-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_9845557-10081830

-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_12-snap.1891-T1
Valid prediction for HiQ_model.g20358.t1
Valid prediction for pasa_asmbl_8848.p1
Valid prediction for GeneMark_model.52741_t
Valid prediction for GlimmerHMM_glimmerT_30555-T1
Valid prediction for GlimmerHMM_glimmerT_30538-T1
Valid prediction for GlimmerHMM_glimmerT_30556-T1
Valid prediction for GlimmerHMM_glimmerT_30540-T1
Valid prediction for GeneMark_model.52763_t
Valid prediction for Augustus_model.g20340.t1
Valid prediction for snap_scaffold_12-snap.1900-T1
Valid prediction for snap_scaffold_12-snap.1899-T1
Valid prediction for GeneMark_model.52765_t
Valid prediction for snap_scaffold_12-snap.1918-T1
Valid prediction for snap_scaffold_12-snap.1882-T1
Valid prediction for GeneMark_model.52727_t
Valid prediction for GeneMark_model.52735_t
Valid prediction for GeneMark_model.52769_t
Valid prediction for GeneMark_model.52759_t
Valid prediction for snap_scaffold_12-snap.1895-T1
Valid prediction for GeneMark_model.52756_t
Valid prediction for GeneMark_model.52733_t
Valid prediction for GlimmerHMM_glimmerT_30528-T1
Valid prediction for snap_scaffold_12-snap.1908-T1
Valid prediction for GeneMark_model.52767_t
Valid prediction for pasa_asmbl_8860.p1
Valid prediction for snap_scaffold_12-snap.1904-T1
Valid prediction for GlimmerHMM_glimmerT_30527-T1
Valid prediction for GeneMark_model.52775_t
Valid prediction for Augustus_model.g20342.t1
Valid prediction for GeneMark_model.52744_t
Valid prediction for GeneMark_model.52753_t
Valid prediction for snap_scaffold_12-snap.1886-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g20351.t1
Valid prediction for CodingQuarry_transcript_10320-T1
Couldn't classify 147506, 148249
Sorry, prediction pasa_asmbl_8867.p1 fails validation.
(TCA)	 TC	147506-148249	CT	AAC
Valid prediction for Augustus_model.g20346.t1
Valid prediction for CodingQuarry_transcript_10316-T1
Valid prediction for Augustus_model.g20354.t1
Valid prediction for pasa_asmbl_8851.p1
Couldn't classify 103146, 103456
Sorry, prediction pasa_asmbl_8864.p1 fails validation.
(GCT)	 AG	103146-103456	GT	TGG
(GGC)	 AG	103674-103750	GT	AGG
(GTA)	 AG	103863-103975	AT	AAA
-recovered pasa_asmbl_8864.p1, terminal, 103863, 103975
-recovered pasa_asmbl_8864.p1, internal, 103146, 103456
-recovered pasa_asmbl_8864.p1, internal, 103674, 103750
Valid prediction for HiQ_model.g20341.t1
Valid prediction for GeneMark_model.52751_t
Valid prediction for Augustus_model.g20343.t1
Valid prediction for snap_scaffold_12-snap.1883-T1
Valid prediction for GeneMark_model.52773_t
Valid prediction for snap_scaffold_12-snap.1898-T1
Valid prediction for snap_scaffold_12-snap.1917-T1
Valid prediction for GeneMark_model.52743_t
Valid prediction for GeneMark_model.52737_t
Valid prediction for GlimmerHMM_glimmerT_30523-T1
Valid prediction for Augustus_model.g20345.t1
Valid prediction for snap_scaffold_12-snap.1881-T1
Valid prediction for Augustus_model.g20367.t1
Couldn't classify 95842, 95904
Sorry, prediction pasa_asmbl_8862.p1 fails validation.
(TTC)	 GC	95842-95904	GT	AGG
(GTG)	 AG	96043-96181	GT	TGG
(ATG)	 AG	96295-96422	GT	AGG
(GCA)	 AG	96500-96556	GT	AGG
(GCA)	 AG	96733-96804	GT	AGG
(GTT)	 AG	96932-97123	GT	AGG
(TCA)	 AG	97300-97539	GT	AGG
(GCT)	 AG	97706-97771	AA	AAA
add_exon() Sorry, pasa_asmbl_8862.p1 96295-96422-initial-1 is invalid.
-recovered pasa_asmbl_8862.p1, initial, 96295, 96422
-recovered pasa_asmbl_8862.p1, terminal, 97706, 97771
-recovered pasa_asmbl_8862.p1, internal, 96043, 96181
-recovered pasa_asmbl_8862.p1, internal, 96295, 96422
-recovered pasa_asmbl_8862.p1, internal, 96500, 96556
-recovered pasa_asmbl_8862.p1, internal, 96733, 96804
-recovered pasa_asmbl_8862.p1, internal, 96932, 97123
-recovered pasa_asmbl_8862.p1, internal, 97300, 97539
Valid prediction for GeneMark_model.52742_t
Couldn't classify 146786, 147352
Sorry, prediction pasa_asmbl_8866.p1 fails validation.
(ATG)	 CA	146236-146667	GT	AGG
(AAT)	 AG	146786-147352	GC	GAG
-recovered pasa_asmbl_8866.p1, initial, 146236, 146667
-recovered pasa_asmbl_8866.p1, internal, 146786, 147352
Valid prediction for GeneMark_model.52734_t
Valid prediction for snap_scaffold_12-snap.1889-T1
Valid prediction for GlimmerHMM_glimmerT_30529-T1
Valid prediction for GeneMark_model.52771_t
Valid prediction for GlimmerHMM_glimmerT_30548-T1
Valid prediction for GlimmerHMM_glimmerT_30525-T1
Valid prediction for GlimmerHMM_glimmerT_30524-T1
Valid prediction for snap_scaffold_12-snap.1884-T1
Valid prediction for Augustus_model.g20350.t1
Valid prediction for snap_scaffold_12-snap.1888-T1
Valid prediction for GlimmerHMM_glimmerT_30535-T1
Valid prediction for GlimmerHMM_glimmerT_30541-T1
Valid prediction for GlimmerHMM_glimmerT_30531-T1
Valid prediction for snap_scaffold_12-snap.1901-T1
Valid prediction for GeneMark_model.52761_t
Valid prediction for GeneMark_model.52728_t
Valid prediction for GeneMark_model.52739_t
Valid prediction for GeneMark_model.52726_t
Valid prediction for HiQ_model.g20352.t1
Valid prediction for GlimmerHMM_glimmerT_30551-T1
Valid prediction for snap_scaffold_12-snap.1903-T1
Couldn't classify 95194, 95208
Sorry, prediction pasa_asmbl_8861.p1 fails validation.
(ATG)	 AC	94213-94416	GT	AGG
(GAT)	 AG	94668-94805	GT	AGG
(GTG)	 AG	94900-95004	GT	AGG
(ATC)	 AG	95194-95208	CA	CAC
-recovered pasa_asmbl_8861.p1, initial, 94213, 94416
-recovered pasa_asmbl_8861.p1, internal, 94668, 94805
-recovered pasa_asmbl_8861.p1, internal, 94900, 95004
Valid prediction for GeneMark_model.52749_t
Valid prediction for snap_scaffold_12-snap.1887-T1
Valid prediction for GeneMark_model.52732_t
Valid prediction for snap_scaffold_12-snap.1913-T1
Couldn't classify 43407, 43505
Sorry, prediction pasa_asmbl_8857.p1 fails validation.
(CAG)	 AA	43407-43505	GT	AGG
(CCT)	 AG	44662-44755	GT	TGG
(GTC)	 AG	45099-45258	GT	GAG
(TTT)	 AG	45487-45592	GA	GAG
-recovered pasa_asmbl_8857.p1, terminal, 45487, 45592
-recovered pasa_asmbl_8857.p1, internal, 44662, 44755
-recovered pasa_asmbl_8857.p1, internal, 45099, 45258
Valid prediction for GlimmerHMM_glimmerT_30547-T1
Valid prediction for snap_scaffold_12-snap.1915-T1
Valid prediction for CodingQuarry_transcript_10315-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 GeneMark_model.52758_t
Valid prediction for Augustus_model.g20365.t1
Valid prediction for pasa_asmbl_7844.p1
Valid prediction for GeneMark_model.52725_t
Valid prediction for Augustus_model.g20356.t1
Valid prediction for GeneMark_model.52776_t
Valid prediction for GeneMark_model.52747_t
Couldn't classify 101858, 101906
Sorry, prediction pasa_asmbl_7835.p1 fails validation.
(AAG)	 TA	101858-101906	GT	GGG
(CCC)	 AG	102025-102127	GT	AGG
(GTA)	 AG	102246-102478	GT	CTG
(CCG)	 AG	102619-102785	GT	AGG
(GTA)	 AG	102915-103023	GT	AGG
(GTT)	 AG	103177-103319	AA	AGA
add_exon() Sorry, pasa_asmbl_7835.p1 102915-103023-terminal-3 is invalid.
-recovered pasa_asmbl_7835.p1, terminal, 102915, 103023
-recovered pasa_asmbl_7835.p1, terminal, 103177, 103319
-recovered pasa_asmbl_7835.p1, internal, 102025, 102127
-recovered pasa_asmbl_7835.p1, internal, 102246, 102478
-recovered pasa_asmbl_7835.p1, internal, 102619, 102785
-recovered pasa_asmbl_7835.p1, internal, 102915, 103023
Valid prediction for snap_scaffold_12-snap.1909-T1
Valid prediction for snap_scaffold_12-snap.1907-T1
Couldn't classify 94934, 95006
Sorry, prediction CodingQuarry_transcript_10323-T1 fails validation.
(ATG)	 GA	92793-92798	GT	GGG
(ACA)	 AG	93293-93388	GT	AGG
(ATT)	 AG	93492-93616	GT	AGG
(AAT)	 AG	93839-93937	GT	CAG
(AAG)	 TA	94934-95006	AT	AAA
-recovered CodingQuarry_transcript_10323-T1, initial, 92793, 92798
-recovered CodingQuarry_transcript_10323-T1, internal, 93293, 93388
-recovered CodingQuarry_transcript_10323-T1, internal, 93492, 93616
-recovered CodingQuarry_transcript_10323-T1, internal, 93839, 93937
Valid prediction for snap_scaffold_12-snap.1910-T1
Valid prediction for CodingQuarry_transcript_10325-T1
Valid prediction for GeneMark_model.52746_t
Valid prediction for Augustus_model.g20347.t1
Couldn't classify 23210, 23278
Couldn't classify 25537, 25636
Sorry, prediction pasa_asmbl_7854.p1 fails validation.
(TTC)	 CC	23210-23278	GT	CGG
(GTG)	 AG	23922-24087	GT	GGG
(ATG)	 AG	24627-24757	GT	AGG
(GTG)	 AG	24857-25003	GT	TGG
(GTG)	 AG	25248-25372	GT	AGG
(GTA)	 AG	25537-25636	AT	AGA
add_exon() Sorry, pasa_asmbl_7854.p1 24627-24757-initial-1 is invalid.
-recovered pasa_asmbl_7854.p1, initial, 24627, 24757
-recovered pasa_asmbl_7854.p1, internal, 23922, 24087
-recovered pasa_asmbl_7854.p1, internal, 24627, 24757
-recovered pasa_asmbl_7854.p1, internal, 24857, 25003
-recovered pasa_asmbl_7854.p1, internal, 25248, 25372
Valid prediction for pasa_asmbl_7845.p1
Valid prediction for CodingQuarry_transcript_10326-T1
Valid prediction for GeneMark_model.52750_t
Valid prediction for snap_scaffold_12-snap.1896-T1
Couldn't classify 76892, 77095
Sorry, prediction pasa_asmbl_7843.p1 fails validation.
(CAG)	 TG	76892-77095	GT	TGG
(GCT)	 AG	77228-77410	GT	AGG
(GCC)	 AG	78018-78263	GT	TAG
(TCC)	 AG	78387-78501	GT	AGG
(ATT)	 AG	78614-78738	GT	AGG
(GAC)	 AG	79028-79194	GT	AGG
(ATA)	 AG	79359-79503	GT	GGG
(ATC)	 AG	79709-79798	CA	AGC
-recovered pasa_asmbl_7843.p1, terminal, 79709, 79798
-recovered pasa_asmbl_7843.p1, internal, 77228, 77410
-recovered pasa_asmbl_7843.p1, internal, 78018, 78263
-recovered pasa_asmbl_7843.p1, internal, 78387, 78501
-recovered pasa_asmbl_7843.p1, internal, 78614, 78738
-recovered pasa_asmbl_7843.p1, internal, 79028, 79194
-recovered pasa_asmbl_7843.p1, internal, 79359, 79503
Valid prediction for pasa_asmbl_7830.p1
Valid prediction for pasa_asmbl_7828.p1
Valid prediction for snap_scaffold_12-snap.1893-T1
Valid prediction for snap_scaffold_12-snap.1911-T1
Valid prediction for Augustus_model.g20339.t1
Valid prediction for GeneMark_model.52748_t
Valid prediction for GlimmerHMM_glimmerT_30530-T1
Valid prediction for GeneMark_model.52766_t
Valid prediction for HiQ_model.g20349.t1
Valid prediction for CodingQuarry_transcript_10318-T1
Valid prediction for GlimmerHMM_glimmerT_30546-T1
Valid prediction for GlimmerHMM_glimmerT_30536-T1
Valid prediction for GlimmerHMM_glimmerT_30553-T1
Valid prediction for snap_scaffold_12-snap.1897-T1
Valid prediction for GeneMark_model.52740_t
Valid prediction for snap_scaffold_12-snap.1892-T1
Valid prediction for Augustus_model.g20344.t1
Valid prediction for GeneMark_model.52760_t
Valid prediction for GeneMark_model.52738_t
Valid prediction for HiQ_model.g20355.t1
Valid prediction for HiQ_model.g20353.t1
Valid prediction for pasa_asmbl_7852.p1
Valid prediction for GlimmerHMM_glimmerT_30532-T1
Valid prediction for GeneMark_model.52774_t
Valid prediction for pasa_asmbl_7829.p1
Valid prediction for GlimmerHMM_glimmerT_30554-T1
Valid prediction for snap_scaffold_12-snap.1912-T1
Valid prediction for GeneMark_model.52755_t
Valid prediction for Augustus_model.g20362.t1
Valid prediction for snap_scaffold_12-snap.1916-T1
Valid prediction for GeneMark_model.52729_t
Valid prediction for HiQ_model.g20357.t1
Valid prediction for CodingQuarry_transcript_10327-T1
Valid prediction for GeneMark_model.52757_t
Valid prediction for GeneMark_model.52762_t
Valid prediction for snap_scaffold_12-snap.1906-T1
Valid prediction for GlimmerHMM_glimmerT_30533-T1
Valid prediction for snap_scaffold_12-snap.1894-T1
Valid prediction for CodingQuarry_transcript_10328-T1
Valid prediction for snap_scaffold_12-snap.1919-T1
Valid prediction for GlimmerHMM_glimmerT_30543-T1
Valid prediction for Augustus_model.g20364.t1
Valid prediction for GlimmerHMM_glimmerT_30550-T1
Valid prediction for snap_scaffold_12-snap.1905-T1
Valid prediction for Augustus_model.g20360.t1
Valid prediction for GeneMark_model.52752_t
Valid prediction for CodingQuarry_transcript_10322-T1
Valid prediction for pasa_asmbl_7833.p1
Valid prediction for GlimmerHMM_glimmerT_30549-T1
Valid prediction for snap_scaffold_12-snap.1914-T1
Valid prediction for GeneMark_model.52772_t
Valid prediction for GeneMark_model.52731_t
Valid prediction for GeneMark_model.52768_t
Valid prediction for CodingQuarry_transcript_10319-T1
Valid prediction for Augustus_model.g20348.t1
Valid prediction for snap_scaffold_12-snap.1885-T1
Valid prediction for GeneMark_model.52736_t
Valid prediction for GeneMark_model.52770_t
Valid prediction for HiQ_model.g20361.t1
Valid prediction for Augustus_model.g20366.t1
Valid prediction for GlimmerHMM_glimmerT_30544-T1
Valid prediction for GlimmerHMM_glimmerT_30526-T1
Valid prediction for GlimmerHMM_glimmerT_30537-T1
Valid prediction for GlimmerHMM_glimmerT_30545-T1
Valid prediction for CodingQuarry_transcript_10317-T1
Valid prediction for snap_scaffold_12-snap.1890-T1
Valid prediction for snap_scaffold_12-snap.1902-T1
Valid prediction for GlimmerHMM_glimmerT_30539-T1
Valid prediction for GlimmerHMM_glimmerT_30534-T1
Valid prediction for GlimmerHMM_glimmerT_30542-T1
Valid prediction for GlimmerHMM_glimmerT_30552-T1
Valid prediction for Augustus_model.g20363.t1
Valid prediction for pasa_asmbl_7831.p1
Valid prediction for CodingQuarry_transcript_10324-T1
Valid prediction for CodingQuarry_transcript_10329-T1
Valid prediction for GeneMark_model.52764_t
Valid prediction for Augustus_model.g20359.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31602, rend_intergenic: 29656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70360, rend_intergenic: 63045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200264, rend_intergenic: 191743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213267, rend_intergenic: 209473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223919, rend_intergenic: 214109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236274
-exon list size: 621


building trellis

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60.2    
60.4    
60.5    
60.7    
60.8    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.6    
63.7    
63.9    
64.0    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.8    
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    
81.9    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
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: 31602, rend_intergenic: 29656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70360, rend_intergenic: 63045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200264, rend_intergenic: 191743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213267, rend_intergenic: 209473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223919, rend_intergenic: 214109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support