-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_6627047-6797428

-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_21-snap.1399-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49110-T1
Valid prediction for HiQ_model.g32913.t1
Valid prediction for GlimmerHMM_glimmerT_49125-T1
Valid prediction for GlimmerHMM_glimmerT_49123-T1
Valid prediction for snap_scaffold_21-snap.1390-T1
Valid prediction for GeneMark_model.85124_t
Valid prediction for GeneMark_model.85142_t
Valid prediction for HiQ_model.g32924.t1
Valid prediction for GeneMark_model.85136_t
Valid prediction for snap_scaffold_21-snap.1370-T1
Valid prediction for snap_scaffold_21-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_49100-T1
Valid prediction for GeneMark_model.85107_t
Valid prediction for GeneMark_model.85116_t
Valid prediction for GeneMark_model.85122_t
Valid prediction for Augustus_model.g32932.t1
Valid prediction for snap_scaffold_21-snap.1392-T1
Valid prediction for GeneMark_model.85134_t
Valid prediction for CodingQuarry_transcript_32542-T1
Valid prediction for snap_scaffold_21-snap.1381-T1
Valid prediction for GlimmerHMM_glimmerT_49116-T1
Valid prediction for Augustus_model.g32925.t1
Valid prediction for Augustus_model.g32923.t1
Valid prediction for GlimmerHMM_glimmerT_49128-T1
Valid prediction for GeneMark_model.85106_t
Valid prediction for Augustus_model.g32936.t1
Valid prediction for snap_scaffold_21-snap.1407-T1
Valid prediction for snap_scaffold_21-snap.1400-T1
Valid prediction for GeneMark_model.85139_t
Valid prediction for GlimmerHMM_glimmerT_49122-T1
Valid prediction for snap_scaffold_21-snap.1389-T1
Valid prediction for HiQ_model.g32926.t1
Valid prediction for GlimmerHMM_glimmerT_49097-T1
Couldn't classify 26025, 26348
Sorry, prediction pasa_asmbl_28706.p1 fails validation.
(GTC)	 CT	26025-26348	AG	GAA
Couldn't classify 21958, 22214
Couldn't classify 25585, 25973
Sorry, prediction pasa_asmbl_28705.p1 fails validation.
(CCA)	 AT	21958-22214	GT	GGG
(AGC)	 AG	22342-22383	GT	AGG
(GCG)	 AG	22613-22724	GT	AGG
(ACT)	 AG	25312-25504	GT	AGG
(AAG)	 AG	25585-25973	AC	CCA
-recovered pasa_asmbl_28705.p1, internal, 22342, 22383
-recovered pasa_asmbl_28705.p1, internal, 22613, 22724
-recovered pasa_asmbl_28705.p1, internal, 25312, 25504
Valid prediction for GlimmerHMM_glimmerT_49098-T1
Valid prediction for GeneMark_model.85143_t
Valid prediction for GeneMark_model.85109_t
Valid prediction for snap_scaffold_21-snap.1401-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1386-T1
Valid prediction for snap_scaffold_21-snap.1388-T1
Valid prediction for HiQ_model.g32935.t1
Valid prediction for pasa_asmbl_28710.p1
Valid prediction for pasa_asmbl_28701.p1
Valid prediction for CodingQuarry_transcript_32538-T1
Valid prediction for GlimmerHMM_glimmerT_49120-T1
Valid prediction for CodingQuarry_transcript_32539-T1
Couldn't classify 97029, 97113
Sorry, prediction pasa_asmbl_28712.p1 fails validation.
(GGG)	 AG	97029-97113	GT	TGG
(GGT)	 AG	97308-97449	GT	AGG
(AAT)	 AG	97577-97682	TT	GAT
-recovered pasa_asmbl_28712.p1, terminal, 97577, 97682
-recovered pasa_asmbl_28712.p1, internal, 97029, 97113
-recovered pasa_asmbl_28712.p1, internal, 97308, 97449
Valid prediction for GlimmerHMM_glimmerT_49099-T1
Valid prediction for GeneMark_model.85112_t
Valid prediction for GlimmerHMM_glimmerT_49114-T1
Couldn't classify 4538, 4612
Sorry, prediction pasa_asmbl_28699.p1 fails validation.
(GTG)	 TG	4538-4612	GT	AAG
(GTA)	 AG	4747-4881	GT	AGG
(TTT)	 AG	5011-5084	GT	AGG
(CAA)	 AG	5209-5305	TC	GAT
-recovered pasa_asmbl_28699.p1, terminal, 5209, 5305
-recovered pasa_asmbl_28699.p1, internal, 4747, 4881
-recovered pasa_asmbl_28699.p1, internal, 5011, 5084
Valid prediction for snap_scaffold_21-snap.1375-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49115-T1
Valid prediction for CodingQuarry_transcript_32536-T1
Couldn't classify 98877, 99185
Couldn't classify 100858, 100959
Sorry, prediction pasa_asmbl_28713.p1 fails validation.
(GAC)	 GT	98877-99185	GT	CAG
(TTG)	 AG	99607-99726	GT	AGG
(GTC)	 AG	99807-99965	GT	AGG
(GAT)	 AG	100131-100222	GT	AAG
(GAA)	 AG	100314-100434	GT	AGG
(GAG)	 AG	100858-100959	AA	ACA
-recovered pasa_asmbl_28713.p1, internal, 99607, 99726
-recovered pasa_asmbl_28713.p1, internal, 99807, 99965
-recovered pasa_asmbl_28713.p1, internal, 100131, 100222
-recovered pasa_asmbl_28713.p1, internal, 100314, 100434
Couldn't classify 85570, 85664
Sorry, prediction pasa_asmbl_28988.p1 fails validation.
(AAG)	 GA	85570-85664	GT	AGG
(GAC)	 AG	86493-86632	GT	ATG
(TTC)	 AG	86842-86887	GT	TGG
(TGA)	 AG	87005-87099	GT	TGG
(TTC)	 AG	87215-87285	GT	AGG
(GAG)	 AG	87564-87704	GT	GAG
(CCA)	 AG	87827-87858	GT	TGG
(GGC)	 AG	88017-88111	GT	GGG
(CTT)	 AG	88293-88376	GT	CGG
(TTC)	 AG	88499-88563	CA	AGC
-recovered pasa_asmbl_28988.p1, terminal, 88499, 88563
-recovered pasa_asmbl_28988.p1, internal, 86493, 86632
-recovered pasa_asmbl_28988.p1, internal, 86842, 86887
-recovered pasa_asmbl_28988.p1, internal, 87005, 87099
-recovered pasa_asmbl_28988.p1, internal, 87215, 87285
-recovered pasa_asmbl_28988.p1, internal, 87564, 87704
-recovered pasa_asmbl_28988.p1, internal, 87827, 87858
-recovered pasa_asmbl_28988.p1, internal, 88017, 88111
-recovered pasa_asmbl_28988.p1, internal, 88293, 88376
Valid prediction for pasa_asmbl_28717.p1
Valid prediction for snap_scaffold_21-snap.1377-T1
Valid prediction for Augustus_model.g32937.t1
Valid prediction for GeneMark_model.85125_t
Valid prediction for GlimmerHMM_glimmerT_49117-T1
Valid prediction for HiQ_model.g32922.t1
Valid prediction for Augustus_model.g32929.t1
Valid prediction for GeneMark_model.85141_t
Valid prediction for snap_scaffold_21-snap.1405-T1
Valid prediction for GlimmerHMM_glimmerT_49126-T1
Valid prediction for Augustus_model.g32931.t1
Valid prediction for snap_scaffold_21-snap.1368-T1
Valid prediction for snap_scaffold_21-snap.1396-T1
Valid prediction for HiQ_model.g32914.t1
Valid prediction for snap_scaffold_21-snap.1365-T1
Couldn't classify 125462, 126169
Sorry, prediction pasa_asmbl_28716.p1 fails validation.
(GTC)	 CT	125462-126169	TA	GAT
Valid prediction for snap_scaffold_21-snap.1397-T1
Valid prediction for Augustus_model.g32933.t1
Valid prediction for GlimmerHMM_glimmerT_49095-T1
Valid prediction for pasa_asmbl_28708.p1
Valid prediction for snap_scaffold_21-snap.1394-T1
Couldn't classify 96796, 96836
Sorry, prediction pasa_asmbl_28711.p1 fails validation.
(ATG)	 CA	95497-95551	GT	AGG
(GTG)	 AG	95660-95804	GT	AGG
(AGA)	 AG	95905-96019	GT	AGG
(TCT)	 AG	96138-96182	GT	AGG
(CCT)	 AG	96533-96683	GT	AGG
(GAC)	 AG	96796-96836	AC	GGA
-recovered pasa_asmbl_28711.p1, initial, 95497, 95551
-recovered pasa_asmbl_28711.p1, internal, 95660, 95804
-recovered pasa_asmbl_28711.p1, internal, 95905, 96019
-recovered pasa_asmbl_28711.p1, internal, 96138, 96182
-recovered pasa_asmbl_28711.p1, internal, 96533, 96683

-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.g32928.t1
Valid prediction for snap_scaffold_21-snap.1371-T1
Valid prediction for GlimmerHMM_glimmerT_49107-T1
Couldn't classify 65668, 65712
Sorry, prediction pasa_asmbl_27770.p1 fails validation.
(ATG)	 TC	64897-65024	GT	TGG
(CCC)	 AG	65402-65537	GT	AGG
(GTG)	 AG	65668-65712	CC	GCC
-recovered pasa_asmbl_27770.p1, initial, 64897, 65024
-recovered pasa_asmbl_27770.p1, internal, 65402, 65537
Valid prediction for snap_scaffold_21-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_49118-T1
Valid prediction for snap_scaffold_21-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_49105-T1
Valid prediction for snap_scaffold_21-snap.1376-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1385-T1
Valid prediction for GeneMark_model.85118_t
Valid prediction for snap_scaffold_21-snap.1383-T1
Valid prediction for Augustus_model.g32918.t1
Valid prediction for GeneMark_model.85113_t
Valid prediction for GeneMark_model.85114_t
Valid prediction for snap_scaffold_21-snap.1406-T1
Valid prediction for snap_scaffold_21-snap.1403-T1
Valid prediction for Augustus_model.g32915.t1
Valid prediction for Augustus_model.g32930.t1
Valid prediction for Augustus_model.g32919.t1
Valid prediction for snap_scaffold_21-snap.1373-T1
Valid prediction for GlimmerHMM_glimmerT_49127-T1
Valid prediction for GeneMark_model.85138_t
Valid prediction for GlimmerHMM_glimmerT_49113-T1
Valid prediction for GlimmerHMM_glimmerT_49096-T1
Valid prediction for GlimmerHMM_glimmerT_49103-T1
Valid prediction for GlimmerHMM_glimmerT_49101-T1
Valid prediction for GeneMark_model.85120_t
Valid prediction for Augustus_model.g32934.t1
Valid prediction for GlimmerHMM_glimmerT_49119-T1
Valid prediction for GeneMark_model.85135_t
Valid prediction for GeneMark_model.85126_t
Valid prediction for GeneMark_model.85123_t
Valid prediction for snap_scaffold_21-snap.1393-T1
Valid prediction for GeneMark_model.85128_t
Valid prediction for CodingQuarry_transcript_32537-T1
Valid prediction for snap_scaffold_21-snap.1372-T1
Valid prediction for snap_scaffold_21-snap.1395-T1
Valid prediction for Augustus_model.g32927.t1
Valid prediction for GeneMark_model.85119_t
Valid prediction for snap_scaffold_21-snap.1384-T1
Valid prediction for GlimmerHMM_glimmerT_49109-T1
Valid prediction for GlimmerHMM_glimmerT_49121-T1
Valid prediction for GeneMark_model.85140_t
Valid prediction for snap_scaffold_21-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_49112-T1
Valid prediction for snap_scaffold_21-snap.1380-T1
Couldn't classify 140646, 140675
Sorry, prediction pasa_asmbl_27766.p1 fails validation.
(CCA)	 CG	140646-140675	GT	AGG
(ATC)	 AG	140804-140905	GT	AGG
(GAC)	 AG	141013-141109	GT	TGG
(TGG)	 AG	141224-141386	GT	AGG
(TCT)	 AG	141528-141630	GT	AGG
(TTG)	 AG	141782-141853	TT	GAT
-recovered pasa_asmbl_27766.p1, terminal, 141782, 141853
-recovered pasa_asmbl_27766.p1, internal, 140804, 140905
-recovered pasa_asmbl_27766.p1, internal, 141013, 141109
-recovered pasa_asmbl_27766.p1, internal, 141224, 141386
-recovered pasa_asmbl_27766.p1, internal, 141528, 141630
Valid prediction for Augustus_model.g32916.t1
Valid prediction for GeneMark_model.85110_t
Valid prediction for GlimmerHMM_glimmerT_49111-T1
Valid prediction for snap_scaffold_21-snap.1402-T1
Valid prediction for Augustus_model.g32917.t1
Valid prediction for snap_scaffold_21-snap.1379-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49108-T1
Valid prediction for GlimmerHMM_glimmerT_49104-T1
Valid prediction for snap_scaffold_21-snap.1382-T1
Valid prediction for GeneMark_model.85117_t
Valid prediction for snap_scaffold_21-snap.1398-T1
Valid prediction for GeneMark_model.85111_t
Couldn't classify 130893, 130919
Sorry, prediction pasa_asmbl_27767.p1 fails validation.
(CCA)	 CG	130893-130919	GT	AGG
(ATA)	 AG	131016-131287	GT	CTG
(ACG)	 AG	131425-131614	GT	AGG
(GTG)	 AG	131789-131875	GT	AGG
(GTG)	 AG	132009-132140	GT	TGG
(GAC)	 AG	132288-132347	GT	TGG
(GCA)	 AG	132516-132581	GT	AGG
(AAC)	 AG	132714-132900	GT	TGG
(GAA)	 AG	132990-133045	GT	AGG
(GTG)	 AG	133243-133400	GT	CGG
(TCC)	 AG	133553-134120	TT	GAT
-recovered pasa_asmbl_27767.p1, terminal, 133553, 134120
-recovered pasa_asmbl_27767.p1, internal, 131016, 131287
-recovered pasa_asmbl_27767.p1, internal, 131425, 131614
-recovered pasa_asmbl_27767.p1, internal, 131789, 131875
-recovered pasa_asmbl_27767.p1, internal, 132009, 132140
-recovered pasa_asmbl_27767.p1, internal, 132288, 132347
-recovered pasa_asmbl_27767.p1, internal, 132516, 132581
-recovered pasa_asmbl_27767.p1, internal, 132714, 132900
-recovered pasa_asmbl_27767.p1, internal, 132990, 133045
-recovered pasa_asmbl_27767.p1, internal, 133243, 133400
Valid prediction for Augustus_model.g32920.t1
Valid prediction for snap_scaffold_21-snap.1369-T1
Valid prediction for Augustus_model.g32921.t1
Valid prediction for GlimmerHMM_glimmerT_49124-T1
Valid prediction for snap_scaffold_21-snap.1366-T1
Valid prediction for GeneMark_model.85108_t
Valid prediction for GeneMark_model.85121_t
Valid prediction for GlimmerHMM_glimmerT_49106-T1
Valid prediction for snap_scaffold_21-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_49102-T1
Valid prediction for snap_scaffold_21-snap.1378-T1
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (5) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 60420, rend_intergenic: 60417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18636, rend_intergenic: 10008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26348, rend_intergenic: 24081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31013, rend_intergenic: 28530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48094, rend_intergenic: 48012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49888, rend_intergenic: 48170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56680, rend_intergenic: 54119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65797, rend_intergenic: 63453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131973, rend_intergenic: 128240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140704, rend_intergenic: 135832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164315, rend_intergenic: 153697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170382
-exon list size: 603


building trellis

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59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.1    
66.3    
66.4    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
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    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 60420, rend_intergenic: 60417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18636, rend_intergenic: 10008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26348, rend_intergenic: 24081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31013, rend_intergenic: 28530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48094, rend_intergenic: 48012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49888, rend_intergenic: 48170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56680, rend_intergenic: 54119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65797, rend_intergenic: 63453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131973, rend_intergenic: 128240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140704, rend_intergenic: 135832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164315, rend_intergenic: 153697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support