-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_7044196-7243064

-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.97236_t
Valid prediction for GlimmerHMM_glimmerT_55751-T1
Valid prediction for GeneMark_model.97252_t
Valid prediction for GeneMark_model.97256_t
Valid prediction for snap_scaffold_25-snap.1538-T1
Valid prediction for snap_scaffold_25-snap.1539-T1
Valid prediction for snap_scaffold_25-snap.1550-T1
Valid prediction for GeneMark_model.97230_t
Valid prediction for GeneMark_model.97273_t
Valid prediction for GeneMark_model.97243_t
Valid prediction for GeneMark_model.97268_t
Valid prediction for GlimmerHMM_glimmerT_55765-T1
Valid prediction for GeneMark_model.97228_t
Valid prediction for snap_scaffold_25-snap.1549-T1
Valid prediction for snap_scaffold_25-snap.1559-T1
Valid prediction for snap_scaffold_25-snap.1566-T1
Valid prediction for GeneMark_model.97271_t
Valid prediction for GeneMark_model.97224_t
Valid prediction for GlimmerHMM_glimmerT_55771-T1
Valid prediction for GeneMark_model.97260_t
Valid prediction for GeneMark_model.97265_t
Valid prediction for GeneMark_model.97258_t
Valid prediction for GeneMark_model.97253_t
Valid prediction for GeneMark_model.97248_t
Valid prediction for snap_scaffold_25-snap.1570-T1
Valid prediction for GeneMark_model.97220_t
Valid prediction for GlimmerHMM_glimmerT_55769-T1
Valid prediction for GeneMark_model.97263_t
Valid prediction for CodingQuarry_transcript_38684-T1
Valid prediction for GlimmerHMM_glimmerT_55766-T1
Valid prediction for snap_scaffold_25-snap.1552-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.97244_t
Valid prediction for Augustus_model.g37202.t1
Valid prediction for GeneMark_model.97234_t
Valid prediction for GeneMark_model.97226_t
Valid prediction for snap_scaffold_25-snap.1545-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g37195.t1
Valid prediction for GlimmerHMM_glimmerT_55760-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.97275_t
Valid prediction for snap_scaffold_25-snap.1556-T1
Valid prediction for Augustus_model.g37201.t1
Valid prediction for pasa_asmbl_33653.p1
Valid prediction for GeneMark_model.97250_t
Valid prediction for GlimmerHMM_glimmerT_55773-T1
Valid prediction for GeneMark_model.97232_t
Valid prediction for CodingQuarry_transcript_38686-T1
Couldn't classify 79709, 79722
Sorry, prediction pasa_asmbl_33654.p1 fails validation.
(AGA)	 GA	79709-79722	GT	AGG
(TCT)	 AG	79846-79954	GT	TGG
(GTC)	 AG	80086-80193	GT	CGG
(AAC)	 AG	80578-80646	GA	AGG
-recovered pasa_asmbl_33654.p1, terminal, 80578, 80646
-recovered pasa_asmbl_33654.p1, internal, 79846, 79954
-recovered pasa_asmbl_33654.p1, internal, 80086, 80193
Valid prediction for GeneMark_model.97241_t
Valid prediction for snap_scaffold_25-snap.1555-T1
Valid prediction for Augustus_model.g37194.t1
Valid prediction for GlimmerHMM_glimmerT_55752-T1
Valid prediction for GeneMark_model.97221_t
Valid prediction for GeneMark_model.97255_t
Valid prediction for GeneMark_model.97237_t
Valid prediction for Augustus_model.g37207.t1
Valid prediction for snap_scaffold_25-snap.1540-T1
Valid prediction for GlimmerHMM_glimmerT_55778-T1
Valid prediction for snap_scaffold_25-snap.1576-T1
Valid prediction for GlimmerHMM_glimmerT_55779-T1
Valid prediction for GeneMark_model.97274_t
Valid prediction for GeneMark_model.97246_t
Valid prediction for snap_scaffold_25-snap.1561-T1
Valid prediction for snap_scaffold_25-snap.1573-T1
Valid prediction for Augustus_model.g37205.t1
Valid prediction for snap_scaffold_25-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_55750-T1
Valid prediction for HiQ_model.g37189.t1
Valid prediction for snap_scaffold_25-snap.1578-T1
Valid prediction for snap_scaffold_25-snap.1554-T1
Valid prediction for snap_scaffold_25-snap.1543-T1
Valid prediction for Augustus_model.g37200.t1
Valid prediction for GlimmerHMM_glimmerT_55776-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_55753-T1
Valid prediction for GeneMark_model.97240_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 snap_scaffold_25-snap.1548-T1
Valid prediction for snap_scaffold_25-snap.1574-T1
Valid prediction for CodingQuarry_transcript_38688-T1
Valid prediction for Augustus_model.g37199.t1
Valid prediction for HiQ_model.g37206.t1
Valid prediction for GeneMark_model.97249_t
Valid prediction for CodingQuarry_transcript_38685-T1
Valid prediction for GeneMark_model.97233_t
Valid prediction for snap_scaffold_25-snap.1568-T1
Valid prediction for Augustus_model.g37191.t1
Valid prediction for GeneMark_model.97272_t
Valid prediction for snap_scaffold_25-snap.1553-T1
Valid prediction for GlimmerHMM_glimmerT_55762-T1
Couldn't classify 134491, 134595
Couldn't classify 135731, 135892
Sorry, prediction pasa_asmbl_34546.p1 fails validation.
(AAC)	 GA	134491-134595	GT	AGG
(GAC)	 AG	134924-135055	GT	AGG
(AAG)	 AG	135731-135892	GA	ACG
-recovered pasa_asmbl_34546.p1, internal, 134924, 135055
Valid prediction for GlimmerHMM_glimmerT_55754-T1
Valid prediction for GeneMark_model.97242_t
Valid prediction for GeneMark_model.97245_t
Valid prediction for GeneMark_model.97266_t
Valid prediction for snap_scaffold_25-snap.1575-T1
Couldn't classify 138956, 139064
Couldn't classify 140376, 140444
Sorry, prediction pasa_asmbl_34357.p1 fails validation.
(GTG)	 AG	138956-139064	GT	GGG
(AGC)	 AG	139190-139353	GT	GGG
(ATG)	 AG	139470-139544	GT	TGG
(GCT)	 AG	139651-139774	GT	AGG
(GCG)	 AG	139880-140025	GT	AGG
(GTG)	 AG	140376-140444	AA	GCA
-recovered pasa_asmbl_34357.p1, initial, 139470, 139544
-recovered pasa_asmbl_34357.p1, internal, 138956, 139064
-recovered pasa_asmbl_34357.p1, internal, 139190, 139353
-recovered pasa_asmbl_34357.p1, internal, 139470, 139544
-recovered pasa_asmbl_34357.p1, internal, 139651, 139774
-recovered pasa_asmbl_34357.p1, internal, 139880, 140025
Valid prediction for GlimmerHMM_glimmerT_55758-T1
Valid prediction for snap_scaffold_25-snap.1541-T1
Valid prediction for GeneMark_model.97223_t
Valid prediction for GeneMark_model.97222_t
Valid prediction for snap_scaffold_25-snap.1542-T1
Valid prediction for Augustus_model.g37190.t1
Valid prediction for GeneMark_model.97257_t
Valid prediction for snap_scaffold_25-snap.1571-T1
Valid prediction for pasa_asmbl_34362.p1
Valid prediction for GlimmerHMM_glimmerT_55774-T1
Valid prediction for snap_scaffold_25-snap.1551-T1
Valid prediction for GeneMark_model.97254_t
Valid prediction for snap_scaffold_25-snap.1572-T1
Valid prediction for Augustus_model.g37193.t1
Valid prediction for pasa_asmbl_34358.p1
Valid prediction for GlimmerHMM_glimmerT_55764-T1
Couldn't classify 148082, 148288
Sorry, prediction pasa_asmbl_34356.p1 fails validation.
(ATC)	 AG	148082-148288	GT	AGG
(GCT)	 AG	148394-148495	GT	AGG
(GAA)	 AG	151361-151503	GT	AGG
(TCT)	 AG	153408-153497	GT	AGG
(TTC)	 AG	153810-154044	GC	AGG
-recovered pasa_asmbl_34356.p1, terminal, 153810, 154044
-recovered pasa_asmbl_34356.p1, internal, 148082, 148288
-recovered pasa_asmbl_34356.p1, internal, 148394, 148495
-recovered pasa_asmbl_34356.p1, internal, 151361, 151503
-recovered pasa_asmbl_34356.p1, internal, 153408, 153497
-recovered pasa_asmbl_34356.p1, internal, 153810, 154044
Valid prediction for CodingQuarry_transcript_38687-T1
Valid prediction for snap_scaffold_25-snap.1544-T1
Valid prediction for GlimmerHMM_glimmerT_55763-T1
Valid prediction for Augustus_model.g37203.t1
Valid prediction for GlimmerHMM_glimmerT_55755-T1
Valid prediction for snap_scaffold_25-snap.1557-T1
Valid prediction for GlimmerHMM_glimmerT_55768-T1
Valid prediction for GlimmerHMM_glimmerT_55770-T1
Valid prediction for GeneMark_model.97259_t
Valid prediction for GlimmerHMM_glimmerT_55761-T1
Valid prediction for snap_scaffold_25-snap.1569-T1
Valid prediction for snap_scaffold_25-snap.1547-T1
Valid prediction for snap_scaffold_25-snap.1565-T1
Valid prediction for GlimmerHMM_glimmerT_55767-T1
Valid prediction for GeneMark_model.97270_t
Valid prediction for snap_scaffold_25-snap.1558-T1
Valid prediction for Augustus_model.g37204.t1
Valid prediction for GeneMark_model.97238_t
Valid prediction for GeneMark_model.97231_t
Valid prediction for snap_scaffold_25-snap.1564-T1
Valid prediction for GlimmerHMM_glimmerT_55759-T1
Valid prediction for Augustus_model.g37197.t1
Valid prediction for GeneMark_model.97239_t
Valid prediction for snap_scaffold_25-snap.1546-T1
Valid prediction for GlimmerHMM_glimmerT_55772-T1
Valid prediction for snap_scaffold_25-snap.1567-T1
Valid prediction for GeneMark_model.97264_t
Valid prediction for snap_scaffold_25-snap.1563-T1
Valid prediction for GeneMark_model.97227_t
Valid prediction for GeneMark_model.97225_t
Valid prediction for GlimmerHMM_glimmerT_55756-T1
Valid prediction for GeneMark_model.97267_t
Valid prediction for Augustus_model.g37192.t1
Valid prediction for GlimmerHMM_glimmerT_55775-T1
Couldn't classify 36238, 36294
Sorry, prediction pasa_asmbl_34360.p1 fails validation.
(CTT)	 AA	36238-36294	GT	TTG
(AGC)	 AG	36865-36949	GT	AGG
(TGG)	 AG	37087-37196	GT	ACG
(GGT)	 AG	37331-37537	GT	CTG
(TGG)	 AG	37759-37953	GT	ACG
(GTC)	 AG	38110-38148	GT	GAG
-recovered pasa_asmbl_34360.p1, terminal, 38110, 38148
-recovered pasa_asmbl_34360.p1, internal, 36865, 36949
-recovered pasa_asmbl_34360.p1, internal, 37087, 37196
-recovered pasa_asmbl_34360.p1, internal, 37331, 37537
-recovered pasa_asmbl_34360.p1, internal, 37759, 37953
-recovered pasa_asmbl_34360.p1, internal, 38110, 38148
Valid prediction for Augustus_model.g37198.t1
Valid prediction for Augustus_model.g37196.t1
Valid prediction for snap_scaffold_25-snap.1577-T1
Valid prediction for GeneMark_model.97247_t
Valid prediction for GeneMark_model.97261_t
Valid prediction for GlimmerHMM_glimmerT_55777-T1
Valid prediction for GeneMark_model.97269_t
Valid prediction for GeneMark_model.97235_t
Valid prediction for GlimmerHMM_glimmerT_55757-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26516, rend_intergenic: 19929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39759, rend_intergenic: 33973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56896, rend_intergenic: 46060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62131, rend_intergenic: 59378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69220, rend_intergenic: 62891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102625, rend_intergenic: 92267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131584, rend_intergenic: 106613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143369, rend_intergenic: 132770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151310, rend_intergenic: 144316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161327, rend_intergenic: 160722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198869
-exon list size: 884


building trellis

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66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 26516, rend_intergenic: 19929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39759, rend_intergenic: 33973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56896, rend_intergenic: 46060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62131, rend_intergenic: 59378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69220, rend_intergenic: 62891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102625, rend_intergenic: 92267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131584, rend_intergenic: 106613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143369, rend_intergenic: 132770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151310, rend_intergenic: 144316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161327, rend_intergenic: 160722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support