-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_21133832-21306982

-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 HiQ_model.g2026.t1
Valid prediction for GeneMark_model.4559_t
Valid prediction for GeneMark_model.4573_t
Valid prediction for Augustus_model.g2028.t1
Valid prediction for GlimmerHMM_glimmerT_2917-T1
Valid prediction for snap_scaffold_1-snap.4016-T1
Valid prediction for snap_scaffold_1-snap.4019-T1
Valid prediction for CodingQuarry_transcript_3042-T1
Valid prediction for snap_scaffold_1-snap.4020-T1
Valid prediction for GlimmerHMM_glimmerT_2909-T1
Valid prediction for Augustus_model.g2030.t1
Valid prediction for GeneMark_model.4561_t
Valid prediction for snap_scaffold_1-snap.4010-T1
Valid prediction for GeneMark_model.4601_t
Valid prediction for snap_scaffold_1-snap.4036-T1
Valid prediction for GeneMark_model.4599_t
Valid prediction for GeneMark_model.4570_t
Valid prediction for pasa_asmbl_2663.p1
Couldn't classify 114325, 114411
Couldn't classify 119554, 119582
Sorry, prediction pasa_asmbl_2665.p1 fails validation.
(TCC)	 GC	114325-114411	GT	AGG
(GTG)	 AG	116015-116111	GT	AGG
(AGG)	 AG	116895-117142	GT	AGG
(ACC)	 AG	117700-117769	GT	AGG
(CTG)	 AG	118531-118685	GT	CAG
(AGA)	 AG	119185-119350	GT	AGG
(AGA)	 AG	119554-119582	TC	CCT
-recovered pasa_asmbl_2665.p1, internal, 116015, 116111
-recovered pasa_asmbl_2665.p1, internal, 116895, 117142
-recovered pasa_asmbl_2665.p1, internal, 117700, 117769
-recovered pasa_asmbl_2665.p1, internal, 118531, 118685
-recovered pasa_asmbl_2665.p1, internal, 119185, 119350
Valid prediction for GeneMark_model.4587_t
Valid prediction for GlimmerHMM_glimmerT_2907-T1
Valid prediction for snap_scaffold_1-snap.4009-T1
Valid prediction for snap_scaffold_1-snap.4023-T1
Valid prediction for Augustus_model.g2033.t1
Valid prediction for Augustus_model.g2031.t1
Valid prediction for GlimmerHMM_glimmerT_2905-T1
Valid prediction for Augustus_model.g2029.t1
Valid prediction for GlimmerHMM_glimmerT_2920-T1
Valid prediction for GeneMark_model.4577_t
Valid prediction for GeneMark_model.4566_t
Valid prediction for GeneMark_model.4596_t
Valid prediction for snap_scaffold_1-snap.4039-T1
Valid prediction for snap_scaffold_1-snap.4005-T1
Valid prediction for snap_scaffold_1-snap.4021-T1
Valid prediction for GlimmerHMM_glimmerT_2910-T1
Valid prediction for GeneMark_model.4574_t
Valid prediction for snap_scaffold_1-snap.4006-T1
Valid prediction for GeneMark_model.4582_t
Valid prediction for GeneMark_model.4580_t
Valid prediction for snap_scaffold_1-snap.4033-T1
Valid prediction for Augustus_model.g2027.t1
Valid prediction for GeneMark_model.4571_t
Valid prediction for GlimmerHMM_glimmerT_2912-T1
Valid prediction for snap_scaffold_1-snap.4029-T1
Valid prediction for GeneMark_model.4563_t
add_exon() Sorry, GeneMark_model.4563_t 28925-29168-terminal-1 is invalid.
Valid prediction for GeneMark_model.4590_t
Valid prediction for snap_scaffold_1-snap.4024-T1
Valid prediction for GlimmerHMM_glimmerT_2922-T1
Valid prediction for GeneMark_model.4565_t
Valid prediction for snap_scaffold_1-snap.4025-T1
Valid prediction for GeneMark_model.4567_t
Valid prediction for GeneMark_model.4595_t
Valid prediction for GlimmerHMM_glimmerT_2911-T1
Valid prediction for snap_scaffold_1-snap.4028-T1
Valid prediction for snap_scaffold_1-snap.4017-T1
Valid prediction for snap_scaffold_1-snap.4012-T1
Valid prediction for GeneMark_model.4578_t
Valid prediction for GlimmerHMM_glimmerT_2916-T1
Valid prediction for GeneMark_model.4585_t
Valid prediction for GeneMark_model.4592_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.4591_t
Valid prediction for GeneMark_model.4576_t
Valid prediction for snap_scaffold_1-snap.4015-T1
Valid prediction for GeneMark_model.4575_t
Valid prediction for GeneMark_model.4600_t
Valid prediction for GeneMark_model.4579_t
Valid prediction for GeneMark_model.4560_t
Valid prediction for Augustus_model.g2034.t1
Valid prediction for snap_scaffold_1-snap.4011-T1
Valid prediction for snap_scaffold_1-snap.4030-T1
Valid prediction for snap_scaffold_1-snap.4026-T1
Valid prediction for GeneMark_model.4602_t
Valid prediction for GeneMark_model.4584_t
Valid prediction for GeneMark_model.4586_t
Valid prediction for GeneMark_model.4562_t
Valid prediction for snap_scaffold_1-snap.4031-T1
Valid prediction for GeneMark_model.4598_t
add_exon() Sorry, GeneMark_model.4598_t 20757-21123-terminal-1 is invalid.
Valid prediction for GeneMark_model.4583_t
Valid prediction for Augustus_model.g2024.t1
Valid prediction for GeneMark_model.4588_t
Valid prediction for GlimmerHMM_glimmerT_2914-T1
Valid prediction for GlimmerHMM_glimmerT_2915-T1
Valid prediction for snap_scaffold_1-snap.4027-T1
Valid prediction for GeneMark_model.4593_t
Valid prediction for snap_scaffold_1-snap.4007-T1
Valid prediction for snap_scaffold_1-snap.4008-T1
Valid prediction for GlimmerHMM_glimmerT_2918-T1
Valid prediction for Augustus_model.g2032.t1
Valid prediction for snap_scaffold_1-snap.4014-T1
Valid prediction for GeneMark_model.4572_t
Valid prediction for snap_scaffold_1-snap.4037-T1
Valid prediction for GeneMark_model.4581_t
Valid prediction for GlimmerHMM_glimmerT_2906-T1
Valid prediction for GeneMark_model.4569_t
Valid prediction for GlimmerHMM_glimmerT_2921-T1
Valid prediction for snap_scaffold_1-snap.4018-T1
Valid prediction for GlimmerHMM_glimmerT_2908-T1
Valid prediction for GeneMark_model.4564_t
Valid prediction for GeneMark_model.4589_t
Valid prediction for Augustus_model.g2025.t1
Valid prediction for snap_scaffold_1-snap.4032-T1
Valid prediction for snap_scaffold_1-snap.4022-T1
Valid prediction for GlimmerHMM_glimmerT_2913-T1
Valid prediction for GeneMark_model.4594_t
Valid prediction for GeneMark_model.4568_t
Valid prediction for GeneMark_model.4597_t
Valid prediction for snap_scaffold_1-snap.4035-T1
Valid prediction for snap_scaffold_1-snap.4038-T1
Valid prediction for GlimmerHMM_glimmerT_2919-T1
Valid prediction for GlimmerHMM_glimmerT_2904-T1
Valid prediction for snap_scaffold_1-snap.4013-T1
Valid prediction for snap_scaffold_1-snap.4034-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9144, rend_intergenic: 7816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41707, rend_intergenic: 15312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52087, rend_intergenic: 44989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54329, rend_intergenic: 52376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65742, rend_intergenic: 62278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77682, rend_intergenic: 71438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89267, rend_intergenic: 86800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105948, rend_intergenic: 102549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120334, rend_intergenic: 106219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126611, rend_intergenic: 122319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133566, rend_intergenic: 133136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136046, rend_intergenic: 133950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149683, rend_intergenic: 144460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165183, rend_intergenic: 149993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171089, rend_intergenic: 165263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173151
-exon list size: 589


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 9144, rend_intergenic: 7816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41707, rend_intergenic: 15312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52087, rend_intergenic: 44989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54329, rend_intergenic: 52376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65742, rend_intergenic: 62278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77682, rend_intergenic: 71438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89267, rend_intergenic: 86800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105948, rend_intergenic: 102549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120334, rend_intergenic: 106219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126611, rend_intergenic: 122319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133566, rend_intergenic: 133136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136046, rend_intergenic: 133950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149683, rend_intergenic: 144460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165183, rend_intergenic: 149993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171089, rend_intergenic: 165263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support