188848, rend_intergenic: 185806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206825, rend_intergenic: 200183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225665, rend_intergenic: 220167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234579, rend_intergenic: 225801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251338, rend_intergenic: 241577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 269857, rend_intergenic: 256242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 285954, rend_intergenic: 278519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 77021, rend_intergenic: 77018  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