-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_11650643-11843916

-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_19-snap.2301-T1
Valid prediction for GeneMark_model.80183_t
Valid prediction for snap_scaffold_19-snap.2277-T1
Valid prediction for GlimmerHMM_glimmerT_46022-T1
Valid prediction for GlimmerHMM_glimmerT_46034-T1
Valid prediction for Augustus_model.g30698.t1
Valid prediction for snap_scaffold_19-snap.2293-T1
Valid prediction for snap_scaffold_19-snap.2300-T1
Valid prediction for snap_scaffold_19-snap.2280-T1
Valid prediction for Augustus_model.g30689.t1
Valid prediction for Augustus_model.g30691.t1
Valid prediction for snap_scaffold_19-snap.2305-T1
Valid prediction for HiQ_model.g30705.t1
Valid prediction for GlimmerHMM_glimmerT_46028-T1
Valid prediction for snap_scaffold_19-snap.2311-T1
Valid prediction for GlimmerHMM_glimmerT_46014-T1
Valid prediction for snap_scaffold_19-snap.2303-T1
Valid prediction for snap_scaffold_19-snap.2282-T1
Valid prediction for snap_scaffold_19-snap.2286-T1
Valid prediction for Augustus_model.g30703.t1
Valid prediction for GlimmerHMM_glimmerT_46016-T1
Valid prediction for GlimmerHMM_glimmerT_46030-T1
Valid prediction for GeneMark_model.80181_t
Valid prediction for Augustus_model.g30690.t1
Valid prediction for Augustus_model.g30700.t1
Couldn't classify 125471, 125510
Sorry, prediction pasa_asmbl_22528.p1 fails validation.
(AAA)	 CC	125471-125510	GT	GGG
(GAA)	 AG	126243-126284	GT	CCG
(ACA)	 AG	126534-126592	GT	TGG
(ATG)	 AG	126921-127016	GT	AGG
(CTC)	 AG	127191-127299	GT	GGG
(ATG)	 AG	127600-127793	GT	CGG
(ATA)	 AG	128271-128354	GT	AGG
(ACA)	 AG	128555-128776	GT	AGG
(AGA)	 AG	129488-129658	GT	ATG
(GTG)	 AG	129999-130160	GT	AGG
(GTG)	 AG	130338-130403	GT	AGG
(ATT)	 AG	130525-130573	GT	AAG
(AAA)	 AG	130793-130827	AC	AAA
-recovered pasa_asmbl_22528.p1, initial, 126921, 127016
-recovered pasa_asmbl_22528.p1, initial, 127600, 127793
-recovered pasa_asmbl_22528.p1, terminal, 130793, 130827
-recovered pasa_asmbl_22528.p1, internal, 126243, 126284
-recovered pasa_asmbl_22528.p1, internal, 126534, 126592
-recovered pasa_asmbl_22528.p1, internal, 126921, 127016
-recovered pasa_asmbl_22528.p1, internal, 127191, 127299
-recovered pasa_asmbl_22528.p1, internal, 127600, 127793
-recovered pasa_asmbl_22528.p1, internal, 128271, 128354
-recovered pasa_asmbl_22528.p1, internal, 128555, 128776
-recovered pasa_asmbl_22528.p1, internal, 129488, 129658
-recovered pasa_asmbl_22528.p1, internal, 129999, 130160
-recovered pasa_asmbl_22528.p1, internal, 130338, 130403
-recovered pasa_asmbl_22528.p1, internal, 130525, 130573
Valid prediction for GeneMark_model.80192_t
Valid prediction for GlimmerHMM_glimmerT_46013-T1
Valid prediction for GlimmerHMM_glimmerT_46037-T1
Valid prediction for snap_scaffold_19-snap.2284-T1
Couldn't classify 176961, 177116
Sorry, prediction pasa_asmbl_22532.p1 fails validation.
(ATG)	 CC	172487-173333	GT	CGG
(ACT)	 AG	174143-174240	GT	AGG
(ATC)	 AG	175108-175209	GT	GGG
(TGG)	 AG	176961-177116	CC	CAC
-recovered pasa_asmbl_22532.p1, initial, 172487, 173333
-recovered pasa_asmbl_22532.p1, internal, 174143, 174240
-recovered pasa_asmbl_22532.p1, internal, 175108, 175209
Valid prediction for GeneMark_model.80187_t
Valid prediction for snap_scaffold_19-snap.2304-T1
Valid prediction for GlimmerHMM_glimmerT_46031-T1
Valid prediction for GeneMark_model.80178_t
Valid prediction for Augustus_model.g30704.t1
Valid prediction for GeneMark_model.80205_t
Valid prediction for GlimmerHMM_glimmerT_46029-T1
Couldn't classify 30394, 30549
Couldn't classify 31971, 32194
Sorry, prediction pasa_asmbl_22520.p1 fails validation.
(GAA)	 CA	30394-30549	GT	AGG
(TCT)	 AG	31639-31729	GT	GAG
(ATC)	 AG	31971-32194	TA	GGT
-recovered pasa_asmbl_22520.p1, internal, 31639, 31729
Valid prediction for snap_scaffold_19-snap.2307-T1
Valid prediction for GeneMark_model.80185_t
Valid prediction for GeneMark_model.80180_t
Valid prediction for snap_scaffold_19-snap.2298-T1
Valid prediction for snap_scaffold_19-snap.2308-T1
Valid prediction for GlimmerHMM_glimmerT_46026-T1
Valid prediction for GlimmerHMM_glimmerT_46019-T1
Valid prediction for GeneMark_model.80197_t
Valid prediction for GeneMark_model.80170_t
Valid prediction for GeneMark_model.80189_t
Couldn't classify 147132, 147149
Sorry, prediction pasa_asmbl_22529.p1 fails validation.
(TCC)	 AC	147132-147149	GT	CAG
(GTG)	 AG	147523-147558	GT	AGG
(GGC)	 AG	148010-148150	GT	AGG
(GAC)	 AG	148415-148585	GT	AGG
(GAG)	 AG	148710-148802	GT	CCG
(AAA)	 AG	149699-149843	GT	GGG
(AGC)	 AG	152454-152503	GT	AGG
(GTG)	 AG	152670-152790	GT	GAG
(GGG)	 AG	153101-153180	GT	ATG
(ATC)	 AG	153355-153459	GT	AGG
(CTG)	 AG	153638-153748	TG	GAT
-recovered pasa_asmbl_22529.p1, terminal, 153638, 153748
-recovered pasa_asmbl_22529.p1, internal, 147523, 147558
-recovered pasa_asmbl_22529.p1, internal, 148010, 148150
-recovered pasa_asmbl_22529.p1, internal, 148415, 148585
-recovered pasa_asmbl_22529.p1, internal, 148710, 148802
-recovered pasa_asmbl_22529.p1, internal, 149699, 149843
-recovered pasa_asmbl_22529.p1, internal, 152454, 152503
-recovered pasa_asmbl_22529.p1, internal, 152670, 152790
-recovered pasa_asmbl_22529.p1, internal, 153101, 153180
-recovered pasa_asmbl_22529.p1, internal, 153355, 153459
Valid prediction for Augustus_model.g30692.t1
Valid prediction for snap_scaffold_19-snap.2288-T1
Valid prediction for GlimmerHMM_glimmerT_46025-T1
Valid prediction for snap_scaffold_19-snap.2312-T1
Valid prediction for GlimmerHMM_glimmerT_46017-T1
Valid prediction for GlimmerHMM_glimmerT_46035-T1
Valid prediction for GlimmerHMM_glimmerT_46023-T1
Valid prediction for GeneMark_model.80196_t
Valid prediction for GlimmerHMM_glimmerT_46020-T1
Valid prediction for GeneMark_model.80202_t
Valid prediction for GeneMark_model.80172_t
Valid prediction for GlimmerHMM_glimmerT_46032-T1
Valid prediction for Augustus_model.g30695.t1
Valid prediction for GeneMark_model.80209_t
Valid prediction for Augustus_model.g30693.t1
Valid prediction for snap_scaffold_19-snap.2295-T1
Valid prediction for Augustus_model.g30702.t1
Valid prediction for GeneMark_model.80194_t
Valid prediction for Augustus_model.g30707.t1
Valid prediction for GeneMark_model.80200_t
Valid prediction for GeneMark_model.80175_t
Valid prediction for GeneMark_model.80168_t

-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_46012-T1
Valid prediction for GeneMark_model.80190_t
Valid prediction for snap_scaffold_19-snap.2299-T1
Valid prediction for GlimmerHMM_glimmerT_46027-T1
Valid prediction for GeneMark_model.80198_t
Valid prediction for snap_scaffold_19-snap.2275-T1
Valid prediction for snap_scaffold_19-snap.2281-T1
Couldn't classify 114559, 114732
Sorry, prediction pasa_asmbl_21644.p1 fails validation.
(CCT)	 CC	114559-114732	GT	AGG
(GTG)	 AG	115052-115153	GT	AGG
(AAG)	 AG	116783-116847	GT	AGG
(AAC)	 AG	117363-117445	GT	TGG
(GTG)	 AG	118654-118761	GT	AGG
(GCT)	 AG	121081-121280	GT	AGG
(GTG)	 AG	122293-122379	GT	AGG
(CTG)	 AG	122927-123104	GT	GGG
(TCC)	 AG	123473-123711	GT	AGG
(ATG)	 AG	123879-124040	AC	GAA
-recovered pasa_asmbl_21644.p1, terminal, 118654, 118761
-recovered pasa_asmbl_21644.p1, terminal, 123879, 124040
-recovered pasa_asmbl_21644.p1, internal, 115052, 115153
-recovered pasa_asmbl_21644.p1, internal, 116783, 116847
-recovered pasa_asmbl_21644.p1, internal, 117363, 117445
-recovered pasa_asmbl_21644.p1, internal, 118654, 118761
-recovered pasa_asmbl_21644.p1, internal, 121081, 121280
-recovered pasa_asmbl_21644.p1, internal, 122293, 122379
-recovered pasa_asmbl_21644.p1, internal, 122927, 123104
-recovered pasa_asmbl_21644.p1, internal, 123473, 123711
Valid prediction for GlimmerHMM_glimmerT_46015-T1
Valid prediction for GeneMark_model.80206_t
Valid prediction for Augustus_model.g30697.t1
Valid prediction for GeneMark_model.80186_t
Valid prediction for GeneMark_model.80201_t
Valid prediction for snap_scaffold_19-snap.2310-T1
Valid prediction for Augustus_model.g30701.t1
Valid prediction for GeneMark_model.80184_t
Valid prediction for snap_scaffold_19-snap.2279-T1
Valid prediction for GeneMark_model.80169_t
Couldn't classify 122104, 122379
Sorry, prediction pasa_asmbl_21645.p1 fails validation.
(TTG)	 GA	122104-122379	GT	AGG
(CTG)	 AG	122927-123104	GT	GGG
(TCC)	 AG	123473-123711	GT	AGG
(ATG)	 AG	123879-124040	AC	GAA
-recovered pasa_asmbl_21645.p1, terminal, 123879, 124040
-recovered pasa_asmbl_21645.p1, internal, 122927, 123104
-recovered pasa_asmbl_21645.p1, internal, 123473, 123711
Valid prediction for GeneMark_model.80174_t
Valid prediction for GlimmerHMM_glimmerT_46018-T1
Valid prediction for GeneMark_model.80193_t
Valid prediction for GlimmerHMM_glimmerT_46038-T1
Valid prediction for snap_scaffold_19-snap.2297-T1
Valid prediction for snap_scaffold_19-snap.2291-T1
Valid prediction for snap_scaffold_19-snap.2276-T1
Valid prediction for snap_scaffold_19-snap.2294-T1
Valid prediction for GeneMark_model.80176_t
Valid prediction for snap_scaffold_19-snap.2287-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2285-T1
Valid prediction for GeneMark_model.80199_t
Valid prediction for snap_scaffold_19-snap.2302-T1
Valid prediction for Augustus_model.g30699.t1
Valid prediction for GeneMark_model.80208_t
Valid prediction for GeneMark_model.80204_t
Valid prediction for GlimmerHMM_glimmerT_46021-T1
Valid prediction for GeneMark_model.80177_t
Valid prediction for snap_scaffold_19-snap.2314-T1
Valid prediction for Augustus_model.g30706.t1
Valid prediction for snap_scaffold_19-snap.2313-T1
Valid prediction for GeneMark_model.80179_t
Valid prediction for Augustus_model.g30694.t1
Valid prediction for snap_scaffold_19-snap.2292-T1
Valid prediction for GeneMark_model.80182_t
Valid prediction for GlimmerHMM_glimmerT_46024-T1
Valid prediction for snap_scaffold_19-snap.2315-T1
Valid prediction for GlimmerHMM_glimmerT_46036-T1
Valid prediction for GeneMark_model.80173_t
Valid prediction for GeneMark_model.80188_t
Valid prediction for snap_scaffold_19-snap.2283-T1
Valid prediction for snap_scaffold_19-snap.2306-T1
Valid prediction for snap_scaffold_19-snap.2290-T1
Valid prediction for snap_scaffold_19-snap.2296-T1
Valid prediction for Augustus_model.g30709.t1
Valid prediction for snap_scaffold_19-snap.2316-T1
Valid prediction for snap_scaffold_19-snap.2309-T1
Valid prediction for snap_scaffold_19-snap.2289-T1
Valid prediction for snap_scaffold_19-snap.2278-T1
Valid prediction for GlimmerHMM_glimmerT_46033-T1
Valid prediction for GeneMark_model.80203_t
Valid prediction for Augustus_model.g30708.t1
Valid prediction for Augustus_model.g30696.t1
Valid prediction for GeneMark_model.80171_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9854, rend_intergenic: 8301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16200, rend_intergenic: 10090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20984, rend_intergenic: 16407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27706, rend_intergenic: 21511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32658, rend_intergenic: 27813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40141, rend_intergenic: 37811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40418, rend_intergenic: 40193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44439, rend_intergenic: 40628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46986, rend_intergenic: 44548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48706, rend_intergenic: 47824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77147, rend_intergenic: 74024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80637, rend_intergenic: 78391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97307, rend_intergenic: 96276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151807, rend_intergenic: 141612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193274
-exon list size: 626


building trellis

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74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9854, rend_intergenic: 8301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16200, rend_intergenic: 10090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20984, rend_intergenic: 16407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27706, rend_intergenic: 21511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32658, rend_intergenic: 27813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40141, rend_intergenic: 37811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40418, rend_intergenic: 40193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44439, rend_intergenic: 40628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46986, rend_intergenic: 44548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48706, rend_intergenic: 47824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77147, rend_intergenic: 74024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80637, rend_intergenic: 78391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97307, rend_intergenic: 96276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151807, rend_intergenic: 141612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support