-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_8612705-8795785

-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 GlimmerHMM_glimmerT_42797-T1
Valid prediction for snap_scaffold_18-snap.1832-T1
Valid prediction for snap_scaffold_18-snap.1821-T1
Valid prediction for Augustus_model.g28553.t1
Valid prediction for Augustus_model.g28552.t1
Valid prediction for GlimmerHMM_glimmerT_42792-T1
Valid prediction for CodingQuarry_transcript_23858-T1
Valid prediction for snap_scaffold_18-snap.1814-T1
Valid prediction for snap_scaffold_18-snap.1847-T1
Valid prediction for snap_scaffold_18-snap.1840-T1
Valid prediction for snap_scaffold_18-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_42804-T1
Valid prediction for GlimmerHMM_glimmerT_42794-T1
Couldn't classify 124449, 124487
Sorry, prediction pasa_asmbl_20867.p1 fails validation.
(CTG)	 TG	124449-124487	GT	AGG
(AAC)	 AG	124787-124910	GT	TGG
(AGC)	 AG	125007-125179	GT	AGG
(TAC)	 AG	125820-125966	CC	GAC
-recovered pasa_asmbl_20867.p1, terminal, 125820, 125966
-recovered pasa_asmbl_20867.p1, internal, 124787, 124910
-recovered pasa_asmbl_20867.p1, internal, 125007, 125179
Valid prediction for Augustus_model.g28560.t1
Valid prediction for snap_scaffold_18-snap.1838-T1
Valid prediction for snap_scaffold_18-snap.1834-T1
Valid prediction for snap_scaffold_18-snap.1836-T1
Valid prediction for pasa_asmbl_20857.p1
Valid prediction for Augustus_model.g28551.t1
Valid prediction for GlimmerHMM_glimmerT_42809-T1
Valid prediction for snap_scaffold_18-snap.1826-T1
Valid prediction for snap_scaffold_18-snap.1823-T1
Valid prediction for snap_scaffold_18-snap.1844-T1
Valid prediction for Augustus_model.g28554.t1
Valid prediction for GlimmerHMM_glimmerT_42802-T1
Couldn't classify 119946, 120001
Sorry, prediction pasa_asmbl_20866.p1 fails validation.
(CAG)	 GA	119946-120001	GT	TGG
(GAA)	 AG	120480-120632	GT	AGG
(GCC)	 AG	120862-121117	GC	AAG
-recovered pasa_asmbl_20866.p1, terminal, 120862, 121117
-recovered pasa_asmbl_20866.p1, internal, 120480, 120632
-recovered pasa_asmbl_20866.p1, internal, 120862, 121117
Valid prediction for GlimmerHMM_glimmerT_42810-T1
Valid prediction for pasa_asmbl_20855.p1
Valid prediction for GlimmerHMM_glimmerT_42796-T1
Valid prediction for snap_scaffold_18-snap.1843-T1
Couldn't classify 64808, 65636
Couldn't classify 65754, 65779
Sorry, prediction pasa_asmbl_20852.p1 fails validation.
(TTC)	 GT	64808-65636	GT	TGG
(CCT)	 AG	65754-65779	GA	GAG
Valid prediction for HiQ_model.g28558.t1
Couldn't classify 66046, 66246
Sorry, prediction pasa_asmbl_20853.p1 fails validation.
(AGG)	 GC	66046-66246	GT	AGG
(TCC)	 AG	66399-66497	GT	TGG
(GTG)	 AG	66673-66754	GT	TGG
(GTG)	 AG	66833-67125	GT	AGG
(ATC)	 AG	67226-67279	GT	AGG
(GTG)	 AG	67364-67741	GC	GAG
-recovered pasa_asmbl_20853.p1, terminal, 67364, 67741
-recovered pasa_asmbl_20853.p1, internal, 66399, 66497
-recovered pasa_asmbl_20853.p1, internal, 66673, 66754
-recovered pasa_asmbl_20853.p1, internal, 66833, 67125
-recovered pasa_asmbl_20853.p1, internal, 67226, 67279
-recovered pasa_asmbl_20853.p1, internal, 67364, 67741
Valid prediction for GlimmerHMM_glimmerT_42799-T1
Valid prediction for snap_scaffold_18-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_42793-T1
Valid prediction for snap_scaffold_18-snap.1828-T1
Valid prediction for GlimmerHMM_glimmerT_42816-T1
Valid prediction for GlimmerHMM_glimmerT_42806-T1
Valid prediction for Augustus_model.g28559.t1
Valid prediction for Augustus_model.g28555.t1
Valid prediction for CodingQuarry_transcript_23859-T1
Valid prediction for GlimmerHMM_glimmerT_42808-T1
Valid prediction for snap_scaffold_18-snap.1819-T1
Valid prediction for snap_scaffold_18-snap.1841-T1
Valid prediction for GlimmerHMM_glimmerT_42798-T1
Valid prediction for snap_scaffold_18-snap.1845-T1
Valid prediction for Augustus_model.g28556.t1
Valid prediction for Augustus_model.g28550.t1
Valid prediction for snap_scaffold_18-snap.1853-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1816-T1
Valid prediction for snap_scaffold_18-snap.1849-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 Augustus_model.g28561.t1
Valid prediction for snap_scaffold_18-snap.1851-T1
Valid prediction for snap_scaffold_18-snap.1846-T1
Couldn't classify 163222, 163356
Couldn't classify 166178, 166362
Sorry, prediction pasa_asmbl_20015.p1 fails validation.
(AAG)	 AG	163222-163356	GT	AGG
(AAT)	 AG	164017-164082	GT	AGG
(ATT)	 AG	164230-164349	GT	AGG
(GTG)	 AG	165822-165954	GT	AGG
(ATG)	 AG	166178-166362	CC	CCC
-recovered pasa_asmbl_20015.p1, internal, 163222, 163356
-recovered pasa_asmbl_20015.p1, internal, 164017, 164082
-recovered pasa_asmbl_20015.p1, internal, 164230, 164349
-recovered pasa_asmbl_20015.p1, internal, 165822, 165954
Valid prediction for GlimmerHMM_glimmerT_42795-T1
Valid prediction for Augustus_model.g28549.t1
Valid prediction for snap_scaffold_18-snap.1812-T1
Valid prediction for snap_scaffold_18-snap.1815-T1
Valid prediction for snap_scaffold_18-snap.1835-T1
Valid prediction for snap_scaffold_18-snap.1827-T1
Valid prediction for snap_scaffold_18-snap.1822-T1
Valid prediction for GlimmerHMM_glimmerT_42819-T1
Valid prediction for GlimmerHMM_glimmerT_42818-T1
Valid prediction for GlimmerHMM_glimmerT_42803-T1
Valid prediction for snap_scaffold_18-snap.1830-T1
Valid prediction for snap_scaffold_18-snap.1833-T1
Valid prediction for GlimmerHMM_glimmerT_42805-T1
Valid prediction for Augustus_model.g28562.t1
Valid prediction for GlimmerHMM_glimmerT_42791-T1
Couldn't classify 70597, 70597
Couldn't classify 76121, 76255
Sorry, prediction pasa_asmbl_20018.p1 fails validation.
(AGT)	 CA	70597-70597	GT	AAG
(TGG)	 AG	70889-70953	GT	CAG
(GGG)	 AG	71037-71252	GT	GGG
(GAG)	 AG	71520-71584	GT	AGG
(AAG)	 AG	72438-72563	GT	AAG
(CGA)	 AG	72664-72836	GT	GAG
(ACA)	 AG	74227-74303	GT	AGG
(GAA)	 AG	76121-76255	AG	TGA
-recovered pasa_asmbl_20018.p1, terminal, 71520, 71584
-recovered pasa_asmbl_20018.p1, internal, 70889, 70953
-recovered pasa_asmbl_20018.p1, internal, 71037, 71252
-recovered pasa_asmbl_20018.p1, internal, 71520, 71584
-recovered pasa_asmbl_20018.p1, internal, 72438, 72563
-recovered pasa_asmbl_20018.p1, internal, 72664, 72836
-recovered pasa_asmbl_20018.p1, internal, 74227, 74303
Valid prediction for GlimmerHMM_glimmerT_42814-T1
Valid prediction for snap_scaffold_18-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_42801-T1
Valid prediction for snap_scaffold_18-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_42811-T1
Valid prediction for GlimmerHMM_glimmerT_42815-T1
Valid prediction for snap_scaffold_18-snap.1850-T1
Valid prediction for snap_scaffold_18-snap.1837-T1
Valid prediction for snap_scaffold_18-snap.1839-T1
Valid prediction for CodingQuarry_transcript_23857-T1
Valid prediction for Augustus_model.g28548.t1
Valid prediction for GlimmerHMM_glimmerT_42807-T1
Valid prediction for snap_scaffold_18-snap.1818-T1
Valid prediction for GlimmerHMM_glimmerT_42813-T1
Valid prediction for GlimmerHMM_glimmerT_42812-T1
Valid prediction for snap_scaffold_18-snap.1820-T1
Valid prediction for snap_scaffold_18-snap.1813-T1
Couldn't classify 11261, 11330
Couldn't classify 12130, 12170
Sorry, prediction pasa_asmbl_20021.p1 fails validation.
(ATC)	 AG	11261-11330	GT	TGG
(TTC)	 AG	11522-11643	GT	AGG
(GTG)	 AG	11808-11997	GT	TCG
(CCC)	 AG	12130-12170	AC	GGA
-recovered pasa_asmbl_20021.p1, internal, 11261, 11330
-recovered pasa_asmbl_20021.p1, internal, 11522, 11643
-recovered pasa_asmbl_20021.p1, internal, 11808, 11997
Valid prediction for snap_scaffold_18-snap.1848-T1
Valid prediction for snap_scaffold_18-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_42800-T1
Valid prediction for snap_scaffold_18-snap.1842-T1
Valid prediction for Augustus_model.g28557.t1
Valid prediction for snap_scaffold_18-snap.1824-T1
Valid prediction for GlimmerHMM_glimmerT_42790-T1
Valid prediction for GlimmerHMM_glimmerT_42817-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15115, rend_intergenic: 13852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16303, rend_intergenic: 15805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21539, rend_intergenic: 16337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31594, rend_intergenic: 29740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45173, rend_intergenic: 37319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49897, rend_intergenic: 45946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56820, rend_intergenic: 49935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63159, rend_intergenic: 59085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71803, rend_intergenic: 69877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82478, rend_intergenic: 82225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95284, rend_intergenic: 82847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103569, rend_intergenic: 95441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107429, rend_intergenic: 105706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121186, rend_intergenic: 117992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125966, rend_intergenic: 124783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132293, rend_intergenic: 127699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144129, rend_intergenic: 139854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149505, rend_intergenic: 144694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151805, rend_intergenic: 149524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164149, rend_intergenic: 152389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178627, rend_intergenic: 170336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183081
-exon list size: 412


building trellis

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28.7    
29.0    
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30.0    
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30.4    
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30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
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33.1    
33.3    
33.6    
33.8    
34.1    
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34.5    
34.8    
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35.5    
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36.7    
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37.9    
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38.6    
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39.1    
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40.6    
40.8    
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42.3    
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43.7    
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97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 15115, rend_intergenic: 13852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16303, rend_intergenic: 15805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21539, rend_intergenic: 16337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31594, rend_intergenic: 29740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45173, rend_intergenic: 37319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49897, rend_intergenic: 45946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56820, rend_intergenic: 49935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63159, rend_intergenic: 59085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71803, rend_intergenic: 69877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82478, rend_intergenic: 82225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95284, rend_intergenic: 82847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103569, rend_intergenic: 95441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107429, rend_intergenic: 105706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121186, rend_intergenic: 117992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125966, rend_intergenic: 124783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132293, rend_intergenic: 127699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144129, rend_intergenic: 139854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149505, rend_intergenic: 144694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151805, rend_intergenic: 149524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164149, rend_intergenic: 152389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178627, rend_intergenic: 170336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15804
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15088
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2382 - 15088
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 3881 - 15088
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support