-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_11835138-12084411

-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_8256-T1
Valid prediction for Augustus_model.g18515.t1
Valid prediction for pasa_asmbl_6004.p1
Valid prediction for GlimmerHMM_glimmerT_27954-T1
Valid prediction for GlimmerHMM_glimmerT_27952-T1
Valid prediction for CodingQuarry_transcript_8255-T1
Valid prediction for snap_scaffold_11-snap.2553-T1
Valid prediction for Augustus_model.g18513.t1
Valid prediction for GlimmerHMM_glimmerT_27946-T1
Valid prediction for snap_scaffold_11-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_27953-T1
Valid prediction for GlimmerHMM_glimmerT_27955-T1
Valid prediction for GlimmerHMM_glimmerT_27961-T1
Valid prediction for CodingQuarry_transcript_8265-T1
Valid prediction for GlimmerHMM_glimmerT_27948-T1
Valid prediction for snap_scaffold_11-snap.2560-T1
Valid prediction for snap_scaffold_11-snap.2528-T1
Valid prediction for snap_scaffold_11-snap.2532-T1
Valid prediction for GlimmerHMM_glimmerT_27949-T1
Valid prediction for snap_scaffold_11-snap.2537-T1
Valid prediction for Augustus_model.g18511.t1
Valid prediction for snap_scaffold_11-snap.2539-T1
Valid prediction for pasa_asmbl_6007.p1
Valid prediction for snap_scaffold_11-snap.2535-T1
Valid prediction for GlimmerHMM_glimmerT_27950-T1
Valid prediction for Augustus_model.g18531.t1
Valid prediction for HiQ_model.g18514.t1
Valid prediction for Augustus_model.g18517.t1
Valid prediction for Augustus_model.g18512.t1
Valid prediction for GlimmerHMM_glimmerT_27969-T1
Valid prediction for GlimmerHMM_glimmerT_27974-T1
Valid prediction for snap_scaffold_11-snap.2533-T1
Valid prediction for Augustus_model.g18518.t1
Couldn't classify 67225, 67296
Couldn't classify 68084, 68155
Sorry, prediction pasa_asmbl_6002.p2 fails validation.
(TGT)	 AG	67225-67296	GT	AGG
(GGG)	 AG	67592-67720	GT	AGG
(GAG)	 AG	67870-67980	GT	AGG
(GAG)	 AG	68084-68155	AA	ACA
-recovered pasa_asmbl_6002.p2, internal, 67225, 67296
-recovered pasa_asmbl_6002.p2, internal, 67592, 67720
-recovered pasa_asmbl_6002.p2, internal, 67870, 67980
Valid prediction for HiQ_model.g18519.t1
Valid prediction for Augustus_model.g18523.t1
Valid prediction for snap_scaffold_11-snap.2526-T1
Valid prediction for snap_scaffold_11-snap.2540-T1
Valid prediction for GlimmerHMM_glimmerT_27951-T1
Valid prediction for GlimmerHMM_glimmerT_27960-T1
Valid prediction for snap_scaffold_11-snap.2538-T1
Valid prediction for GlimmerHMM_glimmerT_27947-T1
Valid prediction for Augustus_model.g18516.t1
Valid prediction for HiQ_model.g18535.t1
Valid prediction for snap_scaffold_11-snap.2557-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 GlimmerHMM_glimmerT_27962-T1
Valid prediction for HiQ_model.g18527.t1
Valid prediction for snap_scaffold_11-snap.2543-T1
Valid prediction for snap_scaffold_11-snap.2550-T1
Valid prediction for snap_scaffold_11-snap.2564-T1
Couldn't classify 63004, 63235
Sorry, prediction pasa_asmbl_7066.p1 fails validation.
(GGT)	 CA	63004-63235	GT	GTG
(GTA)	 AG	63362-63466	GT	AGG
(GCC)	 AG	63567-63638	GT	AGG
(GCC)	 AG	63806-63957	GT	AGG
(GTT)	 AG	64255-64389	GT	AGG
(ATC)	 AG	64624-64728	AC	GAA
-recovered pasa_asmbl_7066.p1, terminal, 64624, 64728
-recovered pasa_asmbl_7066.p1, internal, 63362, 63466
-recovered pasa_asmbl_7066.p1, internal, 63567, 63638
-recovered pasa_asmbl_7066.p1, internal, 63806, 63957
-recovered pasa_asmbl_7066.p1, internal, 64255, 64389
Valid prediction for GlimmerHMM_glimmerT_27945-T1
Valid prediction for snap_scaffold_11-snap.2558-T1
Valid prediction for pasa_asmbl_7054.p1
Valid prediction for snap_scaffold_11-snap.2559-T1
Valid prediction for snap_scaffold_11-snap.2547-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27973-T1
Couldn't classify 147803, 148317
Couldn't classify 149181, 149206
Sorry, prediction CodingQuarry_transcript_8260-T1 fails validation.
(ATG)	 CC	137038-137059	GT	AGG
(GTC)	 AG	138535-138744	GT	TGG
(ATA)	 AG	138922-139005	GT	AGG
(AAC)	 AG	139090-139191	GT	AGG
(GAA)	 AG	139316-139459	GT	AGG
(GAA)	 AG	140097-140240	GT	AGG
(CTG)	 AG	140474-140572	GT	AGG
(GCG)	 AG	140779-140895	GT	AGG
(GGG)	 AG	141082-141201	GT	AGG
(GTG)	 AG	141395-141436	GT	AGG
(GAG)	 AG	141555-141581	GT	AGG
(TTG)	 AG	142537-142653	GT	TGG
(ACA)	 AG	142781-142885	GT	TGG
(CGG)	 AG	142931-144040	GT	AGG
(TTC)	 AG	145051-145107	GT	AGG
(ATC)	 AG	145214-145390	GT	AGG
(AAA)	 AG	145639-145734	GT	AGG
(CTA)	 AG	146011-146210	GT	AGG
(GTG)	 AG	147803-148317	CC	GTC
(TTC)	 GT	149181-149206	GT	GCG
(AAG)	 AG	149313-149360	GT	AGG
(AGA)	 AG	149477-149524	GT	AGG
(AAC)	 AG	149658-149726	GT	AGG
(CAC)	 AG	150192-150233	GT	AGG
(AGC)	 AG	150451-150498	GT	AGG
(TCC)	 AG	150702-150749	GT	AGG
(AAC)	 AG	150838-150885	GT	AGG
(AAC)	 AG	150990-151037	GT	AGG
(AGT)	 AG	151364-151420	GT	AGG
(ATA)	 AG	151518-151568	GT	AGG
(AGG)	 AG	151823-151891	GT	AGG
(AGC)	 AG	151995-152042	GT	AGG
(TTG)	 AG	152362-152418	GT	AGG
(AAC)	 AG	152972-153016	GT	AGG
(CTA)	 AG	153151-153192	GT	AGG
(CAG)	 AG	153365-153409	GT	AGG
(AAC)	 AG	153650-153697	GT	AGG
(AAC)	 AG	153845-153889	GT	AGG
(GGG)	 AG	154188-154229	GT	AGG
(AAC)	 AG	155104-155148	GC	AGG
(AAG)	 AG	155415-155462	GT	AGG
(CTG)	 AG	155601-155636	GT	AGG
(ATG)	 AG	155815-155900	GG	GAG
-recovered CodingQuarry_transcript_8260-T1, initial, 137038, 137059
-recovered CodingQuarry_transcript_8260-T1, terminal, 155815, 155900
-recovered CodingQuarry_transcript_8260-T1, internal, 138535, 138744
-recovered CodingQuarry_transcript_8260-T1, internal, 138922, 139005
-recovered CodingQuarry_transcript_8260-T1, internal, 139090, 139191
-recovered CodingQuarry_transcript_8260-T1, internal, 139316, 139459
-recovered CodingQuarry_transcript_8260-T1, internal, 140097, 140240
-recovered CodingQuarry_transcript_8260-T1, internal, 140474, 140572
-recovered CodingQuarry_transcript_8260-T1, internal, 140779, 140895
-recovered CodingQuarry_transcript_8260-T1, internal, 141082, 141201
-recovered CodingQuarry_transcript_8260-T1, internal, 141395, 141436
-recovered CodingQuarry_transcript_8260-T1, internal, 141555, 141581
-recovered CodingQuarry_transcript_8260-T1, internal, 142537, 142653
-recovered CodingQuarry_transcript_8260-T1, internal, 142781, 142885
-recovered CodingQuarry_transcript_8260-T1, internal, 142931, 144040
-recovered CodingQuarry_transcript_8260-T1, internal, 145051, 145107
-recovered CodingQuarry_transcript_8260-T1, internal, 145214, 145390
-recovered CodingQuarry_transcript_8260-T1, internal, 145639, 145734
-recovered CodingQuarry_transcript_8260-T1, internal, 146011, 146210
-recovered CodingQuarry_transcript_8260-T1, internal, 149313, 149360
-recovered CodingQuarry_transcript_8260-T1, internal, 149477, 149524
-recovered CodingQuarry_transcript_8260-T1, internal, 149658, 149726
-recovered CodingQuarry_transcript_8260-T1, internal, 150192, 150233
-recovered CodingQuarry_transcript_8260-T1, internal, 150451, 150498
-recovered CodingQuarry_transcript_8260-T1, internal, 150702, 150749
-recovered CodingQuarry_transcript_8260-T1, internal, 150838, 150885
-recovered CodingQuarry_transcript_8260-T1, internal, 150990, 151037
-recovered CodingQuarry_transcript_8260-T1, internal, 151364, 151420
-recovered CodingQuarry_transcript_8260-T1, internal, 151518, 151568
-recovered CodingQuarry_transcript_8260-T1, internal, 151823, 151891
-recovered CodingQuarry_transcript_8260-T1, internal, 151995, 152042
-recovered CodingQuarry_transcript_8260-T1, internal, 152362, 152418
-recovered CodingQuarry_transcript_8260-T1, internal, 152972, 153016
-recovered CodingQuarry_transcript_8260-T1, internal, 153151, 153192
-recovered CodingQuarry_transcript_8260-T1, internal, 153365, 153409
-recovered CodingQuarry_transcript_8260-T1, internal, 153650, 153697
-recovered CodingQuarry_transcript_8260-T1, internal, 153845, 153889
-recovered CodingQuarry_transcript_8260-T1, internal, 154188, 154229
-recovered CodingQuarry_transcript_8260-T1, internal, 155104, 155148
-recovered CodingQuarry_transcript_8260-T1, internal, 155415, 155462
-recovered CodingQuarry_transcript_8260-T1, internal, 155601, 155636
Valid prediction for Augustus_model.g18532.t1
Valid prediction for GlimmerHMM_glimmerT_27971-T1
Valid prediction for snap_scaffold_11-snap.2530-T1
Valid prediction for snap_scaffold_11-snap.2563-T1
Valid prediction for HiQ_model.g18533.t1
Valid prediction for GlimmerHMM_glimmerT_27968-T1
Valid prediction for snap_scaffold_11-snap.2542-T1
Valid prediction for snap_scaffold_11-snap.2562-T1
Valid prediction for snap_scaffold_11-snap.2534-T1
Valid prediction for GlimmerHMM_glimmerT_27967-T1
Valid prediction for snap_scaffold_11-snap.2554-T1
Valid prediction for snap_scaffold_11-snap.2541-T1
Valid prediction for snap_scaffold_11-snap.2551-T1
Valid prediction for GlimmerHMM_glimmerT_27959-T1
Valid prediction for Augustus_model.g18522.t1
Valid prediction for CodingQuarry_transcript_8262-T1
Valid prediction for snap_scaffold_11-snap.2561-T1
Valid prediction for snap_scaffold_11-snap.2552-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g18530.t1
Valid prediction for GlimmerHMM_glimmerT_27970-T1
Valid prediction for pasa_asmbl_7057.p1
Valid prediction for snap_scaffold_11-snap.2556-T1
Valid prediction for snap_scaffold_11-snap.2527-T1
Valid prediction for snap_scaffold_11-snap.2536-T1
Valid prediction for Augustus_model.g18528.t1
Valid prediction for GlimmerHMM_glimmerT_27963-T1
Valid prediction for CodingQuarry_transcript_8264-T1
Valid prediction for pasa_asmbl_7043.p1
Valid prediction for Augustus_model.g18536.t1
Valid prediction for GlimmerHMM_glimmerT_27958-T1
Valid prediction for HiQ_model.g18538.t1
Valid prediction for pasa_asmbl_7077.p1
Valid prediction for snap_scaffold_11-snap.2548-T1
Valid prediction for snap_scaffold_11-snap.2555-T1
Valid prediction for snap_scaffold_11-snap.2525-T1
Valid prediction for Augustus_model.g18524.t1
Valid prediction for GlimmerHMM_glimmerT_27956-T1
Valid prediction for Augustus_model.g18525.t1
Valid prediction for Augustus_model.g18521.t1
Valid prediction for GlimmerHMM_glimmerT_27957-T1
Valid prediction for Augustus_model.g18534.t1
Valid prediction for GlimmerHMM_glimmerT_27976-T1
Valid prediction for Augustus_model.g18537.t1
Valid prediction for CodingQuarry_transcript_8259-T1
Couldn't classify 69400, 69544
Couldn't classify 70253, 70745
Sorry, prediction pasa_asmbl_7065.p1 fails validation.
(AAG)	 CC	69400-69544	GT	CGG
(GTG)	 AG	69663-69772	GT	AGG
(GTA)	 AG	69897-69973	GT	AAG
(ATA)	 AG	70253-70745	AC	GAA
add_exon() Sorry, pasa_asmbl_7065.p1 69897-69973-terminal-2 is invalid.
-recovered pasa_asmbl_7065.p1, terminal, 69897, 69973
-recovered pasa_asmbl_7065.p1, internal, 69663, 69772
-recovered pasa_asmbl_7065.p1, internal, 69897, 69973
Valid prediction for HiQ_model.g18520.t1
Valid prediction for snap_scaffold_11-snap.2544-T1
Valid prediction for snap_scaffold_11-snap.2549-T1
Valid prediction for GlimmerHMM_glimmerT_27975-T1
Valid prediction for CodingQuarry_transcript_8261-T1
Valid prediction for CodingQuarry_transcript_8267-T1
Valid prediction for Augustus_model.g18510.t1
Valid prediction for CodingQuarry_transcript_8257-T1
Valid prediction for GlimmerHMM_glimmerT_27965-T1
Valid prediction for pasa_asmbl_7044.p1
Couldn't classify 147913, 147939
Sorry, prediction CodingQuarry_transcript_8258-T1 fails validation.
(ATG)	 GC	144939-145107	GT	AGG
(ATC)	 AG	145214-145390	GT	AGG
(AAA)	 AG	145639-145734	GT	AGG
(CTA)	 AG	146011-146210	GT	AGG
(GTG)	 AG	146690-146902	GT	AGG
(GTC)	 AG	147221-147379	GT	AGG
(GTC)	 AG	147698-147769	GT	AAG
(AGT)	 AA	147913-147939	GG	GAG
-recovered CodingQuarry_transcript_8258-T1, initial, 144939, 145107
-recovered CodingQuarry_transcript_8258-T1, internal, 145214, 145390
-recovered CodingQuarry_transcript_8258-T1, internal, 145639, 145734
-recovered CodingQuarry_transcript_8258-T1, internal, 146011, 146210
-recovered CodingQuarry_transcript_8258-T1, internal, 146690, 146902
-recovered CodingQuarry_transcript_8258-T1, internal, 147221, 147379
-recovered CodingQuarry_transcript_8258-T1, internal, 147698, 147769
Valid prediction for CodingQuarry_transcript_8266-T1
Valid prediction for Augustus_model.g18529.t1
Valid prediction for snap_scaffold_11-snap.2545-T1
Valid prediction for Augustus_model.g18526.t1
Valid prediction for GlimmerHMM_glimmerT_27964-T1
Couldn't classify 27709, 27873
Sorry, prediction pasa_asmbl_7070.p1 fails validation.
(GAT)	 TG	27709-27873	GT	TGG
(GCC)	 AG	28210-28408	GT	CGG
(GCT)	 AG	28682-28828	GT	TGG
(AAA)	 AG	30079-30195	GT	AGG
(GAA)	 AG	31456-31982	TG	GAT
-recovered pasa_asmbl_7070.p1, terminal, 31456, 31982
-recovered pasa_asmbl_7070.p1, internal, 28210, 28408
-recovered pasa_asmbl_7070.p1, internal, 28682, 28828
-recovered pasa_asmbl_7070.p1, internal, 30079, 30195
Valid prediction for snap_scaffold_11-snap.2529-T1
Valid prediction for GlimmerHMM_glimmerT_27972-T1
Valid prediction for CodingQuarry_transcript_8263-T1
Valid prediction for snap_scaffold_11-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_27966-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9435, rend_intergenic: 1970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19381, rend_intergenic: 14205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43670, rend_intergenic: 20022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63026, rend_intergenic: 56826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75121, rend_intergenic: 67568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193149, rend_intergenic: 183537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217838, rend_intergenic: 217293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 249274
-exon list size: 587


building trellis

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56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 9435, rend_intergenic: 1970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19381, rend_intergenic: 14205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43670, rend_intergenic: 20022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63026, rend_intergenic: 56826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75121, rend_intergenic: 67568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193149, rend_intergenic: 183537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217838, rend_intergenic: 217293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support