-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_9656766-9845998

-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.g2993.t1
Valid prediction for GeneMark_model.7157_t
Valid prediction for GeneMark_model.7114_t
Valid prediction for GeneMark_model.7141_t
Valid prediction for GeneMark_model.7152_t
Valid prediction for GeneMark_model.7148_t
Valid prediction for snap_scaffold_2-snap.1956-T1
Valid prediction for snap_scaffold_2-snap.1952-T1
Couldn't classify 15264, 15316
Couldn't classify 15688, 15830
Sorry, prediction pasa_asmbl_25427.p1 fails validation.
(CAT)	 CT	15264-15316	GT	AAG
(GCC)	 AG	15399-15505	GT	AGG
(GGA)	 AG	15688-15830	GT	AGG
-recovered pasa_asmbl_25427.p1, internal, 15399, 15505
-recovered pasa_asmbl_25427.p1, internal, 15688, 15830
Valid prediction for snap_scaffold_2-snap.1957-T1
Valid prediction for GlimmerHMM_glimmerT_4460-T1
Valid prediction for GlimmerHMM_glimmerT_4453-T1
Valid prediction for snap_scaffold_2-snap.1944-T1
Valid prediction for snap_scaffold_2-snap.1946-T1
Valid prediction for pasa_asmbl_24721.p1
Valid prediction for GeneMark_model.7135_t
Valid prediction for GeneMark_model.7162_t
Valid prediction for snap_scaffold_2-snap.1962-T1
Valid prediction for Augustus_model.g2979.t1
Valid prediction for GeneMark_model.7127_t
Valid prediction for GeneMark_model.7116_t
Valid prediction for snap_scaffold_2-snap.1965-T1
Valid prediction for snap_scaffold_2-snap.1947-T1
Valid prediction for GeneMark_model.7136_t
Valid prediction for Augustus_model.g2985.t1
Valid prediction for snap_scaffold_2-snap.1959-T1
Valid prediction for GeneMark_model.7118_t
Valid prediction for GlimmerHMM_glimmerT_4450-T1
Valid prediction for GlimmerHMM_glimmerT_4449-T1
Valid prediction for snap_scaffold_2-snap.1969-T1
Valid prediction for GlimmerHMM_glimmerT_4429-T1
Valid prediction for GeneMark_model.7144_t
Valid prediction for snap_scaffold_2-snap.1951-T1
Valid prediction for HiQ_model.g2989.t1
Valid prediction for GeneMark_model.7137_t
Valid prediction for GeneMark_model.7154_t
Valid prediction for GeneMark_model.7140_t
Valid prediction for GlimmerHMM_glimmerT_4447-T1
Valid prediction for GeneMark_model.7129_t
Valid prediction for GlimmerHMM_glimmerT_4432-T1
Valid prediction for GeneMark_model.7122_t
Valid prediction for Augustus_model.g2982.t1
Valid prediction for snap_scaffold_2-snap.1970-T1
Valid prediction for GlimmerHMM_glimmerT_4442-T1
Valid prediction for GeneMark_model.7124_t
Valid prediction for GlimmerHMM_glimmerT_4435-T1
Valid prediction for GeneMark_model.7139_t
Valid prediction for snap_scaffold_2-snap.1964-T1
Valid prediction for snap_scaffold_2-snap.1961-T1
Valid prediction for snap_scaffold_2-snap.1954-T1
Valid prediction for snap_scaffold_2-snap.1966-T1
Valid prediction for GlimmerHMM_glimmerT_4431-T1
Valid prediction for GlimmerHMM_glimmerT_4446-T1
Valid prediction for Augustus_model.g2987.t1
Valid prediction for GlimmerHMM_glimmerT_4439-T1
Valid prediction for GlimmerHMM_glimmerT_4445-T1
Valid prediction for GlimmerHMM_glimmerT_4437-T1
Valid prediction for snap_scaffold_2-snap.1974-T1
Valid prediction for GeneMark_model.7120_t
Valid prediction for GlimmerHMM_glimmerT_4457-T1
Valid prediction for snap_scaffold_2-snap.1967-T1
Valid prediction for GeneMark_model.7160_t
Valid prediction for GeneMark_model.7156_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 GeneMark_model.7128_t
Valid prediction for pasa_asmbl_23403.p1
Valid prediction for GlimmerHMM_glimmerT_4430-T1
Valid prediction for snap_scaffold_2-snap.1980-T1
Valid prediction for GeneMark_model.7159_t
Valid prediction for GeneMark_model.7133_t
Valid prediction for GlimmerHMM_glimmerT_4454-T1
Valid prediction for GeneMark_model.7145_t
Valid prediction for GeneMark_model.7150_t
Valid prediction for snap_scaffold_2-snap.1979-T1
Valid prediction for snap_scaffold_2-snap.1977-T1
Valid prediction for GlimmerHMM_glimmerT_4436-T1
Valid prediction for snap_scaffold_2-snap.1971-T1
Valid prediction for GlimmerHMM_glimmerT_4444-T1
Valid prediction for GeneMark_model.7155_t
Couldn't classify 43372, 43447
Couldn't classify 44705, 44820
Sorry, prediction pasa_asmbl_23404.p1 fails validation.
(AGG)	 CA	43372-43447	GT	AGG
(TGT)	 AG	43870-44035	GT	AAG
(ATT)	 AG	44431-44570	GT	AGG
(ATG)	 AG	44705-44820	GC	AAG
add_exon() Sorry, pasa_asmbl_23404.p1 44705-44820-initial-1 is invalid.
-recovered pasa_asmbl_23404.p1, initial, 44705, 44820
-recovered pasa_asmbl_23404.p1, internal, 43870, 44035
-recovered pasa_asmbl_23404.p1, internal, 44431, 44570
-recovered pasa_asmbl_23404.p1, internal, 44705, 44820
Valid prediction for snap_scaffold_2-snap.1978-T1
Valid prediction for GeneMark_model.7117_t
Valid prediction for GeneMark_model.7146_t
Valid prediction for GeneMark_model.7161_t
Valid prediction for Augustus_model.g2991.t1
Valid prediction for GlimmerHMM_glimmerT_4434-T1
Valid prediction for GeneMark_model.7158_t
Valid prediction for GlimmerHMM_glimmerT_4458-T1
Valid prediction for Augustus_model.g2983.t1
Valid prediction for Augustus_model.g2986.t1
Valid prediction for GeneMark_model.7121_t
Valid prediction for GeneMark_model.7153_t
Valid prediction for GlimmerHMM_glimmerT_4455-T1
Valid prediction for GlimmerHMM_glimmerT_4433-T1
Valid prediction for GlimmerHMM_glimmerT_4452-T1
Valid prediction for GeneMark_model.7130_t
Valid prediction for GeneMark_model.7143_t
Valid prediction for snap_scaffold_2-snap.1945-T1
Valid prediction for GeneMark_model.7134_t
Valid prediction for GlimmerHMM_glimmerT_4456-T1
Valid prediction for snap_scaffold_2-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_4448-T1
Valid prediction for snap_scaffold_2-snap.1973-T1
Valid prediction for snap_scaffold_2-snap.1963-T1
Valid prediction for snap_scaffold_2-snap.1960-T1
Valid prediction for HiQ_model.g2990.t1
Valid prediction for HiQ_model.g2988.t1
Valid prediction for snap_scaffold_2-snap.1949-T1
Valid prediction for snap_scaffold_2-snap.1958-T1
Valid prediction for snap_scaffold_2-snap.1975-T1
Valid prediction for GlimmerHMM_glimmerT_4441-T1
Valid prediction for CodingQuarry_transcript_28598-T1
Valid prediction for GlimmerHMM_glimmerT_4440-T1
Valid prediction for GeneMark_model.7125_t
Valid prediction for GlimmerHMM_glimmerT_4438-T1
Valid prediction for GlimmerHMM_glimmerT_4443-T1
Valid prediction for Augustus_model.g2980.t1
Valid prediction for pasa_asmbl_23405.p1
Valid prediction for GlimmerHMM_glimmerT_4451-T1
Valid prediction for CodingQuarry_transcript_28597-T1
Valid prediction for Augustus_model.g2996.t1
Valid prediction for GeneMark_model.7115_t
Valid prediction for GeneMark_model.7123_t
Valid prediction for GeneMark_model.7138_t
Valid prediction for GeneMark_model.7132_t
Valid prediction for snap_scaffold_2-snap.1953-T1
Valid prediction for GeneMark_model.7142_t
Valid prediction for GeneMark_model.7131_t
Valid prediction for HiQ_model.g2994.t1
Valid prediction for snap_scaffold_2-snap.1950-T1
Valid prediction for snap_scaffold_2-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_4459-T1
Valid prediction for Augustus_model.g2992.t1
Valid prediction for Augustus_model.g2984.t1
Valid prediction for pasa_asmbl_23402.p1
Valid prediction for snap_scaffold_2-snap.1976-T1
Valid prediction for GeneMark_model.7119_t
Valid prediction for snap_scaffold_2-snap.1972-T1
Valid prediction for Augustus_model.g2981.t1
Valid prediction for snap_scaffold_2-snap.1955-T1
Valid prediction for Augustus_model.g2995.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11086, rend_intergenic: 2984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15266, rend_intergenic: 12006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33650, rend_intergenic: 18124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48073, rend_intergenic: 44875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60007, rend_intergenic: 52744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73011, rend_intergenic: 61306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83634, rend_intergenic: 73661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83939, rend_intergenic: 83663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95242, rend_intergenic: 86904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107350, rend_intergenic: 100722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118480, rend_intergenic: 117322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122662, rend_intergenic: 118486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189233
-exon list size: 657


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 11086, rend_intergenic: 2984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15266, rend_intergenic: 12006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33650, rend_intergenic: 18124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48073, rend_intergenic: 44875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60007, rend_intergenic: 52744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73011, rend_intergenic: 61306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83634, rend_intergenic: 73661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83939, rend_intergenic: 83663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95242, rend_intergenic: 86904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107350, rend_intergenic: 100722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118480, rend_intergenic: 117322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122662, rend_intergenic: 118486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support