-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_2474721-2662148

-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 Augustus_model.g25319.t1
Valid prediction for GlimmerHMM_glimmerT_37969-T1
Valid prediction for GlimmerHMM_glimmerT_37982-T1
Valid prediction for Augustus_model.g25321.t1
Valid prediction for snap_scaffold_16-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_37958-T1
Valid prediction for snap_scaffold_16-snap.431-T1
Valid prediction for GlimmerHMM_glimmerT_37947-T1
Valid prediction for GlimmerHMM_glimmerT_37962-T1
Valid prediction for snap_scaffold_16-snap.438-T1
Valid prediction for snap_scaffold_16-snap.426-T1
Valid prediction for snap_scaffold_16-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_37974-T1
Valid prediction for snap_scaffold_16-snap.427-T1
Valid prediction for GlimmerHMM_glimmerT_37951-T1
Valid prediction for Augustus_model.g25302.t1
Valid prediction for snap_scaffold_16-snap.450-T1
Valid prediction for snap_scaffold_16-snap.433-T1
Valid prediction for GlimmerHMM_glimmerT_37970-T1
Valid prediction for snap_scaffold_16-snap.420-T1
Valid prediction for Augustus_model.g25317.t1
Valid prediction for Augustus_model.g25322.t1
Valid prediction for GlimmerHMM_glimmerT_37956-T1
Valid prediction for GlimmerHMM_glimmerT_37952-T1
Valid prediction for GlimmerHMM_glimmerT_37976-T1
Valid prediction for snap_scaffold_16-snap.439-T1
Valid prediction for Augustus_model.g25315.t1
Valid prediction for snap_scaffold_16-snap.463-T1
Valid prediction for snap_scaffold_16-snap.449-T1
Valid prediction for snap_scaffold_16-snap.419-T1
Valid prediction for Augustus_model.g25323.t1
Valid prediction for snap_scaffold_16-snap.453-T1
Valid prediction for Augustus_model.g25325.t1
Valid prediction for snap_scaffold_16-snap.428-T1
Valid prediction for snap_scaffold_16-snap.423-T1
Valid prediction for snap_scaffold_16-snap.436-T1
Valid prediction for snap_scaffold_16-snap.455-T1
Valid prediction for GlimmerHMM_glimmerT_37946-T1
Valid prediction for snap_scaffold_16-snap.454-T1
Valid prediction for Augustus_model.g25324.t1
Valid prediction for snap_scaffold_16-snap.444-T1
Valid prediction for GlimmerHMM_glimmerT_37954-T1
Valid prediction for GlimmerHMM_glimmerT_37972-T1
Valid prediction for GlimmerHMM_glimmerT_37965-T1
Valid prediction for Augustus_model.g25305.t1
Valid prediction for GlimmerHMM_glimmerT_37960-T1
Valid prediction for GlimmerHMM_glimmerT_37973-T1
Valid prediction for Augustus_model.g25309.t1
Valid prediction for GlimmerHMM_glimmerT_37966-T1
Valid prediction for GlimmerHMM_glimmerT_37950-T1
Valid prediction for snap_scaffold_16-snap.456-T1
Valid prediction for snap_scaffold_16-snap.460-T1
Valid prediction for GlimmerHMM_glimmerT_37949-T1
Valid prediction for snap_scaffold_16-snap.447-T1
Valid prediction for GlimmerHMM_glimmerT_37978-T1
Valid prediction for Augustus_model.g25306.t1
Valid prediction for snap_scaffold_16-snap.430-T1
Valid prediction for GlimmerHMM_glimmerT_37980-T1
Valid prediction for snap_scaffold_16-snap.434-T1
Valid prediction for GlimmerHMM_glimmerT_37959-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.g25318.t1
Valid prediction for snap_scaffold_16-snap.461-T1
Couldn't classify 83900, 83915
Sorry, prediction pasa_asmbl_16974.p1 fails validation.
(GCG)	 TG	83900-83915	GT	GGG
(TCC)	 AG	86297-86419	GT	GGG
(CCC)	 AG	87279-87427	GT	AGG
(GTG)	 AG	87579-87700	GT	GGG
(GAG)	 AG	88758-88956	GT	AGG
(GCG)	 AG	89142-89269	GT	AGG
(GAT)	 AG	89443-89512	GA	GAG
-recovered pasa_asmbl_16974.p1, terminal, 89443, 89512
-recovered pasa_asmbl_16974.p1, internal, 86297, 86419
-recovered pasa_asmbl_16974.p1, internal, 87279, 87427
-recovered pasa_asmbl_16974.p1, internal, 87579, 87700
-recovered pasa_asmbl_16974.p1, internal, 88758, 88956
-recovered pasa_asmbl_16974.p1, internal, 89142, 89269
Valid prediction for snap_scaffold_16-snap.416-T1
Valid prediction for snap_scaffold_16-snap.462-T1
Valid prediction for Augustus_model.g25301.t1
Valid prediction for snap_scaffold_16-snap.458-T1
Valid prediction for GlimmerHMM_glimmerT_37961-T1
Valid prediction for HiQ_model.g25312.t1
Valid prediction for Augustus_model.g25308.t1
Valid prediction for snap_scaffold_16-snap.459-T1
Valid prediction for snap_scaffold_16-snap.457-T1
Valid prediction for Augustus_model.g25311.t1
Valid prediction for snap_scaffold_16-snap.429-T1
Valid prediction for snap_scaffold_16-snap.432-T1
Valid prediction for snap_scaffold_16-snap.437-T1
Valid prediction for snap_scaffold_16-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_37967-T1
Valid prediction for GlimmerHMM_glimmerT_37955-T1
Valid prediction for Augustus_model.g25310.t1
Valid prediction for GlimmerHMM_glimmerT_37968-T1
Valid prediction for GlimmerHMM_glimmerT_37964-T1
Valid prediction for GlimmerHMM_glimmerT_37979-T1
Valid prediction for snap_scaffold_16-snap.421-T1
Valid prediction for snap_scaffold_16-snap.452-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.446-T1
Valid prediction for GlimmerHMM_glimmerT_37948-T1
Valid prediction for snap_scaffold_16-snap.442-T1
Valid prediction for snap_scaffold_16-snap.435-T1
Valid prediction for GlimmerHMM_glimmerT_37981-T1
Valid prediction for GlimmerHMM_glimmerT_37971-T1
Valid prediction for GlimmerHMM_glimmerT_37975-T1
Valid prediction for Augustus_model.g25314.t1
Valid prediction for Augustus_model.g25304.t1
Valid prediction for GlimmerHMM_glimmerT_37953-T1
Valid prediction for Augustus_model.g25313.t1
Valid prediction for snap_scaffold_16-snap.418-T1
Valid prediction for Augustus_model.g25303.t1
Valid prediction for Augustus_model.g25316.t1
Valid prediction for snap_scaffold_16-snap.441-T1
Valid prediction for snap_scaffold_16-snap.443-T1
Valid prediction for Augustus_model.g25320.t1
Valid prediction for snap_scaffold_16-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_37977-T1
Valid prediction for snap_scaffold_16-snap.448-T1
Couldn't classify 98213, 98304
Sorry, prediction pasa_asmbl_16971.p1 fails validation.
(ATG)	 AA	95520-95595	GT	AGG
(GGG)	 AG	97219-97497	GT	AGG
(ATC)	 AG	98213-98304	GC	CGG
-recovered pasa_asmbl_16971.p1, initial, 95520, 95595
-recovered pasa_asmbl_16971.p1, internal, 97219, 97497
-recovered pasa_asmbl_16971.p1, internal, 98213, 98304
Valid prediction for CodingQuarry_transcript_19912-T1
Valid prediction for snap_scaffold_16-snap.424-T1
Valid prediction for snap_scaffold_16-snap.440-T1
Valid prediction for Augustus_model.g25326.t1
Valid prediction for GlimmerHMM_glimmerT_37963-T1
Valid prediction for Augustus_model.g25307.t1
Valid prediction for snap_scaffold_16-snap.451-T1
Valid prediction for GlimmerHMM_glimmerT_37957-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 81096, rend_intergenic: 81093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5450, rend_intergenic: 4586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16321, rend_intergenic: 5465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23253, rend_intergenic: 16343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29104, rend_intergenic: 23859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36404, rend_intergenic: 29752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37448, rend_intergenic: 37101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56610, rend_intergenic: 37544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59313, rend_intergenic: 57403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65540, rend_intergenic: 63211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67669, rend_intergenic: 65754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72194, rend_intergenic: 68988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79534, rend_intergenic: 75632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86632, rend_intergenic: 83384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123541, rend_intergenic: 117188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127573, rend_intergenic: 126022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127769, rend_intergenic: 127658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131470, rend_intergenic: 127785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141970, rend_intergenic: 134246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151993, rend_intergenic: 142040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166943, rend_intergenic: 156060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170349, rend_intergenic: 167231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181713, rend_intergenic: 171308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187428
-exon list size: 462


building trellis

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-found 41 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 81096, rend_intergenic: 81093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5450, rend_intergenic: 4586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16321, rend_intergenic: 5465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23253, rend_intergenic: 16343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29104, rend_intergenic: 23859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36404, rend_intergenic: 29752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37448, rend_intergenic: 37101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56610, rend_intergenic: 37544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59313, rend_intergenic: 57403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65540, rend_intergenic: 63211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67669, rend_intergenic: 65754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72194, rend_intergenic: 68988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79534, rend_intergenic: 75632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86632, rend_intergenic: 83384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123541, rend_intergenic: 117188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127573, rend_intergenic: 126022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127769, rend_intergenic: 127658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131470, rend_intergenic: 127785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141970, rend_intergenic: 134246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151993, rend_intergenic: 142040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166943, rend_intergenic: 156060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170349, rend_intergenic: 167231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181713, rend_intergenic: 171308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support