-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_15746422-15953203

-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_10-snap.3224-T1
Couldn't classify 127672, 127869
Couldn't classify 133786, 134013
Sorry, prediction pasa_asmbl_4971.p1 fails validation.
(ATC)	 TT	127672-127869	GT	AGG
(ATG)	 AG	130388-130523	GT	AGG
(ATG)	 AG	130921-131189	GT	AGG
(GTG)	 AG	133786-134013	AA	AGA
-recovered pasa_asmbl_4971.p1, initial, 130388, 130523
add_exon() Sorry, pasa_asmbl_4971.p1 130921-131189-initial-1 is invalid.
-recovered pasa_asmbl_4971.p1, initial, 130921, 131189
-recovered pasa_asmbl_4971.p1, internal, 130388, 130523
-recovered pasa_asmbl_4971.p1, internal, 130921, 131189
Valid prediction for GeneMark_model.45744_t
Valid prediction for GlimmerHMM_glimmerT_26583-T1
Valid prediction for GeneMark_model.45707_t
Valid prediction for GeneMark_model.45723_t
Valid prediction for GlimmerHMM_glimmerT_26580-T1
Valid prediction for GlimmerHMM_glimmerT_26574-T1
Valid prediction for GlimmerHMM_glimmerT_26592-T1
Valid prediction for GeneMark_model.45698_t
Valid prediction for snap_scaffold_10-snap.3231-T1
Valid prediction for GeneMark_model.45697_t
Valid prediction for GeneMark_model.45719_t
Valid prediction for GeneMark_model.45755_t
Valid prediction for GeneMark_model.45766_t
Valid prediction for GeneMark_model.45715_t
Valid prediction for GlimmerHMM_glimmerT_26575-T1
Valid prediction for Augustus_model.g17827.t1
Valid prediction for GeneMark_model.45731_t
Valid prediction for GeneMark_model.45700_t
Valid prediction for GeneMark_model.45713_t
Valid prediction for snap_scaffold_10-snap.3205-T1
Valid prediction for GeneMark_model.45749_t
Valid prediction for GeneMark_model.45760_t
Valid prediction for HiQ_model.g17826.t1
Valid prediction for snap_scaffold_10-snap.3194-T1
Valid prediction for snap_scaffold_10-snap.3195-T1
Valid prediction for GeneMark_model.45763_t
Valid prediction for snap_scaffold_10-snap.3214-T1
Valid prediction for GeneMark_model.45746_t
Valid prediction for GlimmerHMM_glimmerT_26585-T1
Valid prediction for snap_scaffold_10-snap.3229-T1
Valid prediction for GlimmerHMM_glimmerT_26589-T1
Valid prediction for GeneMark_model.45712_t
Valid prediction for GlimmerHMM_glimmerT_26581-T1
Valid prediction for GlimmerHMM_glimmerT_26582-T1
Valid prediction for Augustus_model.g17819.t1
Couldn't classify 194385, 194629
Sorry, prediction pasa_asmbl_4973.p2 fails validation.
(ATG)	 CC	191714-191744	GT	CTG
(ATA)	 AG	193043-193174	GT	AGG
(GCC)	 AG	194385-194629	AT	AGA
-recovered pasa_asmbl_4973.p2, initial, 191714, 191744
-recovered pasa_asmbl_4973.p2, internal, 193043, 193174
Valid prediction for GeneMark_model.45729_t
Valid prediction for Augustus_model.g17820.t1
Valid prediction for GeneMark_model.45725_t
Valid prediction for GlimmerHMM_glimmerT_26567-T1
Valid prediction for GeneMark_model.45767_t
Valid prediction for GeneMark_model.45727_t
Valid prediction for Augustus_model.g17825.t1
Valid prediction for snap_scaffold_10-snap.3201-T1
Valid prediction for snap_scaffold_10-snap.3221-T1
Valid prediction for GeneMark_model.45769_t
Valid prediction for GeneMark_model.45739_t
Valid prediction for snap_scaffold_10-snap.3197-T1
Valid prediction for GeneMark_model.45734_t
Valid prediction for GeneMark_model.45751_t
Valid prediction for snap_scaffold_10-snap.3206-T1
Valid prediction for snap_scaffold_10-snap.3208-T1
Valid prediction for snap_scaffold_10-snap.3203-T1
Valid prediction for GlimmerHMM_glimmerT_26588-T1
Valid prediction for GeneMark_model.45753_t
Valid prediction for GeneMark_model.45736_t
Valid prediction for snap_scaffold_10-snap.3219-T1
Valid prediction for snap_scaffold_10-snap.3220-T1
Valid prediction for GeneMark_model.45717_t
Valid prediction for GeneMark_model.45740_t
Valid prediction for GeneMark_model.45710_t
Valid prediction for snap_scaffold_10-snap.3222-T1
Valid prediction for GeneMark_model.45764_t
Valid prediction for GeneMark_model.45758_t
Valid prediction for GeneMark_model.45742_t
Valid prediction for GlimmerHMM_glimmerT_26573-T1
Valid prediction for snap_scaffold_10-snap.3217-T1
Valid prediction for GeneMark_model.45741_t
Valid prediction for GeneMark_model.45704_t
Valid prediction for GeneMark_model.45748_t
Valid prediction for GeneMark_model.45765_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 GlimmerHMM_glimmerT_26584-T1
Valid prediction for Augustus_model.g17824.t1
Valid prediction for snap_scaffold_10-snap.3196-T1
Valid prediction for snap_scaffold_10-snap.3218-T1
Valid prediction for snap_scaffold_10-snap.3213-T1
Valid prediction for GeneMark_model.45732_t
Couldn't classify 11498, 11839
Sorry, prediction pasa_asmbl_4975.p1 fails validation.
(ATG)	 CA	11498-11839	TC	CCT
Couldn't classify 108627, 108789
Sorry, prediction pasa_asmbl_3893.p1 fails validation.
(GGT)	 CA	108627-108789	GT	AGG
(AGT)	 AG	109415-109582	GT	AGG
(GGC)	 AG	109743-109924	CG	AGC
add_exon() Sorry, pasa_asmbl_3893.p1 109415-109582-terminal-1 is invalid.
-recovered pasa_asmbl_3893.p1, terminal, 109415, 109582
-recovered pasa_asmbl_3893.p1, terminal, 109743, 109924
-recovered pasa_asmbl_3893.p1, internal, 109415, 109582
Valid prediction for GeneMark_model.45714_t
Valid prediction for GeneMark_model.45759_t
Valid prediction for GeneMark_model.45738_t
Valid prediction for GlimmerHMM_glimmerT_26578-T1
Valid prediction for GeneMark_model.45730_t
Valid prediction for GlimmerHMM_glimmerT_26571-T1
Valid prediction for snap_scaffold_10-snap.3207-T1
Valid prediction for GeneMark_model.45726_t
Couldn't classify 107800, 108455
Sorry, prediction pasa_asmbl_3894.p1 fails validation.
(ATG)	 CC	107163-107601	GT	AGG
(GGA)	 AG	107800-108455	GA	GTG
-recovered pasa_asmbl_3894.p1, initial, 107163, 107601
Valid prediction for Augustus_model.g17817.t1
Valid prediction for GeneMark_model.45705_t
Valid prediction for snap_scaffold_10-snap.3215-T1
Valid prediction for GeneMark_model.45720_t
Valid prediction for GeneMark_model.45762_t
Valid prediction for GeneMark_model.45728_t
Valid prediction for GeneMark_model.45752_t
Valid prediction for snap_scaffold_10-snap.3216-T1
Valid prediction for GeneMark_model.45711_t
Valid prediction for GeneMark_model.45709_t
Valid prediction for snap_scaffold_10-snap.3209-T1
Valid prediction for Augustus_model.g17818.t1
Valid prediction for GlimmerHMM_glimmerT_26586-T1
Valid prediction for GeneMark_model.45722_t
Valid prediction for Augustus_model.g17828.t1
Valid prediction for snap_scaffold_10-snap.3225-T1
Valid prediction for GlimmerHMM_glimmerT_26591-T1
Valid prediction for snap_scaffold_10-snap.3226-T1
Valid prediction for HiQ_model.g17822.t1
Valid prediction for GeneMark_model.45721_t
Valid prediction for GeneMark_model.45745_t
Valid prediction for GeneMark_model.45761_t
Valid prediction for GeneMark_model.45706_t
Valid prediction for snap_scaffold_10-snap.3227-T1
Valid prediction for snap_scaffold_10-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_26587-T1
Valid prediction for GeneMark_model.45750_t
Valid prediction for snap_scaffold_10-snap.3199-T1
Valid prediction for GeneMark_model.45733_t
Valid prediction for GeneMark_model.45754_t
Valid prediction for GeneMark_model.45768_t
Valid prediction for GeneMark_model.45735_t
Valid prediction for Augustus_model.g17823.t1
Valid prediction for GeneMark_model.45724_t
Valid prediction for GeneMark_model.45708_t
Valid prediction for GlimmerHMM_glimmerT_26577-T1
Valid prediction for GeneMark_model.45699_t
Valid prediction for snap_scaffold_10-snap.3228-T1
Valid prediction for GeneMark_model.45702_t
Valid prediction for GlimmerHMM_glimmerT_26579-T1
Valid prediction for snap_scaffold_10-snap.3202-T1
Valid prediction for GlimmerHMM_glimmerT_26570-T1
Valid prediction for snap_scaffold_10-snap.3211-T1
Valid prediction for snap_scaffold_10-snap.3230-T1
Valid prediction for snap_scaffold_10-snap.3193-T1
Valid prediction for GeneMark_model.45747_t
Valid prediction for snap_scaffold_10-snap.3200-T1
Valid prediction for GlimmerHMM_glimmerT_26572-T1
Valid prediction for snap_scaffold_10-snap.3204-T1
Valid prediction for GeneMark_model.45756_t
Valid prediction for GlimmerHMM_glimmerT_26569-T1
Valid prediction for GeneMark_model.45703_t
Valid prediction for pasa_asmbl_3892.p1
Valid prediction for snap_scaffold_10-snap.3198-T1
Valid prediction for snap_scaffold_10-snap.3210-T1
Valid prediction for GlimmerHMM_glimmerT_26576-T1
Valid prediction for snap_scaffold_10-snap.3212-T1
Valid prediction for GeneMark_model.45737_t
Valid prediction for GeneMark_model.45701_t
Valid prediction for snap_scaffold_10-snap.3232-T1
Valid prediction for Augustus_model.g17821.t1
Valid prediction for GlimmerHMM_glimmerT_26568-T1
Valid prediction for GlimmerHMM_glimmerT_26590-T1
Valid prediction for GeneMark_model.45743_t
Valid prediction for GeneMark_model.45716_t
Valid prediction for GeneMark_model.45718_t
Valid prediction for GeneMark_model.45757_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17032, rend_intergenic: 5904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21667, rend_intergenic: 17826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30018, rend_intergenic: 24379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41041, rend_intergenic: 32740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41689, rend_intergenic: 41191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43544, rend_intergenic: 41842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72996, rend_intergenic: 68920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80102, rend_intergenic: 73914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88294, rend_intergenic: 80875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103304, rend_intergenic: 101747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106738, rend_intergenic: 103561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122900, rend_intergenic: 121569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127778, rend_intergenic: 126783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175085, rend_intergenic: 154855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189214, rend_intergenic: 185582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206782
-exon list size: 829


building trellis

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77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 17032, rend_intergenic: 5904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21667, rend_intergenic: 17826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30018, rend_intergenic: 24379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41041, rend_intergenic: 32740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41689, rend_intergenic: 41191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43544, rend_intergenic: 41842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72996, rend_intergenic: 68920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80102, rend_intergenic: 73914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88294, rend_intergenic: 80875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103304, rend_intergenic: 101747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106738, rend_intergenic: 103561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122900, rend_intergenic: 121569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127778, rend_intergenic: 126783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175085, rend_intergenic: 154855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189214, rend_intergenic: 185582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support