-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_8320435-8477387

-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.48547_t
Valid prediction for GlimmerHMM_glimmerT_28092-T1
Valid prediction for GeneMark_model.48568_t
Valid prediction for snap_scaffold_11-snap.1915-T1
Valid prediction for GeneMark_model.48583_t
Couldn't classify 142221, 142335
Couldn't classify 148319, 148404
Sorry, prediction pasa_asmbl_5744.p1 fails validation.
(ACC)	 AG	142221-142335	GT	AGG
(GAG)	 AG	143365-143484	GT	GGG
(AGA)	 AG	145936-146022	GT	AGG
(AAA)	 AG	146260-146347	GT	AGG
(CTG)	 AG	147427-147505	GT	AGG
(GAT)	 AG	147755-147836	GT	GGG
(ACA)	 AG	148319-148404	GT	AGG
-recovered pasa_asmbl_5744.p1, internal, 142221, 142335
-recovered pasa_asmbl_5744.p1, internal, 143365, 143484
-recovered pasa_asmbl_5744.p1, internal, 145936, 146022
-recovered pasa_asmbl_5744.p1, internal, 146260, 146347
-recovered pasa_asmbl_5744.p1, internal, 147427, 147505
-recovered pasa_asmbl_5744.p1, internal, 147755, 147836
-recovered pasa_asmbl_5744.p1, internal, 148319, 148404
Valid prediction for GeneMark_model.48581_t
Valid prediction for GlimmerHMM_glimmerT_28087-T1
Valid prediction for GlimmerHMM_glimmerT_28101-T1
Valid prediction for snap_scaffold_11-snap.1908-T1
Valid prediction for snap_scaffold_11-snap.1913-T1
Valid prediction for snap_scaffold_11-snap.1903-T1
Valid prediction for GlimmerHMM_glimmerT_28106-T1
Valid prediction for GeneMark_model.48554_t
Couldn't classify 6010, 6066
Sorry, prediction pasa_asmbl_6260.p1 fails validation.
(GAA)	 AG	6010-6066	GT	AGG
(GGC)	 AG	6189-6350	GT	GGG
(TAC)	 AG	6721-6822	GT	GAG
-recovered pasa_asmbl_6260.p1, terminal, 6721, 6822
-recovered pasa_asmbl_6260.p1, internal, 6010, 6066
-recovered pasa_asmbl_6260.p1, internal, 6189, 6350
-recovered pasa_asmbl_6260.p1, internal, 6721, 6822
Valid prediction for GlimmerHMM_glimmerT_28110-T1
Valid prediction for GeneMark_model.48578_t
Valid prediction for Augustus_model.g18752.t1
Valid prediction for Augustus_model.g18739.t1
Valid prediction for Augustus_model.g18748.t1
Valid prediction for GlimmerHMM_glimmerT_28108-T1
Valid prediction for pasa_asmbl_5733.p1
Valid prediction for snap_scaffold_11-snap.1921-T1
Valid prediction for pasa_asmbl_5728.p1
Valid prediction for CodingQuarry_transcript_8134-T1
Valid prediction for GlimmerHMM_glimmerT_28102-T1
Valid prediction for Augustus_model.g18742.t1
Valid prediction for GeneMark_model.48546_t
Valid prediction for HiQ_model.g18735.t1
Valid prediction for HiQ_model.g18747.t1
Valid prediction for snap_scaffold_11-snap.1926-T1
Valid prediction for Augustus_model.g18745.t1
Valid prediction for GeneMark_model.48585_t
Valid prediction for snap_scaffold_11-snap.1901-T1
Couldn't classify 30599, 30705
Couldn't classify 32098, 32348
Sorry, prediction pasa_asmbl_6279.p1 fails validation.
(TCA)	 CA	30599-30705	GT	AAG
(GTG)	 AG	30879-31041	GT	AGG
(GCG)	 AG	31878-31995	GT	TGG
(GGA)	 AG	32098-32348	CC	TGC
-recovered pasa_asmbl_6279.p1, internal, 30879, 31041
-recovered pasa_asmbl_6279.p1, internal, 31878, 31995
Valid prediction for GeneMark_model.48556_t
Valid prediction for CodingQuarry_transcript_8133-T1
Valid prediction for GeneMark_model.48544_t
Couldn't classify 123799, 124473
Sorry, prediction pasa_asmbl_5742.p1 fails validation.
(CCT)	 GG	123799-124473	TG	GAT
Valid prediction for GeneMark_model.48576_t
Valid prediction for GeneMark_model.48548_t
Valid prediction for snap_scaffold_11-snap.1922-T1
Valid prediction for GeneMark_model.48559_t
Valid prediction for Augustus_model.g18743.t1
Valid prediction for GlimmerHMM_glimmerT_28100-T1
Valid prediction for snap_scaffold_11-snap.1917-T1
Valid prediction for GlimmerHMM_glimmerT_28107-T1
Valid prediction for GeneMark_model.48565_t
Valid prediction for GlimmerHMM_glimmerT_28089-T1
Couldn't classify 33782, 33829
Sorry, prediction pasa_asmbl_5717.p1 fails validation.
(ATG)	 CC	32502-32594	GT	TTG
(CCA)	 AG	32764-33019	GT	TGG
(GTA)	 AG	33275-33313	GT	AAG
(AGA)	 AG	33534-33637	GT	AGG
(CTG)	 AG	33782-33829	CC	CCC
-recovered pasa_asmbl_5717.p1, initial, 32502, 32594
-recovered pasa_asmbl_5717.p1, internal, 32764, 33019
-recovered pasa_asmbl_5717.p1, internal, 33275, 33313
-recovered pasa_asmbl_5717.p1, internal, 33534, 33637
Valid prediction for snap_scaffold_11-snap.1910-T1
Couldn't classify 100054, 100098
Couldn't classify 110479, 110521
Sorry, prediction pasa_asmbl_5738.p1 fails validation.
(CTA)	 AG	100054-100098	GT	AGG
(GGT)	 AG	100559-100648	GT	AGG
(TAC)	 AG	101140-101265	GT	AGG
(GTG)	 AG	102642-102801	GT	TGG
(ATA)	 AG	103185-103258	GT	AGG
(GAC)	 AG	103719-103799	GT	GGG
(CAG)	 AG	104395-104454	GT	AGG
(GTG)	 AG	104911-105056	GT	AAG
(GCC)	 AG	105218-105308	GT	CAG
(ATG)	 AG	105554-105625	GT	TTG
(GAG)	 AG	105737-105861	GC	AGG
(GCA)	 AG	106030-106162	GT	AGG
(ATC)	 AG	106585-106689	GT	AGG
(TAT)	 AG	107087-107193	GT	TTG
(CTG)	 AG	107415-107569	GT	GGG
(GAT)	 AG	107862-107972	GT	GGG
(GAC)	 AG	108342-108450	GT	AGG
(GAA)	 AG	108894-108926	GT	AGG
(TCT)	 AG	110479-110521	AG	AAA
-recovered pasa_asmbl_5738.p1, initial, 105554, 105625
add_exon() Sorry, pasa_asmbl_5738.p1 104911-105056-terminal-2 is invalid.
-recovered pasa_asmbl_5738.p1, terminal, 104911, 105056
-recovered pasa_asmbl_5738.p1, internal, 100054, 100098
-recovered pasa_asmbl_5738.p1, internal, 100559, 100648
-recovered pasa_asmbl_5738.p1, internal, 101140, 101265
-recovered pasa_asmbl_5738.p1, internal, 102642, 102801
-recovered pasa_asmbl_5738.p1, internal, 103185, 103258
-recovered pasa_asmbl_5738.p1, internal, 103719, 103799
-recovered pasa_asmbl_5738.p1, internal, 104395, 104454
-recovered pasa_asmbl_5738.p1, internal, 104911, 105056
-recovered pasa_asmbl_5738.p1, internal, 105218, 105308
-recovered pasa_asmbl_5738.p1, internal, 105554, 105625
-recovered pasa_asmbl_5738.p1, internal, 105737, 105861
-recovered pasa_asmbl_5738.p1, internal, 106030, 106162
-recovered pasa_asmbl_5738.p1, internal, 106585, 106689
-recovered pasa_asmbl_5738.p1, internal, 107087, 107193
-recovered pasa_asmbl_5738.p1, internal, 107415, 107569
-recovered pasa_asmbl_5738.p1, internal, 107862, 107972
-recovered pasa_asmbl_5738.p1, internal, 108342, 108450
-recovered pasa_asmbl_5738.p1, internal, 108894, 108926
Valid prediction for snap_scaffold_11-snap.1907-T1
Valid prediction for snap_scaffold_11-snap.1904-T1
Valid prediction for snap_scaffold_11-snap.1912-T1
Valid prediction for Augustus_model.g18753.t1
Valid prediction for snap_scaffold_11-snap.1927-T1
Valid prediction for GlimmerHMM_glimmerT_28103-T1
Valid prediction for GlimmerHMM_glimmerT_28091-T1
Valid prediction for GlimmerHMM_glimmerT_28111-T1
Valid prediction for pasa_asmbl_5723.p1
Valid prediction for GeneMark_model.48560_t
Valid prediction for GeneMark_model.48572_t
Valid prediction for CodingQuarry_transcript_8135-T1
Valid prediction for HiQ_model.g18733.t1
Valid prediction for GeneMark_model.48549_t
Valid prediction for GlimmerHMM_glimmerT_28097-T1
Valid prediction for HiQ_model.g18744.t1
Valid prediction for snap_scaffold_11-snap.1914-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_8137-T1
Valid prediction for snap_scaffold_11-snap.1924-T1
Valid prediction for HiQ_model.g18746.t1
Valid prediction for GeneMark_model.48564_t
Valid prediction for pasa_asmbl_5715.p1
Valid prediction for GlimmerHMM_glimmerT_28090-T1
Valid prediction for snap_scaffold_11-snap.1916-T1
Valid prediction for CodingQuarry_transcript_8130-T1
Valid prediction for Augustus_model.g18737.t1
Valid prediction for pasa_asmbl_5722.p1
Valid prediction for GlimmerHMM_glimmerT_28093-T1
Valid prediction for Augustus_model.g18750.t1
Valid prediction for GlimmerHMM_glimmerT_28104-T1
Valid prediction for CodingQuarry_transcript_8128-T1
Valid prediction for GlimmerHMM_glimmerT_28096-T1
Valid prediction for GeneMark_model.48574_t
Valid prediction for GeneMark_model.48562_t
Valid prediction for GeneMark_model.48551_t
Valid prediction for GeneMark_model.48587_t
Valid prediction for GeneMark_model.48570_t
Couldn't classify 44438, 44510
Couldn't classify 46860, 47071
Sorry, prediction pasa_asmbl_5719.p1 fails validation.
(TGC)	 AG	44438-44510	GT	AGG
(AGC)	 AG	46309-46396	GT	TGG
(GTT)	 AG	46506-46561	GT	AGG
(GAT)	 AG	46722-46766	GT	CGG
(GTG)	 AG	46860-47071	AC	GGA
-recovered pasa_asmbl_5719.p1, internal, 44438, 44510
-recovered pasa_asmbl_5719.p1, internal, 46309, 46396
-recovered pasa_asmbl_5719.p1, internal, 46506, 46561
-recovered pasa_asmbl_5719.p1, internal, 46722, 46766
Valid prediction for GlimmerHMM_glimmerT_28109-T1
Valid prediction for snap_scaffold_11-snap.1919-T1
Valid prediction for Augustus_model.g18751.t1
Valid prediction for CodingQuarry_transcript_8136-T1
Valid prediction for GlimmerHMM_glimmerT_28112-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_11-snap.1920-T1
Valid prediction for GlimmerHMM_glimmerT_28098-T1
Valid prediction for snap_scaffold_11-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_28105-T1
Valid prediction for GeneMark_model.48553_t
Valid prediction for GeneMark_model.48552_t
Valid prediction for snap_scaffold_11-snap.1902-T1
Valid prediction for GeneMark_model.48545_t
Valid prediction for Augustus_model.g18736.t1
Valid prediction for HiQ_model.g18740.t1
Valid prediction for snap_scaffold_11-snap.1928-T1
Valid prediction for GeneMark_model.48586_t
Valid prediction for GlimmerHMM_glimmerT_28099-T1
Valid prediction for snap_scaffold_11-snap.1929-T1
Valid prediction for CodingQuarry_transcript_8127-T1
Valid prediction for snap_scaffold_11-snap.1911-T1
Valid prediction for snap_scaffold_11-snap.1923-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g18741.t1
Valid prediction for GeneMark_model.48575_t
Valid prediction for snap_scaffold_11-snap.1918-T1
Valid prediction for GeneMark_model.48584_t
Valid prediction for GeneMark_model.48557_t
Valid prediction for GeneMark_model.48582_t
Valid prediction for Augustus_model.g18738.t1
Valid prediction for snap_scaffold_11-snap.1906-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.48573_t
Valid prediction for GeneMark_model.48558_t
Valid prediction for GeneMark_model.48571_t
Valid prediction for HiQ_model.g18734.t1
Valid prediction for GeneMark_model.48579_t
Valid prediction for GeneMark_model.48561_t
Valid prediction for GeneMark_model.48567_t
Valid prediction for GeneMark_model.48566_t
Valid prediction for GeneMark_model.48577_t
Valid prediction for pasa_asmbl_6838.p1
Valid prediction for GeneMark_model.48563_t
Valid prediction for GlimmerHMM_glimmerT_28094-T1
Valid prediction for GeneMark_model.48555_t
Couldn't classify 99944, 100003
Couldn't classify 100105, 100177
Sorry, prediction CodingQuarry_transcript_8132-T1 fails validation.
(ATG)	 AA	98409-98411	GT	TGG
(AGT)	 AG	99290-99386	GT	CAG
(TGA)	 AG	99514-99563	GC	AGG
(GAT)	 AG	99944-100003	AT	TCA
(TAT)	 TC	100105-100177	GT	GGG
(GAT)	 AG	100285-100358	GT	AGG
(GTT)	 AG	100638-100709	AA	AGA
-recovered CodingQuarry_transcript_8132-T1, initial, 98409, 98411
-recovered CodingQuarry_transcript_8132-T1, terminal, 100638, 100709
-recovered CodingQuarry_transcript_8132-T1, internal, 99290, 99386
-recovered CodingQuarry_transcript_8132-T1, internal, 99514, 99563
-recovered CodingQuarry_transcript_8132-T1, internal, 100285, 100358
Valid prediction for GeneMark_model.48580_t
Valid prediction for Augustus_model.g18749.t1
Valid prediction for GlimmerHMM_glimmerT_28088-T1
Valid prediction for snap_scaffold_11-snap.1905-T1
Valid prediction for GeneMark_model.48569_t
Valid prediction for CodingQuarry_transcript_8131-T1
Valid prediction for GlimmerHMM_glimmerT_28095-T1
Valid prediction for GeneMark_model.48550_t
Valid prediction for snap_scaffold_11-snap.1909-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24135, rend_intergenic: 18830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27119, rend_intergenic: 24336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39048, rend_intergenic: 37140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94186, rend_intergenic: 88388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100687, rend_intergenic: 96375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102917, rend_intergenic: 101098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103792, rend_intergenic: 103130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124473, rend_intergenic: 119727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135417, rend_intergenic: 133702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141910, rend_intergenic: 135776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148601, rend_intergenic: 141949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156953
-exon list size: 663


building trellis

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62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
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    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
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    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
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 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 24135, rend_intergenic: 18830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27119, rend_intergenic: 24336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39048, rend_intergenic: 37140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94186, rend_intergenic: 88388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100687, rend_intergenic: 96375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102917, rend_intergenic: 101098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103792, rend_intergenic: 103130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124473, rend_intergenic: 119727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135417, rend_intergenic: 133702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141910, rend_intergenic: 135776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148601, rend_intergenic: 141949  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