-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_11686105-11890878

-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.53081_t
Valid prediction for GeneMark_model.53089_t
Valid prediction for GeneMark_model.53075_t
Valid prediction for snap_scaffold_12-snap.2180-T1
Valid prediction for GeneMark_model.53083_t
Valid prediction for snap_scaffold_12-snap.2190-T1
Valid prediction for snap_scaffold_12-snap.2195-T1
Valid prediction for Augustus_model.g20520.t1
Valid prediction for Augustus_model.g20517.t1
Valid prediction for GeneMark_model.53071_t
Valid prediction for snap_scaffold_12-snap.2185-T1
Valid prediction for GlimmerHMM_glimmerT_30769-T1
Valid prediction for GeneMark_model.53087_t
Valid prediction for snap_scaffold_12-snap.2199-T1
Valid prediction for GeneMark_model.53097_t
Valid prediction for Augustus_model.g20507.t1
Valid prediction for GlimmerHMM_glimmerT_30762-T1
Valid prediction for Augustus_model.g20510.t1
Valid prediction for GlimmerHMM_glimmerT_30770-T1
Valid prediction for GeneMark_model.53065_t
Valid prediction for snap_scaffold_12-snap.2183-T1
Valid prediction for snap_scaffold_12-snap.2181-T1
Valid prediction for GlimmerHMM_glimmerT_30766-T1
Valid prediction for GlimmerHMM_glimmerT_30758-T1
Valid prediction for GeneMark_model.53080_t
Couldn't classify 112110, 113873
Sorry, prediction pasa_asmbl_8932.p1 fails validation.
(CAT)	 GA	112110-113873	GG	AGG
Valid prediction for GeneMark_model.53073_t
Valid prediction for GeneMark_model.53067_t
Valid prediction for snap_scaffold_12-snap.2198-T1
Valid prediction for snap_scaffold_12-snap.2187-T1
Valid prediction for snap_scaffold_12-snap.2201-T1
Valid prediction for GlimmerHMM_glimmerT_30761-T1
Valid prediction for GeneMark_model.53088_t
Valid prediction for GeneMark_model.53069_t
Valid prediction for GeneMark_model.53085_t
Valid prediction for GeneMark_model.53076_t
Valid prediction for GeneMark_model.53068_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_12-snap.2188-T1
Valid prediction for CodingQuarry_transcript_10365-T1
Valid prediction for GeneMark_model.53093_t
Valid prediction for GeneMark_model.53063_t
Valid prediction for Augustus_model.g20506.t1
Valid prediction for snap_scaffold_12-snap.2192-T1
Valid prediction for GlimmerHMM_glimmerT_30754-T1
Valid prediction for snap_scaffold_12-snap.2197-T1
Valid prediction for snap_scaffold_12-snap.2189-T1
Valid prediction for Augustus_model.g20505.t1
Valid prediction for GeneMark_model.53066_t
Valid prediction for GeneMark_model.53084_t
Valid prediction for snap_scaffold_12-snap.2203-T1
Valid prediction for CodingQuarry_transcript_10367-T1
Couldn't classify 174720, 174892
Couldn't classify 177940, 178035
Sorry, prediction pasa_asmbl_7958.p1 fails validation.
(GCC)	 AG	174720-174892	GT	AGG
(GGT)	 AG	176059-176242	GT	AGG
(TTC)	 AG	177940-178035	CT	TCC
-recovered pasa_asmbl_7958.p1, internal, 174720, 174892
-recovered pasa_asmbl_7958.p1, internal, 176059, 176242
Valid prediction for pasa_asmbl_7962.p1
Valid prediction for Augustus_model.g20522.t1
Couldn't classify 162862, 162933
Couldn't classify 168592, 168660
Sorry, prediction pasa_asmbl_7959.p1 fails validation.
(AGC)	 AC	162862-162933	GT	CGG
(GAC)	 AG	163187-163271	GT	GGG
(GTC)	 AG	163570-163709	GT	AGG
(AAC)	 AG	165642-165780	GT	CGG
(GAC)	 AG	168277-168341	GT	ACG
(CCA)	 AG	168592-168660	AA	GGA
-recovered pasa_asmbl_7959.p1, internal, 163187, 163271
-recovered pasa_asmbl_7959.p1, internal, 163570, 163709
-recovered pasa_asmbl_7959.p1, internal, 165642, 165780
-recovered pasa_asmbl_7959.p1, internal, 168277, 168341
Valid prediction for snap_scaffold_12-snap.2179-T1
Valid prediction for Augustus_model.g20508.t1
Valid prediction for snap_scaffold_12-snap.2196-T1
Valid prediction for Augustus_model.g20512.t1
Valid prediction for GeneMark_model.53092_t
Valid prediction for Augustus_model.g20511.t1
Valid prediction for GeneMark_model.53086_t
Valid prediction for GeneMark_model.53070_t
Valid prediction for GlimmerHMM_glimmerT_30757-T1
Valid prediction for GlimmerHMM_glimmerT_30753-T1
Valid prediction for snap_scaffold_12-snap.2200-T1
Valid prediction for snap_scaffold_12-snap.2202-T1
Valid prediction for GlimmerHMM_glimmerT_30760-T1
Valid prediction for Augustus_model.g20516.t1
Valid prediction for snap_scaffold_12-snap.2178-T1
Valid prediction for Augustus_model.g20504.t1
Valid prediction for GeneMark_model.53095_t
Valid prediction for GeneMark_model.53064_t
Valid prediction for GlimmerHMM_glimmerT_30756-T1
Valid prediction for GlimmerHMM_glimmerT_30768-T1
Valid prediction for HiQ_model.g20518.t1
Valid prediction for Augustus_model.g20515.t1
Valid prediction for GeneMark_model.53072_t
Valid prediction for CodingQuarry_transcript_10368-T1
Valid prediction for GlimmerHMM_glimmerT_30765-T1
Valid prediction for GeneMark_model.53077_t
Couldn't classify 94954, 95106
Sorry, prediction pasa_asmbl_7963.p1 fails validation.
(GTT)	 AA	94954-95106	GT	GCG
(GTC)	 AG	95682-95708	GT	AGG
(GTT)	 AG	95999-96087	GT	GAG
(AAC)	 AG	96611-96680	GT	AGG
(GCA)	 AG	96886-97033	GT	AGG
(GGG)	 AG	97154-97208	GT	AAG
(GCG)	 AG	97399-97498	GT	GGG
(GTG)	 AG	97652-97738	GT	AGG
(GTG)	 AG	97932-98099	GT	TGG
(GGT)	 AG	98347-98458	GT	TGG
(TGG)	 AG	98568-98699	GT	AGG
(AGG)	 AG	98927-99060	GT	AGG
(GTG)	 AG	99215-99364	CC	AGC
add_exon() Sorry, pasa_asmbl_7963.p1 97154-97208-terminal-3 is invalid.
-recovered pasa_asmbl_7963.p1, terminal, 97154, 97208
-recovered pasa_asmbl_7963.p1, terminal, 99215, 99364
-recovered pasa_asmbl_7963.p1, internal, 95682, 95708
-recovered pasa_asmbl_7963.p1, internal, 95999, 96087
-recovered pasa_asmbl_7963.p1, internal, 96611, 96680
-recovered pasa_asmbl_7963.p1, internal, 96886, 97033
-recovered pasa_asmbl_7963.p1, internal, 97154, 97208
-recovered pasa_asmbl_7963.p1, internal, 97399, 97498
-recovered pasa_asmbl_7963.p1, internal, 97652, 97738
-recovered pasa_asmbl_7963.p1, internal, 97932, 98099
-recovered pasa_asmbl_7963.p1, internal, 98347, 98458
-recovered pasa_asmbl_7963.p1, internal, 98568, 98699
-recovered pasa_asmbl_7963.p1, internal, 98927, 99060
Valid prediction for GlimmerHMM_glimmerT_30764-T1
Valid prediction for GlimmerHMM_glimmerT_30767-T1
Valid prediction for snap_scaffold_12-snap.2184-T1
Valid prediction for snap_scaffold_12-snap.2186-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.2191-T1
Valid prediction for GeneMark_model.53091_t
Valid prediction for HiQ_model.g20519.t1
Valid prediction for snap_scaffold_12-snap.2182-T1
Valid prediction for GlimmerHMM_glimmerT_30763-T1
Valid prediction for snap_scaffold_12-snap.2193-T1
Valid prediction for CodingQuarry_transcript_10366-T1
Valid prediction for GeneMark_model.53096_t
Valid prediction for GeneMark_model.53079_t
Valid prediction for GeneMark_model.53090_t
Valid prediction for snap_scaffold_12-snap.2194-T1
Valid prediction for GeneMark_model.53082_t
Valid prediction for GeneMark_model.53094_t
Couldn't classify 197466, 197524
Sorry, prediction pasa_asmbl_7956.p1 fails validation.
(TGG)	 TC	197466-197524	GT	GTG
(GGT)	 AG	197965-198057	GT	AGG
(TTT)	 AG	198938-199029	GT	CCG
(ACG)	 AG	200287-200384	GA	GAG
-recovered pasa_asmbl_7956.p1, terminal, 200287, 200384
-recovered pasa_asmbl_7956.p1, internal, 197965, 198057
-recovered pasa_asmbl_7956.p1, internal, 198938, 199029
Valid prediction for GlimmerHMM_glimmerT_30759-T1
Valid prediction for Augustus_model.g20521.t1
Valid prediction for Augustus_model.g20513.t1
Couldn't classify 144712, 144743
Couldn't classify 147033, 147197
Sorry, prediction pasa_asmbl_7960.p1 fails validation.
(CTC)	 AC	144712-144743	GT	AGG
(TGA)	 AG	145983-146052	GT	AGG
(GGG)	 AG	146147-146274	GT	AGG
(CAC)	 AG	146726-146837	GT	AGG
(AAC)	 AG	147033-147197	TG	ACT
-recovered pasa_asmbl_7960.p1, internal, 145983, 146052
-recovered pasa_asmbl_7960.p1, internal, 146147, 146274
-recovered pasa_asmbl_7960.p1, internal, 146726, 146837
Valid prediction for GeneMark_model.53078_t
Valid prediction for GlimmerHMM_glimmerT_30755-T1
Valid prediction for Augustus_model.g20514.t1
Valid prediction for GeneMark_model.53074_t
Valid prediction for Augustus_model.g20509.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30022, rend_intergenic: 19680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33311, rend_intergenic: 32087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43019, rend_intergenic: 36817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66010, rend_intergenic: 63177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204774
-exon list size: 429


building trellis

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19.0    
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22.7    
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23.9    
24.1    
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24.8    
25.1    
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25.5    
25.8    
26.0    
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26.5    
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27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
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54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.3    
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61.7    
61.9    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.8    
71.0    
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71.5    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.5    
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74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 30022, rend_intergenic: 19680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33311, rend_intergenic: 32087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43019, rend_intergenic: 36817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66010, rend_intergenic: 63177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 189766 - 204774
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 3 predictions from path traversal

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