-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_9402100-9692176

-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_20-snap.2096-T1
Valid prediction for pasa_asmbl_26872.p1
Valid prediction for snap_scaffold_20-snap.2074-T1
Valid prediction for snap_scaffold_20-snap.2104-T1
Valid prediction for snap_scaffold_20-snap.2072-T1
Valid prediction for snap_scaffold_20-snap.2073-T1
Valid prediction for Augustus_model.g30981.t1
Valid prediction for snap_scaffold_20-snap.2095-T1
Couldn't classify 96164, 96197
Sorry, prediction pasa_asmbl_26850.p1 fails validation.
(GTT)	 CT	96164-96197	GT	CGG
(CGT)	 AG	96520-96717	GT	AGG
(AAT)	 AG	96881-96965	GT	GTG
(GCC)	 AG	97094-97229	CA	GAC
-recovered pasa_asmbl_26850.p1, terminal, 97094, 97229
-recovered pasa_asmbl_26850.p1, internal, 96520, 96717
-recovered pasa_asmbl_26850.p1, internal, 96881, 96965
Valid prediction for GlimmerHMM_glimmerT_46615-T1
Valid prediction for CodingQuarry_transcript_30610-T1
Valid prediction for GlimmerHMM_glimmerT_46618-T1
Valid prediction for snap_scaffold_20-snap.2080-T1
Couldn't classify 244712, 244958
Couldn't classify 250135, 250207
Sorry, prediction pasa_asmbl_26875.p1 fails validation.
(AAA)	 GC	244712-244958	GT	CGG
(CCA)	 AG	246128-246228	GT	AGG
(CAC)	 AG	248536-248693	GT	AGG
(GTG)	 AG	248982-249577	GT	TGG
(GTG)	 AG	249703-249763	GT	AGG
(TCT)	 AG	250135-250207	CC	AGC
-recovered pasa_asmbl_26875.p1, internal, 246128, 246228
-recovered pasa_asmbl_26875.p1, internal, 248536, 248693
-recovered pasa_asmbl_26875.p1, internal, 248982, 249577
-recovered pasa_asmbl_26875.p1, internal, 249703, 249763
Valid prediction for snap_scaffold_20-snap.2098-T1
Valid prediction for snap_scaffold_20-snap.2054-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_30605-T1
Valid prediction for CodingQuarry_transcript_30606-T1
Valid prediction for snap_scaffold_20-snap.2066-T1
Valid prediction for CodingQuarry_transcript_30607-T1
Valid prediction for GlimmerHMM_glimmerT_46637-T1
Valid prediction for GlimmerHMM_glimmerT_46627-T1
Valid prediction for HiQ_model.g30960.t1
Valid prediction for Augustus_model.g30977.t1
Valid prediction for snap_scaffold_20-snap.2079-T1
Valid prediction for snap_scaffold_20-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_46622-T1
Valid prediction for snap_scaffold_20-snap.2068-T1
Valid prediction for snap_scaffold_20-snap.2099-T1
Valid prediction for CodingQuarry_transcript_30609-T1
Valid prediction for CodingQuarry_transcript_30608-T1
Valid prediction for snap_scaffold_20-snap.2069-T1
Valid prediction for snap_scaffold_20-snap.2065-T1
Valid prediction for Augustus_model.g30978.t1
Couldn't classify 107252, 107407
Sorry, prediction pasa_asmbl_26857.p1 fails validation.
(ATG)	 GG	106722-107063	GT	ACG
(ACA)	 AG	107252-107407	GG	AAG
-recovered pasa_asmbl_26857.p1, initial, 106722, 107063
Valid prediction for HiQ_model.g30979.t1
Valid prediction for pasa_asmbl_26864.p1
Valid prediction for GlimmerHMM_glimmerT_46616-T1
Valid prediction for Augustus_model.g30957.t1
Valid prediction for GlimmerHMM_glimmerT_46634-T1
Valid prediction for Augustus_model.g30973.t1
Valid prediction for Augustus_model.g30963.t1
Valid prediction for snap_scaffold_20-snap.2100-T1
Couldn't classify 149190, 149215
Couldn't classify 155276, 155367
Sorry, prediction pasa_asmbl_26867.p1 fails validation.
(CAC)	 GG	149190-149215	GT	AGG
(CGA)	 AG	149638-149757	GT	AGG
(TTT)	 AG	150093-150274	GT	AGG
(ATC)	 AG	150518-150738	GT	AGG
(ATC)	 AG	151603-151745	GT	TGG
(GTG)	 AG	152023-152156	GT	AGG
(AGC)	 AG	152263-152465	GT	CGG
(GTG)	 AG	152773-153000	GT	AGG
(GTG)	 AG	153349-153591	GT	AGG
(CTG)	 AG	153921-154139	GT	AGG
(GTG)	 AG	154643-154703	GT	AGG
(CGA)	 AG	154830-154949	GT	AGG
(CTG)	 AG	155276-155367	CT	AGC
-recovered pasa_asmbl_26867.p1, internal, 149638, 149757
-recovered pasa_asmbl_26867.p1, internal, 150093, 150274
-recovered pasa_asmbl_26867.p1, internal, 150518, 150738
-recovered pasa_asmbl_26867.p1, internal, 151603, 151745
-recovered pasa_asmbl_26867.p1, internal, 152023, 152156
-recovered pasa_asmbl_26867.p1, internal, 152263, 152465
-recovered pasa_asmbl_26867.p1, internal, 152773, 153000
-recovered pasa_asmbl_26867.p1, internal, 153349, 153591
-recovered pasa_asmbl_26867.p1, internal, 153921, 154139
-recovered pasa_asmbl_26867.p1, internal, 154643, 154703
-recovered pasa_asmbl_26867.p1, internal, 154830, 154949
Valid prediction for snap_scaffold_20-snap.2067-T1
Couldn't classify 141029, 141184
Sorry, prediction pasa_asmbl_26865.p1 fails validation.
(ATG)	 CA	140376-140528	GT	AGG
(AAG)	 AG	141029-141184	GA	AAG
-recovered pasa_asmbl_26865.p1, initial, 140376, 140528
Valid prediction for GlimmerHMM_glimmerT_46628-T1
Valid prediction for HiQ_model.g30959.t1
Valid prediction for snap_scaffold_20-snap.2055-T1
Valid prediction for snap_scaffold_20-snap.2077-T1
Valid prediction for snap_scaffold_20-snap.2101-T1
Valid prediction for CodingQuarry_transcript_30604-T1
Valid prediction for snap_scaffold_20-snap.2052-T1
Valid prediction for snap_scaffold_20-snap.2093-T1
Valid prediction for GlimmerHMM_glimmerT_46635-T1
Valid prediction for snap_scaffold_20-snap.2086-T1
Valid prediction for CodingQuarry_transcript_30599-T1
Valid prediction for pasa_asmbl_26882.p1
Valid prediction for GlimmerHMM_glimmerT_46630-T1
Valid prediction for GlimmerHMM_glimmerT_46633-T1
Valid prediction for GlimmerHMM_glimmerT_46614-T1
Valid prediction for snap_scaffold_20-snap.2091-T1
Valid prediction for HiQ_model.g30961.t1
Valid prediction for HiQ_model.g30975.t1
Valid prediction for HiQ_model.g30958.t1
Valid prediction for snap_scaffold_20-snap.2094-T1
Valid prediction for snap_scaffold_20-snap.2061-T1
Couldn't classify 250280, 250547
Sorry, prediction pasa_asmbl_26877.p1 fails validation.
(GGC)	 CG	250280-250547	GT	AGG
(CTG)	 AG	251016-251374	GT	AGG
(CGA)	 AG	251565-251699	GT	AGG
(GTG)	 AG	252012-252138	GT	CGG
(ACG)	 AG	252619-252709	GT	ACG
(GGC)	 AG	252971-253044	GT	AGG
(AGA)	 AG	253258-253372	GT	AGG
(GGA)	 AG	253499-253545	GT	AGG
(ACT)	 AG	253674-253819	AA	GAA
-recovered pasa_asmbl_26877.p1, terminal, 253674, 253819
-recovered pasa_asmbl_26877.p1, internal, 251016, 251374
-recovered pasa_asmbl_26877.p1, internal, 251565, 251699
-recovered pasa_asmbl_26877.p1, internal, 252012, 252138
-recovered pasa_asmbl_26877.p1, internal, 252619, 252709
-recovered pasa_asmbl_26877.p1, internal, 252971, 253044
-recovered pasa_asmbl_26877.p1, internal, 253258, 253372
-recovered pasa_asmbl_26877.p1, internal, 253499, 253545
Valid prediction for snap_scaffold_20-snap.2070-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 Augustus_model.g30953.t1
Valid prediction for CodingQuarry_transcript_30598-T1
Valid prediction for snap_scaffold_20-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_46609-T1
Valid prediction for GlimmerHMM_glimmerT_46629-T1
Valid prediction for snap_scaffold_20-snap.2090-T1
Valid prediction for snap_scaffold_20-snap.2053-T1
Valid prediction for snap_scaffold_20-snap.2078-T1
Valid prediction for snap_scaffold_20-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_46607-T1
Valid prediction for pasa_asmbl_26045.p1
Valid prediction for snap_scaffold_20-snap.2088-T1
Valid prediction for snap_scaffold_20-snap.2071-T1
Valid prediction for CodingQuarry_transcript_30602-T1
Valid prediction for Augustus_model.g30955.t1
Valid prediction for HiQ_model.g30950.t1
Valid prediction for pasa_asmbl_26039.p1
Valid prediction for snap_scaffold_20-snap.2056-T1
Couldn't classify 268621, 268625
Sorry, prediction GlimmerHMM_glimmerT_46608-T1 fails validation.
(ATG)	 GC	262585-262699	GT	GGG
(GGC)	 AG	264344-264475	GT	GGG
(AGT)	 AG	268621-268625	NN	ANN
-recovered GlimmerHMM_glimmerT_46608-T1, initial, 262585, 262699
-recovered GlimmerHMM_glimmerT_46608-T1, internal, 264344, 264475
Valid prediction for GlimmerHMM_glimmerT_46636-T1
Valid prediction for GlimmerHMM_glimmerT_46612-T1
Valid prediction for GlimmerHMM_glimmerT_46626-T1
Valid prediction for Augustus_model.g30966.t1
Valid prediction for HiQ_model.g30972.t1
Valid prediction for GlimmerHMM_glimmerT_46621-T1
Valid prediction for GlimmerHMM_glimmerT_46619-T1
Couldn't classify 279974, 279992
Couldn't classify 280660, 280674
Sorry, prediction pasa_asmbl_26259.p1 fails validation.
(CTT)	 TC	279974-279992	GT	GGG
(ACT)	 AG	280104-280468	GT	AGG
(AAC)	 AG	280660-280674	GA	GGG
-recovered pasa_asmbl_26259.p1, internal, 280104, 280468
Valid prediction for GlimmerHMM_glimmerT_46632-T1
Valid prediction for Augustus_model.g30976.t1
Valid prediction for pasa_asmbl_26041.p1
Valid prediction for GlimmerHMM_glimmerT_46624-T1
Valid prediction for snap_scaffold_20-snap.2075-T1
Valid prediction for Augustus_model.g30971.t1
Valid prediction for snap_scaffold_20-snap.2085-T1
Valid prediction for GlimmerHMM_glimmerT_46623-T1
Valid prediction for snap_scaffold_20-snap.2076-T1
Valid prediction for Augustus_model.g30974.t1
Valid prediction for snap_scaffold_20-snap.2103-T1
Valid prediction for Augustus_model.g30970.t1
Valid prediction for snap_scaffold_20-snap.2084-T1
Valid prediction for snap_scaffold_20-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_46613-T1
Valid prediction for HiQ_model.g30956.t1
Valid prediction for snap_scaffold_20-snap.2063-T1
Couldn't classify 107124, 107453
Sorry, prediction pasa_asmbl_26044.p1 fails validation.
(TTC)	 CG	107124-107453	TG	AGT
Valid prediction for snap_scaffold_20-snap.2083-T1
Valid prediction for CodingQuarry_transcript_30600-T1
Couldn't classify 55646, 55708
Sorry, prediction pasa_asmbl_26051.p1 fails validation.
(ATG)	 AG	51889-51931	GT	CAG
(ATA)	 AG	52443-52527	GT	GGG
(ACC)	 AG	53181-53256	GT	CGG
(GTC)	 AG	53639-53737	GT	AGG
(TAT)	 AG	53875-53998	GT	GGG
(GTA)	 AG	54460-54560	GT	AGG
(ACG)	 AG	54754-54834	GT	AAG
(GAC)	 AG	55245-55382	GT	AGG
(GAC)	 AG	55646-55708	GA	AGG
-recovered pasa_asmbl_26051.p1, initial, 51889, 51931
-recovered pasa_asmbl_26051.p1, internal, 51889, 51931
-recovered pasa_asmbl_26051.p1, internal, 52443, 52527
-recovered pasa_asmbl_26051.p1, internal, 53181, 53256
-recovered pasa_asmbl_26051.p1, internal, 53639, 53737
-recovered pasa_asmbl_26051.p1, internal, 53875, 53998
-recovered pasa_asmbl_26051.p1, internal, 54460, 54560
-recovered pasa_asmbl_26051.p1, internal, 54754, 54834
-recovered pasa_asmbl_26051.p1, internal, 55245, 55382
Valid prediction for CodingQuarry_transcript_30596-T1
Valid prediction for HiQ_model.g30965.t1
Couldn't classify 243916, 243958
Sorry, prediction pasa_asmbl_26035.p1 fails validation.
(TGG)	 AG	243916-243958	GT	TTG
(CTC)	 AG	244402-244549	GT	ACG
(GGC)	 AG	244871-244918	GT	AGG
(TAA)	 AG	245987-246293	AA	AAA
-recovered pasa_asmbl_26035.p1, terminal, 245987, 246293
-recovered pasa_asmbl_26035.p1, internal, 243916, 243958
-recovered pasa_asmbl_26035.p1, internal, 244402, 244549
-recovered pasa_asmbl_26035.p1, internal, 244871, 244918
Valid prediction for GlimmerHMM_glimmerT_46631-T1
Valid prediction for GlimmerHMM_glimmerT_46606-T1
Valid prediction for HiQ_model.g30962.t1
Valid prediction for snap_scaffold_20-snap.2081-T1
Valid prediction for snap_scaffold_20-snap.2051-T1
Valid prediction for snap_scaffold_20-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_46617-T1
Valid prediction for GlimmerHMM_glimmerT_46605-T1
Valid prediction for Augustus_model.g30952.t1
Valid prediction for CodingQuarry_transcript_30603-T1
Valid prediction for Augustus_model.g30969.t1
Couldn't classify 56135, 56204
Couldn't classify 57381, 57486
Sorry, prediction pasa_asmbl_26050.p1 fails validation.
(AAC)	 TC	56135-56204	GT	AGG
(GAA)	 AG	56394-56537	GT	AGG
(GTC)	 AG	56770-56834	GT	AGG
(TCA)	 AG	56934-57124	GT	TGG
(GGA)	 AG	57381-57486	GC	CGG
add_exon() Sorry, pasa_asmbl_26050.p1 56394-56537-terminal-1 is invalid.
-recovered pasa_asmbl_26050.p1, terminal, 56394, 56537
-recovered pasa_asmbl_26050.p1, internal, 56394, 56537
-recovered pasa_asmbl_26050.p1, internal, 56770, 56834
-recovered pasa_asmbl_26050.p1, internal, 56934, 57124
-recovered pasa_asmbl_26050.p1, internal, 57381, 57486
Valid prediction for Augustus_model.g30951.t1
Couldn't classify 241869, 241965
Couldn't classify 242712, 242812
Sorry, prediction pasa_asmbl_26037.p1 fails validation.
(GGT)	 TA	241869-241965	GT	AGG
(GGA)	 AG	242121-242181	GT	GTG
(ATT)	 AG	242502-242605	GT	AAG
(CTG)	 AG	242712-242812	AG	CGA
-recovered pasa_asmbl_26037.p1, internal, 242121, 242181
-recovered pasa_asmbl_26037.p1, internal, 242502, 242605
Valid prediction for snap_scaffold_20-snap.2064-T1
Valid prediction for Augustus_model.g30964.t1
Valid prediction for GlimmerHMM_glimmerT_46625-T1
Valid prediction for GlimmerHMM_glimmerT_46610-T1
Valid prediction for CodingQuarry_transcript_30597-T1
Valid prediction for GlimmerHMM_glimmerT_46611-T1
Valid prediction for snap_scaffold_20-snap.2087-T1
Valid prediction for snap_scaffold_20-snap.2050-T1
Valid prediction for snap_scaffold_20-snap.2059-T1
Valid prediction for snap_scaffold_20-snap.2060-T1
Valid prediction for snap_scaffold_20-snap.2058-T1
Valid prediction for snap_scaffold_20-snap.2057-T1
Valid prediction for Augustus_model.g30967.t1
Valid prediction for pasa_asmbl_26032.p1
Valid prediction for HiQ_model.g30968.t1
Valid prediction for HiQ_model.g30954.t1
Valid prediction for Augustus_model.g30980.t1
Valid prediction for GlimmerHMM_glimmerT_46620-T1
Valid prediction for snap_scaffold_20-snap.2089-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20349, rend_intergenic: 13936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24046, rend_intergenic: 20351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69816, rend_intergenic: 67977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131488, rend_intergenic: 124002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164395, rend_intergenic: 161401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201197, rend_intergenic: 189429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 290077
-exon list size: 580


building trellis

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54.6    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.8    
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    
58.8    
58.9    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.4    
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    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 47 predictions from path traversal
Error with prediction: snap lend_intergenic: 20349, rend_intergenic: 13936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24046, rend_intergenic: 20351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69816, rend_intergenic: 67977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131488, rend_intergenic: 124002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164395, rend_intergenic: 161401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201197, rend_intergenic: 189429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support