-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_13843955-14136782

-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 GeneMark_model.2629_t
Valid prediction for GeneMark_model.2618_t
Valid prediction for GeneMark_model.2587_t
Valid prediction for GlimmerHMM_glimmerT_1883-T1
Valid prediction for GlimmerHMM_glimmerT_1898-T1
Valid prediction for snap_scaffold_1-snap.2437-T1
Valid prediction for GlimmerHMM_glimmerT_1897-T1
Valid prediction for Augustus_model.g1383.t1
Valid prediction for CodingQuarry_transcript_2891-T1
Valid prediction for pasa_asmbl_2303.p1
Valid prediction for GeneMark_model.2621_t
Valid prediction for GeneMark_model.2617_t
Valid prediction for snap_scaffold_1-snap.2412-T1
Valid prediction for GlimmerHMM_glimmerT_1879-T1
Valid prediction for Augustus_model.g1386.t1
Valid prediction for GlimmerHMM_glimmerT_1889-T1
Valid prediction for GeneMark_model.2594_t
Valid prediction for snap_scaffold_1-snap.2421-T1
Valid prediction for snap_scaffold_1-snap.2431-T1
Valid prediction for GlimmerHMM_glimmerT_1881-T1
Valid prediction for snap_scaffold_1-snap.2445-T1
Couldn't classify 224253, 224361
Couldn't classify 224638, 224892
Sorry, prediction pasa_asmbl_2743.p1 fails validation.
(AAA)	 AG	224253-224361	GT	TGG
(CAA)	 AG	224487-224536	GT	TGG
(CCC)	 AG	224638-224892	GC	AGG
-recovered pasa_asmbl_2743.p1, internal, 224253, 224361
-recovered pasa_asmbl_2743.p1, internal, 224487, 224536
-recovered pasa_asmbl_2743.p1, internal, 224638, 224892
Valid prediction for GlimmerHMM_glimmerT_1896-T1
Valid prediction for GeneMark_model.2613_t
Valid prediction for snap_scaffold_1-snap.2443-T1
Valid prediction for snap_scaffold_1-snap.2433-T1
Valid prediction for snap_scaffold_1-snap.2432-T1
Couldn't classify 215759, 215833
Couldn't classify 222754, 222938
Sorry, prediction pasa_asmbl_2311.p1 fails validation.
(TCT)	 AC	215759-215833	GT	AGG
(GTG)	 AG	217454-217520	GT	TGG
(AGA)	 AG	219707-219864	GT	AGG
(CTG)	 AG	220888-221080	GT	AGG
(TGT)	 AG	222754-222938	GT	TGG
-recovered pasa_asmbl_2311.p1, internal, 217454, 217520
-recovered pasa_asmbl_2311.p1, internal, 219707, 219864
-recovered pasa_asmbl_2311.p1, internal, 220888, 221080
-recovered pasa_asmbl_2311.p1, internal, 222754, 222938
Valid prediction for GlimmerHMM_glimmerT_1880-T1
Valid prediction for snap_scaffold_1-snap.2406-T1
Valid prediction for Augustus_model.g1394.t1
Valid prediction for Augustus_model.g1384.t1
Couldn't classify 228151, 228185
Sorry, prediction pasa_asmbl_2312.p1 fails validation.
(ACC)	 TG	228151-228185	GT	AGG
(GAG)	 AG	229060-229151	GT	AGG
(ATG)	 AG	231585-231676	GT	AGG
(GAT)	 AG	231858-231965	CC	GAC
add_exon() Sorry, pasa_asmbl_2312.p1 231585-231676-initial-1 is invalid.
-recovered pasa_asmbl_2312.p1, initial, 231585, 231676
-recovered pasa_asmbl_2312.p1, terminal, 231858, 231965
-recovered pasa_asmbl_2312.p1, internal, 229060, 229151
-recovered pasa_asmbl_2312.p1, internal, 231585, 231676
Valid prediction for snap_scaffold_1-snap.2410-T1
Valid prediction for snap_scaffold_1-snap.2416-T1
Valid prediction for GeneMark_model.2611_t
Valid prediction for HiQ_model.g1382.t1
Valid prediction for GeneMark_model.2590_t
Valid prediction for GeneMark_model.2623_t
Valid prediction for GlimmerHMM_glimmerT_1890-T1
Valid prediction for snap_scaffold_1-snap.2413-T1
Valid prediction for GeneMark_model.2625_t
Valid prediction for pasa_asmbl_2308.p1
Valid prediction for GeneMark_model.2602_t
Valid prediction for GeneMark_model.2614_t
Valid prediction for GlimmerHMM_glimmerT_1884-T1
Valid prediction for HiQ_model.g1395.t1
Valid prediction for snap_scaffold_1-snap.2409-T1
Valid prediction for Augustus_model.g1389.t1
Valid prediction for GeneMark_model.2596_t
Valid prediction for snap_scaffold_1-snap.2411-T1
Valid prediction for GlimmerHMM_glimmerT_1878-T1
Valid prediction for pasa_asmbl_2313.p1
Valid prediction for GlimmerHMM_glimmerT_1894-T1
Valid prediction for GeneMark_model.2593_t
Valid prediction for GeneMark_model.2607_t
Valid prediction for snap_scaffold_1-snap.2417-T1
Valid prediction for CodingQuarry_transcript_2888-T1
Valid prediction for snap_scaffold_1-snap.2436-T1
Valid prediction for GeneMark_model.2595_t
Valid prediction for snap_scaffold_1-snap.2434-T1
Valid prediction for GeneMark_model.2627_t
Valid prediction for GeneMark_model.2598_t
Valid prediction for GlimmerHMM_glimmerT_1895-T1
Valid prediction for GeneMark_model.2615_t
Valid prediction for Augustus_model.g1393.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.2631_t
Valid prediction for GeneMark_model.2630_t
Valid prediction for GeneMark_model.2600_t
Valid prediction for snap_scaffold_1-snap.2444-T1
Valid prediction for pasa_asmbl_855.p1
Valid prediction for GeneMark_model.2591_t
Valid prediction for Augustus_model.g1388.t1
Valid prediction for GeneMark_model.2619_t
Valid prediction for snap_scaffold_1-snap.2438-T1
Valid prediction for snap_scaffold_1-snap.2423-T1
Valid prediction for snap_scaffold_1-snap.2428-T1
Valid prediction for Augustus_model.g1401.t1
Valid prediction for snap_scaffold_1-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_1888-T1
Valid prediction for snap_scaffold_1-snap.2415-T1
Valid prediction for snap_scaffold_1-snap.2420-T1
Valid prediction for snap_scaffold_1-snap.2418-T1
Valid prediction for Augustus_model.g1399.t1
Valid prediction for snap_scaffold_1-snap.2414-T1
Valid prediction for GlimmerHMM_glimmerT_1893-T1
Valid prediction for snap_scaffold_1-snap.2405-T1
Valid prediction for GeneMark_model.2599_t
Valid prediction for snap_scaffold_1-snap.2442-T1
Valid prediction for GeneMark_model.2616_t
Couldn't classify 200041, 200172
Sorry, prediction pasa_asmbl_869.p1 fails validation.
(TAT)	 AC	200041-200172	GT	AGG
(CCT)	 AG	200568-200720	GT	AGG
(ACC)	 AG	200820-200936	GT	TGG
(CAC)	 AG	201025-201093	GT	AGG
(ATT)	 AG	201220-201318	GT	AGG
(GAT)	 AG	201425-201510	GT	AGG
(AAA)	 AG	201616-201707	GT	TGG
(GGT)	 AG	201787-202003	GT	AGG
(AGA)	 AG	202083-202224	GT	AGG
(ATC)	 AG	202339-202424	GT	AGG
(CCA)	 AG	202731-203010	GT	AGG
(GTT)	 AG	203110-203215	GT	AAG
(GGA)	 AG	203399-204038	GT	AGG
(GAC)	 AG	204181-204392	GT	AGG
(AGG)	 AG	204589-204774	GT	AGG
(GAG)	 AG	204875-205032	GT	AGG
(GAT)	 AG	205126-205371	GT	AGG
(GAA)	 AG	205489-205634	GT	AGG
(GGT)	 AG	205765-205922	GT	GGG
(GTA)	 AG	206217-206400	GT	AGG
(GAA)	 AG	206495-206702	GT	AGG
(TCC)	 AG	206889-207087	GT	AGG
(AGC)	 AG	207184-207255	GT	AGG
(GTA)	 AG	208349-208416	GT	AGG
(CCG)	 AG	208558-208771	GC	AGG
(CCC)	 AG	208851-209014	AA	AGA
add_exon() Sorry, pasa_asmbl_869.p1 203110-203215-terminal-3 is invalid.
-recovered pasa_asmbl_869.p1, terminal, 203110, 203215
add_exon() Sorry, pasa_asmbl_869.p1 203399-204038-terminal-3 is invalid.
-recovered pasa_asmbl_869.p1, terminal, 203399, 204038
-recovered pasa_asmbl_869.p1, terminal, 208851, 209014
-recovered pasa_asmbl_869.p1, internal, 200568, 200720
-recovered pasa_asmbl_869.p1, internal, 200820, 200936
-recovered pasa_asmbl_869.p1, internal, 201025, 201093
-recovered pasa_asmbl_869.p1, internal, 201220, 201318
-recovered pasa_asmbl_869.p1, internal, 201425, 201510
-recovered pasa_asmbl_869.p1, internal, 201616, 201707
-recovered pasa_asmbl_869.p1, internal, 201787, 202003
-recovered pasa_asmbl_869.p1, internal, 202083, 202224
-recovered pasa_asmbl_869.p1, internal, 202339, 202424
-recovered pasa_asmbl_869.p1, internal, 202731, 203010
-recovered pasa_asmbl_869.p1, internal, 203110, 203215
-recovered pasa_asmbl_869.p1, internal, 203399, 204038
-recovered pasa_asmbl_869.p1, internal, 204181, 204392
-recovered pasa_asmbl_869.p1, internal, 204589, 204774
-recovered pasa_asmbl_869.p1, internal, 204875, 205032
-recovered pasa_asmbl_869.p1, internal, 205126, 205371
-recovered pasa_asmbl_869.p1, internal, 205489, 205634
-recovered pasa_asmbl_869.p1, internal, 205765, 205922
-recovered pasa_asmbl_869.p1, internal, 206217, 206400
-recovered pasa_asmbl_869.p1, internal, 206495, 206702
-recovered pasa_asmbl_869.p1, internal, 206889, 207087
-recovered pasa_asmbl_869.p1, internal, 207184, 207255
-recovered pasa_asmbl_869.p1, internal, 208349, 208416
-recovered pasa_asmbl_869.p1, internal, 208558, 208771
Valid prediction for Augustus_model.g1398.t1
Valid prediction for GlimmerHMM_glimmerT_1886-T1
Valid prediction for Augustus_model.g1396.t1
Valid prediction for GeneMark_model.2605_t
Valid prediction for GeneMark_model.2606_t
Valid prediction for snap_scaffold_1-snap.2435-T1
Valid prediction for pasa_asmbl_868.p1
Valid prediction for Augustus_model.g1390.t1
Valid prediction for Augustus_model.g1381.t1
Valid prediction for snap_scaffold_1-snap.2425-T1
Valid prediction for snap_scaffold_1-snap.2446-T1
Valid prediction for Augustus_model.g1397.t1
Valid prediction for GlimmerHMM_glimmerT_1887-T1
Valid prediction for snap_scaffold_1-snap.2419-T1
Valid prediction for snap_scaffold_1-snap.2430-T1
Valid prediction for GeneMark_model.2597_t
Valid prediction for Augustus_model.g1400.t1
Valid prediction for GeneMark_model.2628_t
Valid prediction for GlimmerHMM_glimmerT_1892-T1
Valid prediction for snap_scaffold_1-snap.2426-T1
Valid prediction for snap_scaffold_1-snap.2424-T1
Valid prediction for snap_scaffold_1-snap.2427-T1
Valid prediction for GlimmerHMM_glimmerT_1882-T1
Valid prediction for Augustus_model.g1385.t1
Valid prediction for CodingQuarry_transcript_2889-T1
Valid prediction for GlimmerHMM_glimmerT_1875-T1
Valid prediction for GeneMark_model.2609_t
Valid prediction for GlimmerHMM_glimmerT_1877-T1
Valid prediction for snap_scaffold_1-snap.2407-T1
Valid prediction for GeneMark_model.2588_t
Valid prediction for snap_scaffold_1-snap.2429-T1
Valid prediction for snap_scaffold_1-snap.2440-T1
Valid prediction for snap_scaffold_1-snap.2441-T1
Couldn't classify 270901, 270946
Couldn't classify 272632, 272807
Sorry, prediction pasa_asmbl_856.p1 fails validation.
(GGT)	 CA	270901-270946	GT	AGG
(GTG)	 AG	271295-271429	GT	CAG
(AGC)	 AG	271734-271839	GT	CAG
(TTT)	 AG	271952-272179	GT	TGG
(CGA)	 AG	272278-272351	GT	AGG
(AGC)	 AG	272632-272807	GA	AGG
-recovered pasa_asmbl_856.p1, internal, 271295, 271429
-recovered pasa_asmbl_856.p1, internal, 271734, 271839
-recovered pasa_asmbl_856.p1, internal, 271952, 272179
-recovered pasa_asmbl_856.p1, internal, 272278, 272351
Valid prediction for GeneMark_model.2626_t
Valid prediction for CodingQuarry_transcript_2890-T1
Valid prediction for GeneMark_model.2601_t
Valid prediction for GeneMark_model.2610_t
Valid prediction for GlimmerHMM_glimmerT_1901-T1
Valid prediction for GeneMark_model.2624_t
Valid prediction for GlimmerHMM_glimmerT_1876-T1
Valid prediction for GeneMark_model.2612_t
Valid prediction for GeneMark_model.2592_t
Valid prediction for HiQ_model.g1387.t1
Valid prediction for Augustus_model.g1391.t1
Valid prediction for Augustus_model.g1392.t1
Valid prediction for GeneMark_model.2589_t
Valid prediction for GlimmerHMM_glimmerT_1891-T1
Valid prediction for GeneMark_model.2622_t
Valid prediction for snap_scaffold_1-snap.2439-T1
Valid prediction for GeneMark_model.2608_t
Valid prediction for snap_scaffold_1-snap.2422-T1
Couldn't classify 209393, 209568
Sorry, prediction pasa_asmbl_865.p1 fails validation.
(CAA)	 GT	209393-209568	GT	AGG
(GCG)	 AG	210290-210603	GT	AGG
(TAT)	 AG	210720-210841	GT	AGG
(ATC)	 AG	210962-211106	GC	AGG
(TAG)	 AG	211251-211404	GT	CAG
(GTA)	 AG	211520-211691	GT	AGG
(ATA)	 AG	212068-212163	GT	AGG
(GTT)	 AG	212313-212525	GT	AGG
(CTG)	 AG	212679-212822	GT	AGG
(GTG)	 AG	212936-213082	GT	AGG
(GCT)	 AG	213188-213281	GT	AGG
(CGC)	 AG	213460-213782	GT	AGG
(GTG)	 AG	213921-214043	GT	TGG
(GCT)	 AG	214266-214345	GT	GGG
(GTG)	 AG	214440-214527	AC	AGA
-recovered pasa_asmbl_865.p1, terminal, 214440, 214527
-recovered pasa_asmbl_865.p1, internal, 210290, 210603
-recovered pasa_asmbl_865.p1, internal, 210720, 210841
-recovered pasa_asmbl_865.p1, internal, 210962, 211106
-recovered pasa_asmbl_865.p1, internal, 211251, 211404
-recovered pasa_asmbl_865.p1, internal, 211520, 211691
-recovered pasa_asmbl_865.p1, internal, 212068, 212163
-recovered pasa_asmbl_865.p1, internal, 212313, 212525
-recovered pasa_asmbl_865.p1, internal, 212679, 212822
-recovered pasa_asmbl_865.p1, internal, 212936, 213082
-recovered pasa_asmbl_865.p1, internal, 213188, 213281
-recovered pasa_asmbl_865.p1, internal, 213460, 213782
-recovered pasa_asmbl_865.p1, internal, 213921, 214043
-recovered pasa_asmbl_865.p1, internal, 214266, 214345
Valid prediction for GlimmerHMM_glimmerT_1900-T1
Valid prediction for GlimmerHMM_glimmerT_1899-T1
Valid prediction for GeneMark_model.2604_t
Valid prediction for GlimmerHMM_glimmerT_1885-T1
Valid prediction for GeneMark_model.2620_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28174, rend_intergenic: 25754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28766, rend_intergenic: 28174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68375, rend_intergenic: 65123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225405, rend_intergenic: 221699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229081, rend_intergenic: 225986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 292828
-exon list size: 647


building trellis

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59.0    
59.2    
59.3    
59.5    
59.6    
59.8    
59.9    
60.1    
60.2    
60.4    
60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.2    
65.3    
65.5    
65.6    
65.8    
65.9    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 28174, rend_intergenic: 25754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28766, rend_intergenic: 28174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68375, rend_intergenic: 65123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225405, rend_intergenic: 221699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229081, rend_intergenic: 225986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17841
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13509
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12833
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2583 - 12833
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2583 - 12648
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support