-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_11534586-11747972

-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_41118-T1
Valid prediction for GlimmerHMM_glimmerT_41117-T1
Valid prediction for snap_scaffold_17-snap.2358-T1
Valid prediction for GlimmerHMM_glimmerT_41126-T1
Valid prediction for Augustus_model.g27428.t1
Valid prediction for Augustus_model.g27432.t1
Valid prediction for GlimmerHMM_glimmerT_41122-T1
Valid prediction for snap_scaffold_17-snap.2353-T1
Valid prediction for CodingQuarry_transcript_22180-T1
Valid prediction for snap_scaffold_17-snap.2345-T1
Valid prediction for Augustus_model.g27434.t1
Valid prediction for GlimmerHMM_glimmerT_41102-T1
Valid prediction for snap_scaffold_17-snap.2363-T1
Valid prediction for Augustus_model.g27419.t1
Valid prediction for snap_scaffold_17-snap.2341-T1
Valid prediction for CodingQuarry_transcript_22178-T1
Valid prediction for snap_scaffold_17-snap.2369-T1
Valid prediction for snap_scaffold_17-snap.2367-T1
Valid prediction for snap_scaffold_17-snap.2377-T1
Valid prediction for Augustus_model.g27431.t1
Valid prediction for snap_scaffold_17-snap.2339-T1
Valid prediction for snap_scaffold_17-snap.2359-T1
Valid prediction for GlimmerHMM_glimmerT_41100-T1
Valid prediction for Augustus_model.g27427.t1
Valid prediction for Augustus_model.g27415.t1
Valid prediction for CodingQuarry_transcript_22179-T1
Valid prediction for GlimmerHMM_glimmerT_41120-T1
Valid prediction for snap_scaffold_17-snap.2332-T1
Valid prediction for snap_scaffold_17-snap.2335-T1
Valid prediction for snap_scaffold_17-snap.2342-T1
Valid prediction for snap_scaffold_17-snap.2352-T1
Valid prediction for snap_scaffold_17-snap.2379-T1
Valid prediction for GlimmerHMM_glimmerT_41110-T1
Valid prediction for GlimmerHMM_glimmerT_41119-T1
Valid prediction for pasa_asmbl_19238.p1
Valid prediction for GlimmerHMM_glimmerT_41104-T1
Valid prediction for GlimmerHMM_glimmerT_41127-T1
Valid prediction for snap_scaffold_17-snap.2375-T1
Valid prediction for Augustus_model.g27417.t1
Valid prediction for GlimmerHMM_glimmerT_41115-T1
Valid prediction for CodingQuarry_transcript_22181-T1
Valid prediction for Augustus_model.g27430.t1
Valid prediction for Augustus_model.g27422.t1
Valid prediction for snap_scaffold_17-snap.2370-T1
Couldn't classify 41331, 41642
Sorry, prediction pasa_asmbl_19486.p1 fails validation.
(TGT)	 TC	41331-41642	AT	CCA
Valid prediction for snap_scaffold_17-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_41107-T1
Couldn't classify 42399, 43262
Sorry, prediction pasa_asmbl_19240.p1 fails validation.
(GTG)	 AC	42399-43262	AA	GAA
Valid prediction for snap_scaffold_17-snap.2365-T1
Valid prediction for snap_scaffold_17-snap.2351-T1
Valid prediction for snap_scaffold_17-snap.2334-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 snap_scaffold_17-snap.2333-T1
Valid prediction for GlimmerHMM_glimmerT_41124-T1
Valid prediction for GlimmerHMM_glimmerT_41123-T1
Valid prediction for snap_scaffold_17-snap.2343-T1
Valid prediction for snap_scaffold_17-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_41112-T1
Valid prediction for GlimmerHMM_glimmerT_41114-T1
Valid prediction for snap_scaffold_17-snap.2362-T1
Valid prediction for snap_scaffold_17-snap.2372-T1
Valid prediction for Augustus_model.g27429.t1
Valid prediction for snap_scaffold_17-snap.2366-T1
Valid prediction for CodingQuarry_transcript_22187-T1
Valid prediction for GlimmerHMM_glimmerT_41116-T1
Valid prediction for GlimmerHMM_glimmerT_41113-T1
Valid prediction for Augustus_model.g27425.t1
Couldn't classify 143320, 143457
Sorry, prediction pasa_asmbl_18292.p1 fails validation.
(GAA)	 CA	143320-143457	GT	TGG
(GCA)	 AG	143818-144132	GG	AGG
-recovered pasa_asmbl_18292.p1, terminal, 143818, 144132
Valid prediction for pasa_asmbl_18286.p1
Valid prediction for snap_scaffold_17-snap.2346-T1
Valid prediction for pasa_asmbl_18300.p1
Valid prediction for CodingQuarry_transcript_22185-T1
Valid prediction for pasa_asmbl_18290.p1
Valid prediction for snap_scaffold_17-snap.2340-T1
Valid prediction for Augustus_model.g27420.t1
Valid prediction for GlimmerHMM_glimmerT_41121-T1
Valid prediction for snap_scaffold_17-snap.2378-T1
Valid prediction for snap_scaffold_17-snap.2364-T1
Valid prediction for snap_scaffold_17-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_41108-T1
Valid prediction for GlimmerHMM_glimmerT_41125-T1
Valid prediction for HiQ_model.g27424.t1
Valid prediction for snap_scaffold_17-snap.2337-T1
Valid prediction for Augustus_model.g27416.t1
Valid prediction for GlimmerHMM_glimmerT_41103-T1
Valid prediction for CodingQuarry_transcript_22183-T1
Valid prediction for snap_scaffold_17-snap.2338-T1
Valid prediction for Augustus_model.g27426.t1
Valid prediction for HiQ_model.g27423.t1
Valid prediction for snap_scaffold_17-snap.2344-T1
Couldn't classify 135427, 135579
Sorry, prediction pasa_asmbl_18296.p1 fails validation.
(GAA)	 AG	135427-135579	GT	AGG
(GAG)	 AG	135933-136047	GT	GAG
(CTC)	 AG	136382-136558	GT	CGG
(AGA)	 AG	137045-137189	GT	GGG
(GTT)	 AG	137417-137816	AG	GAA
-recovered pasa_asmbl_18296.p1, terminal, 137417, 137816
-recovered pasa_asmbl_18296.p1, internal, 135427, 135579
-recovered pasa_asmbl_18296.p1, internal, 135933, 136047
-recovered pasa_asmbl_18296.p1, internal, 136382, 136558
-recovered pasa_asmbl_18296.p1, internal, 137045, 137189
Couldn't classify 141052, 141109
Couldn't classify 143066, 143223
Sorry, prediction pasa_asmbl_18293.p1 fails validation.
(GTA)	 CT	141052-141109	GT	AGG
(GTA)	 AG	141261-141406	GT	CGG
(GGT)	 AG	141519-141704	GT	AGG
(GAC)	 AG	141832-141984	GT	AGG
(AAC)	 AG	142216-142360	GT	GGG
(GCT)	 AG	142684-142911	GT	AGG
(GAA)	 AG	143066-143223	CC	CCC
-recovered pasa_asmbl_18293.p1, internal, 141261, 141406
-recovered pasa_asmbl_18293.p1, internal, 141519, 141704
-recovered pasa_asmbl_18293.p1, internal, 141832, 141984
-recovered pasa_asmbl_18293.p1, internal, 142216, 142360
-recovered pasa_asmbl_18293.p1, internal, 142684, 142911
Valid prediction for CodingQuarry_transcript_22186-T1
Valid prediction for GlimmerHMM_glimmerT_41111-T1
Valid prediction for snap_scaffold_17-snap.2347-T1
Valid prediction for snap_scaffold_17-snap.2373-T1
Valid prediction for snap_scaffold_17-snap.2356-T1
Valid prediction for snap_scaffold_17-snap.2371-T1
Valid prediction for snap_scaffold_17-snap.2355-T1
Valid prediction for GlimmerHMM_glimmerT_41101-T1
Valid prediction for snap_scaffold_17-snap.2354-T1
Couldn't classify 204628, 204672
Sorry, prediction pasa_asmbl_18285.p1 fails validation.
(CGG)	 GA	204628-204672	GT	AGG
(ATG)	 AG	204928-204998	GT	AAG
(GTC)	 AG	205357-205457	GT	AGG
(CGT)	 AG	205633-205816	GT	GGG
(AGG)	 AG	206075-206129	GT	AGG
(GTT)	 AG	206250-206276	GT	AAG
-recovered pasa_asmbl_18285.p1, initial, 204928, 204998
add_exon() Sorry, pasa_asmbl_18285.p1 205357-205457-terminal-2 is invalid.
-recovered pasa_asmbl_18285.p1, terminal, 205357, 205457
-recovered pasa_asmbl_18285.p1, terminal, 206250, 206276
-recovered pasa_asmbl_18285.p1, internal, 204928, 204998
-recovered pasa_asmbl_18285.p1, internal, 205357, 205457
-recovered pasa_asmbl_18285.p1, internal, 205633, 205816
-recovered pasa_asmbl_18285.p1, internal, 206075, 206129
-recovered pasa_asmbl_18285.p1, internal, 206250, 206276
Valid prediction for snap_scaffold_17-snap.2361-T1
Valid prediction for Augustus_model.g27433.t1
Valid prediction for snap_scaffold_17-snap.2368-T1
Valid prediction for snap_scaffold_17-snap.2336-T1
Valid prediction for Augustus_model.g27418.t1
Valid prediction for snap_scaffold_17-snap.2349-T1
Valid prediction for snap_scaffold_17-snap.2350-T1
Valid prediction for GlimmerHMM_glimmerT_41109-T1
Valid prediction for GlimmerHMM_glimmerT_41106-T1
Valid prediction for snap_scaffold_17-snap.2348-T1
Valid prediction for Augustus_model.g27421.t1
Valid prediction for GlimmerHMM_glimmerT_41105-T1
Valid prediction for CodingQuarry_transcript_22184-T1
Valid prediction for snap_scaffold_17-snap.2374-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10839, rend_intergenic: 9003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21305, rend_intergenic: 12833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29212, rend_intergenic: 26258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119052, rend_intergenic: 106370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146577, rend_intergenic: 139864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164022, rend_intergenic: 160243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171305, rend_intergenic: 168017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173157, rend_intergenic: 171801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177396, rend_intergenic: 173414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185084, rend_intergenic: 180633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190412, rend_intergenic: 188830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194678, rend_intergenic: 190570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197886, rend_intergenic: 194962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208842, rend_intergenic: 202622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213387
-exon list size: 366


building trellis

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10.6    
10.9    
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11.7    
12.0    
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13.3    
13.6    
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17.9    
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18.8    
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19.6    
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27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
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59.0    
59.2    
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60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
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63.9    
64.1    
64.4    
64.7    
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65.2    
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66.3    
66.6    
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67.1    
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72.6    
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75.8    
76.1    
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76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 10839, rend_intergenic: 9003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21305, rend_intergenic: 12833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29212, rend_intergenic: 26258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119052, rend_intergenic: 106370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146577, rend_intergenic: 139864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164022, rend_intergenic: 160243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171305, rend_intergenic: 168017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173157, rend_intergenic: 171801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177396, rend_intergenic: 173414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185084, rend_intergenic: 180633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190412, rend_intergenic: 188830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194678, rend_intergenic: 190570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197886, rend_intergenic: 194962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208842, rend_intergenic: 202622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support