-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_8435765-8626021

-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_4-snap.1795-T1
Valid prediction for GeneMark_model.16259_t
Valid prediction for GeneMark_model.16247_t
Valid prediction for GeneMark_model.16211_t
Valid prediction for snap_scaffold_4-snap.1791-T1
Valid prediction for GeneMark_model.16232_t
Valid prediction for GlimmerHMM_glimmerT_9989-T1
Valid prediction for GeneMark_model.16253_t
Valid prediction for snap_scaffold_4-snap.1777-T1
Valid prediction for GlimmerHMM_glimmerT_9980-T1
Valid prediction for snap_scaffold_4-snap.1805-T1
Valid prediction for GeneMark_model.16238_t
Valid prediction for snap_scaffold_4-snap.1778-T1
Valid prediction for snap_scaffold_4-snap.1765-T1
Valid prediction for GeneMark_model.16245_t
Valid prediction for snap_scaffold_4-snap.1798-T1
Valid prediction for GeneMark_model.16231_t
Valid prediction for Augustus_model.g6551.t1
Valid prediction for GeneMark_model.16217_t
Valid prediction for pasa_asmbl_42898.p1
Valid prediction for snap_scaffold_4-snap.1775-T1
Valid prediction for GeneMark_model.16209_t
Valid prediction for snap_scaffold_4-snap.1801-T1
Valid prediction for GeneMark_model.16228_t
Valid prediction for snap_scaffold_4-snap.1797-T1
Valid prediction for Augustus_model.g6542.t1
Valid prediction for GlimmerHMM_glimmerT_9992-T1
Valid prediction for GeneMark_model.16255_t
Valid prediction for GeneMark_model.16220_t
Valid prediction for GlimmerHMM_glimmerT_9998-T1
Couldn't classify 43174, 43253
Sorry, prediction pasa_asmbl_42899.p1 fails validation.
(ATG)	 TC	41972-42074	GC	ATG
(ATG)	 AG	42310-42404	GT	CAG
(GGA)	 AG	42501-42637	GT	AGG
(AGC)	 AG	42760-42926	GT	AGG
(AGC)	 AG	43174-43253	AG	CCA
-recovered pasa_asmbl_42899.p1, initial, 41972, 42074
-recovered pasa_asmbl_42899.p1, initial, 42310, 42404
-recovered pasa_asmbl_42899.p1, internal, 42310, 42404
-recovered pasa_asmbl_42899.p1, internal, 42501, 42637
-recovered pasa_asmbl_42899.p1, internal, 42760, 42926
Valid prediction for GeneMark_model.16207_t
Valid prediction for GeneMark_model.16241_t
Valid prediction for GeneMark_model.16214_t
Valid prediction for GeneMark_model.16221_t
Valid prediction for GeneMark_model.16243_t
Valid prediction for GeneMark_model.16236_t
Valid prediction for snap_scaffold_4-snap.1794-T1
Valid prediction for snap_scaffold_4-snap.1771-T1
Valid prediction for GeneMark_model.16257_t
Valid prediction for GeneMark_model.16239_t
Valid prediction for GlimmerHMM_glimmerT_9984-T1
Valid prediction for snap_scaffold_4-snap.1792-T1
Valid prediction for snap_scaffold_4-snap.1788-T1
Valid prediction for snap_scaffold_4-snap.1802-T1
Valid prediction for snap_scaffold_4-snap.1800-T1
Valid prediction for snap_scaffold_4-snap.1781-T1
Valid prediction for HiQ_model.g6539.t1
Valid prediction for snap_scaffold_4-snap.1774-T1
Valid prediction for GeneMark_model.16234_t
Valid prediction for GlimmerHMM_glimmerT_10001-T1
Valid prediction for GeneMark_model.16222_t
Valid prediction for snap_scaffold_4-snap.1786-T1
Valid prediction for Augustus_model.g6545.t1
Valid prediction for snap_scaffold_4-snap.1782-T1
Valid prediction for snap_scaffold_4-snap.1783-T1
Valid prediction for GeneMark_model.16251_t
Valid prediction for GeneMark_model.16226_t
Valid prediction for GeneMark_model.16216_t
Valid prediction for snap_scaffold_4-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_9993-T1
Valid prediction for GeneMark_model.16218_t
Valid prediction for CodingQuarry_transcript_48972-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 GeneMark_model.16224_t
Valid prediction for snap_scaffold_4-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_10003-T1
Valid prediction for Augustus_model.g6556.t1
Valid prediction for GeneMark_model.16230_t
Valid prediction for GeneMark_model.16237_t
Valid prediction for GeneMark_model.16233_t
Valid prediction for Augustus_model.g6541.t1
Valid prediction for GeneMark_model.16229_t
Valid prediction for snap_scaffold_4-snap.1773-T1
Valid prediction for GeneMark_model.16235_t
Valid prediction for GeneMark_model.16208_t
Valid prediction for GeneMark_model.16256_t
Valid prediction for GeneMark_model.16212_t
Valid prediction for GeneMark_model.16219_t
Valid prediction for Augustus_model.g6547.t1
Valid prediction for GlimmerHMM_glimmerT_10005-T1
Valid prediction for GeneMark_model.16246_t
Valid prediction for GeneMark_model.16210_t
Valid prediction for GlimmerHMM_glimmerT_10000-T1
Valid prediction for Augustus_model.g6560.t1
Valid prediction for GlimmerHMM_glimmerT_9981-T1
Valid prediction for GeneMark_model.16213_t
Valid prediction for snap_scaffold_4-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_9997-T1
Valid prediction for pasa_asmbl_41519.p1
Valid prediction for GeneMark_model.16252_t
Valid prediction for GlimmerHMM_glimmerT_9983-T1
Valid prediction for GeneMark_model.16258_t
Valid prediction for Augustus_model.g6557.t1
Valid prediction for GeneMark_model.16242_t
Valid prediction for snap_scaffold_4-snap.1789-T1
Valid prediction for HiQ_model.g6544.t1
Valid prediction for Augustus_model.g6548.t1
Valid prediction for Augustus_model.g6553.t1
Valid prediction for Augustus_model.g6550.t1
Valid prediction for GlimmerHMM_glimmerT_9985-T1
Valid prediction for snap_scaffold_4-snap.1787-T1
Valid prediction for snap_scaffold_4-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_9988-T1
Valid prediction for snap_scaffold_4-snap.1776-T1
Valid prediction for GeneMark_model.16225_t
Valid prediction for snap_scaffold_4-snap.1799-T1
Valid prediction for GeneMark_model.16254_t
Valid prediction for Augustus_model.g6554.t1
Valid prediction for pasa_asmbl_41517.p1
Valid prediction for GeneMark_model.16244_t
Valid prediction for Augustus_model.g6555.t1
Valid prediction for GeneMark_model.16215_t
Valid prediction for GlimmerHMM_glimmerT_9999-T1
Valid prediction for GeneMark_model.16227_t
Valid prediction for snap_scaffold_4-snap.1803-T1
Valid prediction for snap_scaffold_4-snap.1779-T1
Valid prediction for GeneMark_model.16240_t
Valid prediction for GeneMark_model.16250_t
Valid prediction for Augustus_model.g6558.t1
Valid prediction for snap_scaffold_4-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_9991-T1
Valid prediction for Augustus_model.g6543.t1
Valid prediction for Augustus_model.g6540.t1
Valid prediction for GlimmerHMM_glimmerT_10002-T1
Valid prediction for Augustus_model.g6549.t1
Valid prediction for GlimmerHMM_glimmerT_9986-T1
Valid prediction for snap_scaffold_4-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_9990-T1
Valid prediction for snap_scaffold_4-snap.1780-T1
Valid prediction for GlimmerHMM_glimmerT_9987-T1
Valid prediction for GlimmerHMM_glimmerT_10004-T1
Valid prediction for snap_scaffold_4-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_9982-T1
Valid prediction for CodingQuarry_transcript_48973-T1
Valid prediction for GlimmerHMM_glimmerT_9995-T1
Couldn't classify 188512, 188553
Sorry, prediction pasa_asmbl_41515.p1 fails validation.
(GGT)	 GA	188512-188553	GT	AGG
(CTT)	 AG	188819-189808	TG	GAT
-recovered pasa_asmbl_41515.p1, terminal, 188819, 189808
Valid prediction for snap_scaffold_4-snap.1769-T1
Valid prediction for GlimmerHMM_glimmerT_9994-T1
Valid prediction for CodingQuarry_transcript_48975-T1
Valid prediction for Augustus_model.g6552.t1
Valid prediction for snap_scaffold_4-snap.1766-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.16248_t
Valid prediction for snap_scaffold_4-snap.1785-T1
Valid prediction for snap_scaffold_4-snap.1790-T1
Valid prediction for snap_scaffold_4-snap.1784-T1
Valid prediction for snap_scaffold_4-snap.1767-T1
Valid prediction for GeneMark_model.16223_t
Valid prediction for Augustus_model.g6546.t1
Valid prediction for HiQ_model.g6559.t1
Valid prediction for GlimmerHMM_glimmerT_9996-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13170, rend_intergenic: 5798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60958, rend_intergenic: 51951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78613, rend_intergenic: 68911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98274, rend_intergenic: 82442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104995, rend_intergenic: 99443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111195, rend_intergenic: 107389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121230, rend_intergenic: 111259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144133, rend_intergenic: 121859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147020, rend_intergenic: 145731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150461, rend_intergenic: 147382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153661, rend_intergenic: 151089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161817, rend_intergenic: 154137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165641, rend_intergenic: 162206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176836, rend_intergenic: 165975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188319, rend_intergenic: 184016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190257
-exon list size: 786


building trellis

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89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 13170, rend_intergenic: 5798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60958, rend_intergenic: 51951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78613, rend_intergenic: 68911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98274, rend_intergenic: 82442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104995, rend_intergenic: 99443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111195, rend_intergenic: 107389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121230, rend_intergenic: 111259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144133, rend_intergenic: 121859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147020, rend_intergenic: 145731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150461, rend_intergenic: 147382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153661, rend_intergenic: 151089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161817, rend_intergenic: 154137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165641, rend_intergenic: 162206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176836, rend_intergenic: 165975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188319, rend_intergenic: 184016  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