-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_19400082-19580349

-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_3-snap.3860-T1
Valid prediction for GlimmerHMM_glimmerT_8689-T1
Valid prediction for GlimmerHMM_glimmerT_8690-T1
Valid prediction for GeneMark_model.14101_t
Valid prediction for snap_scaffold_3-snap.3870-T1
Valid prediction for snap_scaffold_3-snap.3845-T1
Valid prediction for Augustus_model.g5748.t1
Valid prediction for snap_scaffold_3-snap.3879-T1
Valid prediction for GeneMark_model.14105_t
Valid prediction for GeneMark_model.14116_t
Valid prediction for Augustus_model.g5749.t1
Valid prediction for GeneMark_model.14103_t
Valid prediction for GeneMark_model.14121_t
Valid prediction for GeneMark_model.14098_t
Valid prediction for snap_scaffold_3-snap.3850-T1
Valid prediction for GlimmerHMM_glimmerT_8662-T1
Valid prediction for snap_scaffold_3-snap.3857-T1
Valid prediction for GlimmerHMM_glimmerT_8674-T1
Valid prediction for GlimmerHMM_glimmerT_8682-T1
Valid prediction for GeneMark_model.14093_t
Valid prediction for GeneMark_model.14118_t
Valid prediction for GlimmerHMM_glimmerT_8673-T1
Valid prediction for GlimmerHMM_glimmerT_8685-T1
Valid prediction for GeneMark_model.14087_t
Valid prediction for GlimmerHMM_glimmerT_8671-T1
Valid prediction for GlimmerHMM_glimmerT_8661-T1
Valid prediction for GlimmerHMM_glimmerT_8668-T1
Valid prediction for GlimmerHMM_glimmerT_8664-T1
Valid prediction for GlimmerHMM_glimmerT_8670-T1
Valid prediction for snap_scaffold_3-snap.3868-T1
Valid prediction for GlimmerHMM_glimmerT_8691-T1
Valid prediction for GeneMark_model.14114_t
Valid prediction for snap_scaffold_3-snap.3858-T1
Valid prediction for GlimmerHMM_glimmerT_8683-T1
Valid prediction for Augustus_model.g5745.t1
Valid prediction for Augustus_model.g5751.t1
Valid prediction for GeneMark_model.14081_t
Couldn't classify 62075, 62204
Sorry, prediction pasa_asmbl_40766.p1 fails validation.
(GGG)	 GA	62075-62204	GT	AGG
(ATA)	 AG	64089-64256	GT	AGG
(GGA)	 AG	64888-65044	GT	AGG
(GTA)	 AG	66540-66664	GT	GGG
(GAA)	 AG	68624-68754	GT	AGG
(GCT)	 AG	69691-69816	CC	AGC
-recovered pasa_asmbl_40766.p1, terminal, 69691, 69816
-recovered pasa_asmbl_40766.p1, internal, 64089, 64256
-recovered pasa_asmbl_40766.p1, internal, 64888, 65044
-recovered pasa_asmbl_40766.p1, internal, 66540, 66664
-recovered pasa_asmbl_40766.p1, internal, 68624, 68754
Valid prediction for Augustus_model.g5746.t1
Valid prediction for GeneMark_model.14122_t
Valid prediction for GlimmerHMM_glimmerT_8666-T1
Valid prediction for snap_scaffold_3-snap.3861-T1
Valid prediction for GeneMark_model.14120_t
Valid prediction for GeneMark_model.14095_t
Valid prediction for GeneMark_model.14083_t
Valid prediction for GeneMark_model.14110_t
Valid prediction for GeneMark_model.14107_t
Valid prediction for snap_scaffold_3-snap.3854-T1
Valid prediction for GlimmerHMM_glimmerT_8675-T1
Valid prediction for GlimmerHMM_glimmerT_8692-T1
Valid prediction for snap_scaffold_3-snap.3874-T1
Valid prediction for GlimmerHMM_glimmerT_8688-T1
Valid prediction for snap_scaffold_3-snap.3864-T1
Valid prediction for GlimmerHMM_glimmerT_8672-T1
Valid prediction for snap_scaffold_3-snap.3849-T1
Valid prediction for GlimmerHMM_glimmerT_8680-T1
Valid prediction for snap_scaffold_3-snap.3878-T1
Valid prediction for snap_scaffold_3-snap.3843-T1
Valid prediction for Augustus_model.g5752.t1
Valid prediction for GeneMark_model.14096_t
Valid prediction for GlimmerHMM_glimmerT_8660-T1
Valid prediction for snap_scaffold_3-snap.3875-T1
Valid prediction for GeneMark_model.14097_t
Valid prediction for Augustus_model.g5750.t1
Valid prediction for GlimmerHMM_glimmerT_8686-T1
Valid prediction for GlimmerHMM_glimmerT_8676-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 GlimmerHMM_glimmerT_8677-T1
Valid prediction for GlimmerHMM_glimmerT_8669-T1
Valid prediction for snap_scaffold_3-snap.3863-T1
Valid prediction for snap_scaffold_3-snap.3873-T1
Valid prediction for GeneMark_model.14094_t
Valid prediction for GlimmerHMM_glimmerT_8667-T1
Valid prediction for CodingQuarry_transcript_46377-T1
Valid prediction for GeneMark_model.14104_t
Valid prediction for GeneMark_model.14086_t
Valid prediction for GeneMark_model.14119_t
Valid prediction for snap_scaffold_3-snap.3851-T1
Valid prediction for snap_scaffold_3-snap.3872-T1
Valid prediction for GeneMark_model.14099_t
Valid prediction for snap_scaffold_3-snap.3853-T1
Valid prediction for GeneMark_model.14091_t
Valid prediction for snap_scaffold_3-snap.3862-T1
Valid prediction for snap_scaffold_3-snap.3847-T1
Valid prediction for GeneMark_model.14090_t
Couldn't classify 92733, 92836
Couldn't classify 95002, 95055
Sorry, prediction pasa_asmbl_39600.p1 fails validation.
(AAC)	 AT	92733-92836	GT	AGG
(ATG)	 AG	93025-93142	GT	AGG
(ATC)	 AG	93556-93882	GT	TGG
(GTT)	 AG	94295-94378	GT	AGG
(AGT)	 AG	94597-94743	GT	TGG
(GCG)	 AG	95002-95055	CT	GGC
-recovered pasa_asmbl_39600.p1, initial, 93025, 93142
-recovered pasa_asmbl_39600.p1, internal, 93025, 93142
-recovered pasa_asmbl_39600.p1, internal, 93556, 93882
-recovered pasa_asmbl_39600.p1, internal, 94295, 94378
-recovered pasa_asmbl_39600.p1, internal, 94597, 94743
Valid prediction for GeneMark_model.14082_t
Valid prediction for GeneMark_model.14106_t
Valid prediction for snap_scaffold_3-snap.3866-T1
Valid prediction for GlimmerHMM_glimmerT_8679-T1
Valid prediction for Augustus_model.g5753.t1
Valid prediction for GeneMark_model.14112_t
Valid prediction for GlimmerHMM_glimmerT_8665-T1
Valid prediction for GeneMark_model.14113_t
Valid prediction for Augustus_model.g5747.t1
Valid prediction for GlimmerHMM_glimmerT_8684-T1
Valid prediction for GeneMark_model.14085_t
Valid prediction for GeneMark_model.14088_t
Valid prediction for snap_scaffold_3-snap.3871-T1
Valid prediction for GeneMark_model.14089_t
Valid prediction for GeneMark_model.14092_t
Valid prediction for GlimmerHMM_glimmerT_8687-T1
Valid prediction for snap_scaffold_3-snap.3856-T1
Valid prediction for snap_scaffold_3-snap.3869-T1
Valid prediction for snap_scaffold_3-snap.3867-T1
Valid prediction for GlimmerHMM_glimmerT_8663-T1
Couldn't classify 89358, 90107
Sorry, prediction pasa_asmbl_39601.p1 fails validation.
(CAC)	 AA	89358-90107	GT	CCG
Valid prediction for CodingQuarry_transcript_46378-T1
Valid prediction for GlimmerHMM_glimmerT_8659-T1
Valid prediction for snap_scaffold_3-snap.3865-T1
Valid prediction for Augustus_model.g5754.t1
Valid prediction for snap_scaffold_3-snap.3848-T1
Valid prediction for snap_scaffold_3-snap.3846-T1
Valid prediction for snap_scaffold_3-snap.3855-T1
Valid prediction for GeneMark_model.14109_t
Valid prediction for GeneMark_model.14102_t
Valid prediction for snap_scaffold_3-snap.3877-T1
Valid prediction for GeneMark_model.14111_t
Valid prediction for pasa_asmbl_39594.p1
Valid prediction for GeneMark_model.14115_t
Valid prediction for GeneMark_model.14117_t
Valid prediction for GlimmerHMM_glimmerT_8678-T1
Valid prediction for snap_scaffold_3-snap.3852-T1
Valid prediction for snap_scaffold_3-snap.3859-T1
Valid prediction for HiQ_model.g5744.t1
Valid prediction for GlimmerHMM_glimmerT_8681-T1
Valid prediction for snap_scaffold_3-snap.3844-T1
Valid prediction for snap_scaffold_3-snap.3880-T1
Valid prediction for snap_scaffold_3-snap.3876-T1
Valid prediction for GeneMark_model.14084_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 36572, rend_intergenic: 36569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13849, rend_intergenic: 12198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24464, rend_intergenic: 16957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35806, rend_intergenic: 25650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43554, rend_intergenic: 36361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67177, rend_intergenic: 52540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71173, rend_intergenic: 68238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83353, rend_intergenic: 77399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107439, rend_intergenic: 102583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110276, rend_intergenic: 109402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121207, rend_intergenic: 118592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133913, rend_intergenic: 122095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151435, rend_intergenic: 147913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170841, rend_intergenic: 158990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180268
-exon list size: 635


building trellis

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-found 33 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 36572, rend_intergenic: 36569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13849, rend_intergenic: 12198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24464, rend_intergenic: 16957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35806, rend_intergenic: 25650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43554, rend_intergenic: 36361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67177, rend_intergenic: 52540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71173, rend_intergenic: 68238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83353, rend_intergenic: 77399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107439, rend_intergenic: 102583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110276, rend_intergenic: 109402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121207, rend_intergenic: 118592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133913, rend_intergenic: 122095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151435, rend_intergenic: 147913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170841, rend_intergenic: 158990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support