-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_13151299-13393228

-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 CodingQuarry_transcript_52321-T1
Valid prediction for snap_scaffold_5-snap.2447-T1
Valid prediction for snap_scaffold_5-snap.2441-T1
Valid prediction for snap_scaffold_5-snap.2455-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g8559.t1
Valid prediction for snap_scaffold_5-snap.2463-T1
Valid prediction for snap_scaffold_5-snap.2437-T1
Valid prediction for snap_scaffold_5-snap.2457-T1
Valid prediction for GlimmerHMM_glimmerT_12920-T1
Valid prediction for snap_scaffold_5-snap.2449-T1
Valid prediction for CodingQuarry_transcript_52325-T1
Valid prediction for Augustus_model.g8554.t1
Valid prediction for GlimmerHMM_glimmerT_12918-T1
Couldn't classify 139702, 139803
Sorry, prediction pasa_asmbl_45876.p1 fails validation.
(GGG)	 CA	139702-139803	GT	TGG
(GCC)	 AG	140340-140463	GT	AGG
(AGT)	 AG	140961-141022	GT	AGG
(GAT)	 AG	141138-141183	GT	AGG
(GCC)	 AG	141285-141410	GT	AGG
(GAT)	 AG	141575-141619	GT	AGG
(ATT)	 AG	141877-141920	GT	TGG
(GTG)	 AG	142160-142216	GT	AGG
(ATG)	 AG	142969-143021	GT	GGG
(GCT)	 AG	143149-143357	GT	CGG
(ACG)	 AG	143602-143793	GT	AGG
(ATC)	 AG	143893-143938	GT	AGG
(GTC)	 AG	144085-144198	GT	TGG
(TGT)	 AG	145474-145529	GT	CGG
(ACT)	 AG	145975-146132	GT	GGG
(GAT)	 AG	146240-146377	GT	AGG
(GCC)	 AG	148609-148676	GT	GGG
(GGA)	 AG	150187-150337	GT	AGG
(AGC)	 AG	150522-150614	GT	GTG
(CTA)	 AG	151963-152042	GT	AGG
(CAA)	 AG	152199-152279	GT	GGG
(AGT)	 AG	152470-152575	GT	AGG
(CTG)	 AG	152986-153144	GT	AGG
(CTC)	 AG	154056-154163	GT	TGG
(TCC)	 AG	156431-156544	GT	AGG
(AAA)	 AG	157486-157587	GT	AGG
(GTG)	 AG	157757-157879	GT	AGG
(CTC)	 AG	158002-158085	AA	AAA
-recovered pasa_asmbl_45876.p1, initial, 142969, 143021
-recovered pasa_asmbl_45876.p1, terminal, 158002, 158085
-recovered pasa_asmbl_45876.p1, internal, 140340, 140463
-recovered pasa_asmbl_45876.p1, internal, 140961, 141022
-recovered pasa_asmbl_45876.p1, internal, 141138, 141183
-recovered pasa_asmbl_45876.p1, internal, 141285, 141410
-recovered pasa_asmbl_45876.p1, internal, 141575, 141619
-recovered pasa_asmbl_45876.p1, internal, 141877, 141920
-recovered pasa_asmbl_45876.p1, internal, 142160, 142216
-recovered pasa_asmbl_45876.p1, internal, 142969, 143021
-recovered pasa_asmbl_45876.p1, internal, 143149, 143357
-recovered pasa_asmbl_45876.p1, internal, 143602, 143793
-recovered pasa_asmbl_45876.p1, internal, 143893, 143938
-recovered pasa_asmbl_45876.p1, internal, 144085, 144198
-recovered pasa_asmbl_45876.p1, internal, 145474, 145529
-recovered pasa_asmbl_45876.p1, internal, 145975, 146132
-recovered pasa_asmbl_45876.p1, internal, 146240, 146377
-recovered pasa_asmbl_45876.p1, internal, 148609, 148676
-recovered pasa_asmbl_45876.p1, internal, 150187, 150337
-recovered pasa_asmbl_45876.p1, internal, 150522, 150614
-recovered pasa_asmbl_45876.p1, internal, 151963, 152042
-recovered pasa_asmbl_45876.p1, internal, 152199, 152279
-recovered pasa_asmbl_45876.p1, internal, 152470, 152575
-recovered pasa_asmbl_45876.p1, internal, 152986, 153144
-recovered pasa_asmbl_45876.p1, internal, 154056, 154163
-recovered pasa_asmbl_45876.p1, internal, 156431, 156544
-recovered pasa_asmbl_45876.p1, internal, 157486, 157587
-recovered pasa_asmbl_45876.p1, internal, 157757, 157879
Couldn't classify 101331, 101804
Sorry, prediction pasa_asmbl_45874.p1 fails validation.
(TCA)	 TG	101331-101804	TA	AGT
Valid prediction for Augustus_model.g8575.t1
Valid prediction for snap_scaffold_5-snap.2460-T1
Valid prediction for GlimmerHMM_glimmerT_12896-T1
Valid prediction for snap_scaffold_5-snap.2450-T1
Valid prediction for CodingQuarry_transcript_52320-T1
Valid prediction for snap_scaffold_5-snap.2435-T1
Valid prediction for GlimmerHMM_glimmerT_12915-T1
Valid prediction for HiQ_model.g8570.t1
Valid prediction for Augustus_model.g8572.t1
Valid prediction for pasa_asmbl_45878.p1
Valid prediction for snap_scaffold_5-snap.2428-T1
Valid prediction for Augustus_model.g8557.t1
Valid prediction for GlimmerHMM_glimmerT_12919-T1
Valid prediction for GlimmerHMM_glimmerT_12908-T1
Valid prediction for GlimmerHMM_glimmerT_12904-T1
Valid prediction for GlimmerHMM_glimmerT_12916-T1
Valid prediction for HiQ_model.g8562.t1
Valid prediction for CodingQuarry_transcript_52317-T1
Valid prediction for GlimmerHMM_glimmerT_12906-T1
Valid prediction for Augustus_model.g8563.t1
Valid prediction for snap_scaffold_5-snap.2434-T1
Valid prediction for Augustus_model.g8569.t1
Valid prediction for HiQ_model.g8561.t1
Valid prediction for snap_scaffold_5-snap.2440-T1
Valid prediction for GlimmerHMM_glimmerT_12924-T1
Valid prediction for pasa_asmbl_45868.p1
Valid prediction for CodingQuarry_transcript_52328-T1
Valid prediction for Augustus_model.g8552.t1
Valid prediction for Augustus_model.g8571.t1
Valid prediction for CodingQuarry_transcript_52326-T1
Valid prediction for CodingQuarry_transcript_52324-T1
Valid prediction for GlimmerHMM_glimmerT_12917-T1
Valid prediction for snap_scaffold_5-snap.2439-T1
Valid prediction for pasa_asmbl_45865.p1
Valid prediction for snap_scaffold_5-snap.2442-T1
Valid prediction for GlimmerHMM_glimmerT_12902-T1
Valid prediction for GlimmerHMM_glimmerT_12907-T1
Valid prediction for snap_scaffold_5-snap.2446-T1
Valid prediction for snap_scaffold_5-snap.2456-T1
Valid prediction for GlimmerHMM_glimmerT_12925-T1
Valid prediction for snap_scaffold_5-snap.2458-T1
Valid prediction for CodingQuarry_transcript_52323-T1
Valid prediction for snap_scaffold_5-snap.2452-T1
Couldn't classify 100474, 100722
Sorry, prediction pasa_asmbl_45873.p1 fails validation.
(ATG)	 CC	99798-99957	GT	ACG
(CAA)	 AG	100081-100343	GT	AAG
(CTG)	 AG	100474-100722	TG	ACT
-recovered pasa_asmbl_45873.p1, initial, 99798, 99957
-recovered pasa_asmbl_45873.p1, internal, 100081, 100343
Valid prediction for HiQ_model.g8567.t1
Valid prediction for GlimmerHMM_glimmerT_12898-T1
Valid prediction for GlimmerHMM_glimmerT_12911-T1
Valid prediction for snap_scaffold_5-snap.2431-T1
Valid prediction for snap_scaffold_5-snap.2459-T1
Valid prediction for snap_scaffold_5-snap.2461-T1
Valid prediction for snap_scaffold_5-snap.2443-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_5-snap.2454-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g8558.t1
Valid prediction for GlimmerHMM_glimmerT_12894-T1
Valid prediction for CodingQuarry_transcript_52322-T1
Valid prediction for snap_scaffold_5-snap.2453-T1
Valid prediction for HiQ_model.g8568.t1
Valid prediction for GlimmerHMM_glimmerT_12914-T1
Valid prediction for GlimmerHMM_glimmerT_12921-T1
Valid prediction for GlimmerHMM_glimmerT_12901-T1
Valid prediction for GlimmerHMM_glimmerT_12922-T1
Valid prediction for Augustus_model.g8577.t1
Valid prediction for GlimmerHMM_glimmerT_12897-T1
Valid prediction for snap_scaffold_5-snap.2430-T1
Valid prediction for CodingQuarry_transcript_52327-T1
Valid prediction for snap_scaffold_5-snap.2438-T1
Valid prediction for GlimmerHMM_glimmerT_12895-T1
Valid prediction for Augustus_model.g8566.t1
Valid prediction for GlimmerHMM_glimmerT_12912-T1
Valid prediction for CodingQuarry_transcript_52319-T1
Valid prediction for Augustus_model.g8564.t1
Valid prediction for GlimmerHMM_glimmerT_12899-T1
Valid prediction for pasa_asmbl_44534.p1
Valid prediction for GlimmerHMM_glimmerT_12900-T1
Valid prediction for snap_scaffold_5-snap.2445-T1
Couldn't classify 72920, 73029
Couldn't classify 76148, 76226
Couldn't classify 76531, 76681
Sorry, prediction pasa_asmbl_44539.p1 fails validation.
(CAG)	 TC	72920-73029	GT	AGG
(ACA)	 AG	73136-73257	GT	CGG
(TGA)	 AG	73411-73588	GT	TGG
(CCC)	 AG	73835-73919	GT	CGG
(GTG)	 AG	74087-74147	GT	GTG
(TAT)	 AG	74449-74525	GT	AGG
(GGG)	 AG	74630-74776	GT	AGG
(GAT)	 AG	74967-75073	GT	AAG
(GTA)	 AG	75819-75907	GT	AGG
(ATC)	 AG	76148-76226	AT	CAA
(CTA)	 AC	76531-76681	GT	AGG
(AGG)	 AG	76800-76882	GT	GTG
(GCT)	 AG	76978-77008	GT	AGG
(GCC)	 AG	77103-77181	GT	AGG
(TGT)	 AG	77272-77409	GT	AGG
(AGC)	 AG	77551-77648	GT	TGG
(ACG)	 AG	77938-78063	GT	AGG
(GTA)	 AG	78667-78848	GT	GTG
(TTT)	 AG	79148-79238	GT	AGG
(AGA)	 AG	79327-79377	GT	TGG
(GAT)	 AG	79559-79646	GT	AGG
(ACA)	 AG	79756-79820	GT	TGG
(CGC)	 AG	79961-80015	GT	TGG
(TGC)	 AG	80258-80329	GT	ATG
(ATT)	 AG	80420-80538	GG	AAG
add_exon() Sorry, pasa_asmbl_44539.p1 75819-75907-terminal-2 is invalid.
-recovered pasa_asmbl_44539.p1, terminal, 75819, 75907
-recovered pasa_asmbl_44539.p1, terminal, 80420, 80538
-recovered pasa_asmbl_44539.p1, internal, 73136, 73257
-recovered pasa_asmbl_44539.p1, internal, 73411, 73588
-recovered pasa_asmbl_44539.p1, internal, 73835, 73919
-recovered pasa_asmbl_44539.p1, internal, 74087, 74147
-recovered pasa_asmbl_44539.p1, internal, 74449, 74525
-recovered pasa_asmbl_44539.p1, internal, 74630, 74776
-recovered pasa_asmbl_44539.p1, internal, 74967, 75073
-recovered pasa_asmbl_44539.p1, internal, 75819, 75907
-recovered pasa_asmbl_44539.p1, internal, 76800, 76882
-recovered pasa_asmbl_44539.p1, internal, 76978, 77008
-recovered pasa_asmbl_44539.p1, internal, 77103, 77181
-recovered pasa_asmbl_44539.p1, internal, 77272, 77409
-recovered pasa_asmbl_44539.p1, internal, 77551, 77648
-recovered pasa_asmbl_44539.p1, internal, 77938, 78063
-recovered pasa_asmbl_44539.p1, internal, 78667, 78848
-recovered pasa_asmbl_44539.p1, internal, 79148, 79238
-recovered pasa_asmbl_44539.p1, internal, 79327, 79377
-recovered pasa_asmbl_44539.p1, internal, 79559, 79646
-recovered pasa_asmbl_44539.p1, internal, 79756, 79820
-recovered pasa_asmbl_44539.p1, internal, 79961, 80015
-recovered pasa_asmbl_44539.p1, internal, 80258, 80329
Couldn't classify 160538, 160682
Sorry, prediction pasa_asmbl_44535.p1 fails validation.
(CAT)	 AC	160538-160682	GT	AGG
(GTT)	 AG	161360-161478	GT	AGG
(ATA)	 AG	161577-161825	GT	CTG
(CCC)	 AG	161960-162088	CA	AAC
-recovered pasa_asmbl_44535.p1, terminal, 161960, 162088
-recovered pasa_asmbl_44535.p1, internal, 161360, 161478
-recovered pasa_asmbl_44535.p1, internal, 161577, 161825
Valid prediction for Augustus_model.g8553.t1
Valid prediction for snap_scaffold_5-snap.2465-T1
Valid prediction for CodingQuarry_transcript_52318-T1
Valid prediction for snap_scaffold_5-snap.2464-T1
Valid prediction for GlimmerHMM_glimmerT_12909-T1
Valid prediction for Augustus_model.g8576.t1
Valid prediction for GlimmerHMM_glimmerT_12905-T1
Valid prediction for HiQ_model.g8551.t1
Valid prediction for pasa_asmbl_44533.p1
Valid prediction for Augustus_model.g8556.t1
Valid prediction for Augustus_model.g8574.t1
Valid prediction for HiQ_model.g8555.t1
Valid prediction for GlimmerHMM_glimmerT_12910-T1
Valid prediction for Augustus_model.g8560.t1
Valid prediction for snap_scaffold_5-snap.2432-T1
Valid prediction for snap_scaffold_5-snap.2436-T1
Valid prediction for snap_scaffold_5-snap.2451-T1
Valid prediction for snap_scaffold_5-snap.2444-T1
Valid prediction for snap_scaffold_5-snap.2433-T1
Valid prediction for snap_scaffold_5-snap.2462-T1
Valid prediction for GlimmerHMM_glimmerT_12923-T1
Valid prediction for snap_scaffold_5-snap.2427-T1
Valid prediction for Augustus_model.g8573.t1
Valid prediction for CodingQuarry_transcript_52316-T1
Valid prediction for GlimmerHMM_glimmerT_12903-T1
Valid prediction for GlimmerHMM_glimmerT_12913-T1
Valid prediction for pasa_asmbl_44529.p1
Valid prediction for snap_scaffold_5-snap.2429-T1
Valid prediction for snap_scaffold_5-snap.2448-T1
Valid prediction for Augustus_model.g8565.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 135282, rend_intergenic: 134733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148680, rend_intergenic: 144052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151829, rend_intergenic: 148913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158085, rend_intergenic: 153031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174839, rend_intergenic: 163445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 241930
-exon list size: 514


building trellis

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84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 135282, rend_intergenic: 134733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148680, rend_intergenic: 144052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151829, rend_intergenic: 148913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158085, rend_intergenic: 153031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174839, rend_intergenic: 163445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support