-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_10349903-10550582

-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_2-snap.2071-T1
Valid prediction for GeneMark_model.7269_t
Valid prediction for Augustus_model.g3036.t1
Valid prediction for snap_scaffold_2-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_4534-T1
Valid prediction for GlimmerHMM_glimmerT_4526-T1
Valid prediction for snap_scaffold_2-snap.2073-T1
Valid prediction for GeneMark_model.7283_t
Valid prediction for Augustus_model.g3034.t1
Valid prediction for snap_scaffold_2-snap.2077-T1
Valid prediction for GeneMark_model.7266_t
Couldn't classify 42825, 43293
Couldn't classify 45070, 45255
Sorry, prediction pasa_asmbl_24739.p1 fails validation.
(GAA)	 CA	42825-43293	GT	CGG
(TCC)	 AG	43614-43738	GT	AAG
(CGT)	 AG	45070-45255	GA	AGG
-recovered pasa_asmbl_24739.p1, internal, 43614, 43738
Valid prediction for GlimmerHMM_glimmerT_4524-T1
Valid prediction for GeneMark_model.7264_t
Valid prediction for GeneMark_model.7271_t
Valid prediction for snap_scaffold_2-snap.2083-T1
Valid prediction for CodingQuarry_transcript_28605-T1
Valid prediction for snap_scaffold_2-snap.2079-T1
Valid prediction for snap_scaffold_2-snap.2076-T1
Valid prediction for GeneMark_model.7277_t
Valid prediction for GeneMark_model.7281_t
Valid prediction for snap_scaffold_2-snap.2098-T1
Valid prediction for GeneMark_model.7253_t
Valid prediction for snap_scaffold_2-snap.2100-T1
Valid prediction for GeneMark_model.7262_t
Valid prediction for GeneMark_model.7258_t
Valid prediction for GeneMark_model.7246_t
Valid prediction for GeneMark_model.7272_t
Valid prediction for GeneMark_model.7251_t
Valid prediction for snap_scaffold_2-snap.2070-T1
Valid prediction for GeneMark_model.7270_t
Valid prediction for Augustus_model.g3037.t1
Valid prediction for snap_scaffold_2-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_4520-T1
Valid prediction for GeneMark_model.7261_t
Valid prediction for GeneMark_model.7268_t
Valid prediction for snap_scaffold_2-snap.2085-T1
Valid prediction for snap_scaffold_2-snap.2068-T1
Valid prediction for Augustus_model.g3040.t1
Valid prediction for snap_scaffold_2-snap.2087-T1
Valid prediction for snap_scaffold_2-snap.2096-T1
Valid prediction for snap_scaffold_2-snap.2093-T1
Valid prediction for snap_scaffold_2-snap.2088-T1
Valid prediction for GeneMark_model.7244_t
Valid prediction for GlimmerHMM_glimmerT_4525-T1
Valid prediction for GlimmerHMM_glimmerT_4522-T1
Valid prediction for GlimmerHMM_glimmerT_4537-T1
Valid prediction for snap_scaffold_2-snap.2064-T1
Valid prediction for snap_scaffold_2-snap.2103-T1
Valid prediction for GlimmerHMM_glimmerT_4523-T1
Valid prediction for snap_scaffold_2-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_4527-T1
Valid prediction for snap_scaffold_2-snap.2089-T1
Valid prediction for GeneMark_model.7286_t
Valid prediction for GeneMark_model.7260_t
Valid prediction for Augustus_model.g3033.t1
Valid prediction for snap_scaffold_2-snap.2081-T1
Valid prediction for GeneMark_model.7250_t
Valid prediction for GeneMark_model.7285_t
Valid prediction for GeneMark_model.7273_t
Valid prediction for snap_scaffold_2-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_4521-T1
Valid prediction for snap_scaffold_2-snap.2095-T1
Valid prediction for Augustus_model.g3031.t1
Valid prediction for GeneMark_model.7255_t
Valid prediction for GeneMark_model.7263_t
Valid prediction for GeneMark_model.7275_t
Valid prediction for GlimmerHMM_glimmerT_4530-T1
Valid prediction for snap_scaffold_2-snap.2069-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_2-snap.2097-T1
Valid prediction for snap_scaffold_2-snap.2090-T1
Couldn't classify 191131, 191181
Couldn't classify 195346, 195465
Sorry, prediction pasa_asmbl_23426.p1 fails validation.
(CAG)	 CC	191131-191181	GT	AGG
(CAG)	 AG	191399-191508	GT	GGG
(GAG)	 AG	191913-192080	GT	AGG
(GAG)	 AG	192304-192663	GT	AGG
(GTG)	 AG	192937-193089	GT	AGG
(TAT)	 AG	193217-193431	GT	AGG
(CCT)	 AG	194993-195114	GT	AGG
(GTG)	 AG	195346-195465	AC	CCA
-recovered pasa_asmbl_23426.p1, internal, 191399, 191508
-recovered pasa_asmbl_23426.p1, internal, 191913, 192080
-recovered pasa_asmbl_23426.p1, internal, 192304, 192663
-recovered pasa_asmbl_23426.p1, internal, 192937, 193089
-recovered pasa_asmbl_23426.p1, internal, 193217, 193431
-recovered pasa_asmbl_23426.p1, internal, 194993, 195114
Valid prediction for Augustus_model.g3028.t1
Valid prediction for GeneMark_model.7278_t
Valid prediction for snap_scaffold_2-snap.2067-T1
Valid prediction for snap_scaffold_2-snap.2086-T1
Valid prediction for snap_scaffold_2-snap.2066-T1
Valid prediction for GeneMark_model.7247_t
Valid prediction for GlimmerHMM_glimmerT_4539-T1
Valid prediction for pasa_asmbl_23429.p1
Couldn't classify 189018, 189131
Couldn't classify 190677, 190757
Sorry, prediction pasa_asmbl_23427.p1 fails validation.
(TAC)	 GC	189018-189131	GT	AGG
(ACC)	 AG	189327-189413	GT	ATG
(GTG)	 AG	189515-189699	GT	CAG
(CGT)	 AG	190249-190408	GT	AGG
(GCC)	 AG	190677-190757	AC	ACA
-recovered pasa_asmbl_23427.p1, internal, 189327, 189413
-recovered pasa_asmbl_23427.p1, internal, 189515, 189699
-recovered pasa_asmbl_23427.p1, internal, 190249, 190408
Valid prediction for snap_scaffold_2-snap.2074-T1
Valid prediction for GlimmerHMM_glimmerT_4540-T1
Valid prediction for snap_scaffold_2-snap.2082-T1
Valid prediction for snap_scaffold_2-snap.2078-T1
Valid prediction for GeneMark_model.7257_t
Valid prediction for Augustus_model.g3042.t1
Valid prediction for Augustus_model.g3043.t1
Valid prediction for CodingQuarry_transcript_28604-T1
Valid prediction for GlimmerHMM_glimmerT_4519-T1
Valid prediction for GeneMark_model.7248_t
Valid prediction for snap_scaffold_2-snap.2072-T1
Valid prediction for snap_scaffold_2-snap.2099-T1
Valid prediction for GlimmerHMM_glimmerT_4518-T1
Valid prediction for GeneMark_model.7279_t
Valid prediction for Augustus_model.g3039.t1
Valid prediction for HiQ_model.g3029.t1
Valid prediction for GeneMark_model.7265_t
Valid prediction for GlimmerHMM_glimmerT_4528-T1
Valid prediction for GeneMark_model.7267_t
Valid prediction for GeneMark_model.7284_t
Valid prediction for GeneMark_model.7274_t
Valid prediction for snap_scaffold_2-snap.2101-T1
Valid prediction for snap_scaffold_2-snap.2063-T1
Valid prediction for GeneMark_model.7259_t
Valid prediction for GlimmerHMM_glimmerT_4535-T1
Valid prediction for Augustus_model.g3032.t1
Valid prediction for snap_scaffold_2-snap.2094-T1
Valid prediction for Augustus_model.g3038.t1
Valid prediction for GeneMark_model.7256_t
Valid prediction for snap_scaffold_2-snap.2091-T1
Valid prediction for GlimmerHMM_glimmerT_4532-T1
Valid prediction for GlimmerHMM_glimmerT_4533-T1
Valid prediction for CodingQuarry_transcript_28606-T1
Valid prediction for GlimmerHMM_glimmerT_4536-T1
Valid prediction for GeneMark_model.7252_t
Valid prediction for GeneMark_model.7280_t
Valid prediction for GlimmerHMM_glimmerT_4529-T1
Valid prediction for GeneMark_model.7276_t
Valid prediction for GeneMark_model.7243_t
Valid prediction for GeneMark_model.7254_t
Couldn't classify 181675, 181851
Sorry, prediction pasa_asmbl_23428.p1 fails validation.
(ATG)	 TT	180285-181352	GT	AGG
(GTG)	 AG	181675-181851	TA	ACT
-recovered pasa_asmbl_23428.p1, initial, 180285, 181352
Valid prediction for snap_scaffold_2-snap.2065-T1
Valid prediction for snap_scaffold_2-snap.2084-T1
Valid prediction for Augustus_model.g3041.t1
Valid prediction for GeneMark_model.7282_t
Valid prediction for GlimmerHMM_glimmerT_4538-T1
Valid prediction for GeneMark_model.7249_t
Valid prediction for Augustus_model.g3030.t1
Valid prediction for Augustus_model.g3035.t1
Valid prediction for GlimmerHMM_glimmerT_4531-T1
Valid prediction for GeneMark_model.7245_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12094, rend_intergenic: 9455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74260, rend_intergenic: 63189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88282, rend_intergenic: 81824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114325, rend_intergenic: 109890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161591, rend_intergenic: 157317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172733, rend_intergenic: 162434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175199, rend_intergenic: 173791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183379, rend_intergenic: 175223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187034, rend_intergenic: 185049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191681, rend_intergenic: 188174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200680
-exon list size: 623


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 12094, rend_intergenic: 9455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74260, rend_intergenic: 63189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88282, rend_intergenic: 81824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114325, rend_intergenic: 109890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161591, rend_intergenic: 157317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172733, rend_intergenic: 162434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175199, rend_intergenic: 173791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183379, rend_intergenic: 175223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187034, rend_intergenic: 185049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191681, rend_intergenic: 188174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support