-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_8824706-9044594

-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: +)Couldn't classify 197362, 197411
Sorry, prediction pasa_asmbl_1948.p1 fails validation.
(ATG)	 GG	194758-194843	GT	GGG
(GTG)	 AG	195058-195218	GT	AGG
(GAA)	 AG	196465-196565	GT	AGG
(GCC)	 AG	196778-196952	GT	AGG
(CTC)	 AG	197041-197226	GT	AGG
(ACC)	 AG	197362-197411	AG	AGA
-recovered pasa_asmbl_1948.p1, initial, 194758, 194843
-recovered pasa_asmbl_1948.p1, internal, 195058, 195218
-recovered pasa_asmbl_1948.p1, internal, 196465, 196565
-recovered pasa_asmbl_1948.p1, internal, 196778, 196952
-recovered pasa_asmbl_1948.p1, internal, 197041, 197226
Valid prediction for GlimmerHMM_glimmerT_1246-T1
Valid prediction for GlimmerHMM_glimmerT_1248-T1
Valid prediction for GlimmerHMM_glimmerT_1264-T1
Valid prediction for snap_scaffold_1-snap.1583-T1
Valid prediction for snap_scaffold_1-snap.1593-T1
Valid prediction for GlimmerHMM_glimmerT_1237-T1
Valid prediction for snap_scaffold_1-snap.1610-T1
Valid prediction for snap_scaffold_1-snap.1591-T1
Valid prediction for GlimmerHMM_glimmerT_1263-T1
Valid prediction for snap_scaffold_1-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_1262-T1
Valid prediction for GlimmerHMM_glimmerT_1235-T1
Valid prediction for snap_scaffold_1-snap.1589-T1
Valid prediction for Augustus_model.g916.t1
Valid prediction for snap_scaffold_1-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_1239-T1
Valid prediction for GlimmerHMM_glimmerT_1267-T1
Valid prediction for snap_scaffold_1-snap.1605-T1
Valid prediction for snap_scaffold_1-snap.1588-T1
Valid prediction for Augustus_model.g920.t1
Couldn't classify 144976, 145003
Sorry, prediction pasa_asmbl_2839.p1 fails validation.
(ATG)	 AA	143404-143703	GT	AAG
(TCA)	 AG	143834-143899	GT	CAG
(GCA)	 AG	144057-144089	GT	AAG
(AAT)	 AG	144240-144294	GT	TGG
(ATT)	 AG	144372-144450	GT	TGG
(GTT)	 AG	144581-144647	GT	AGG
(GCT)	 AG	144737-144885	GT	AGG
(AAA)	 AG	144976-145003	AG	CCA
-recovered pasa_asmbl_2839.p1, initial, 143404, 143703
-recovered pasa_asmbl_2839.p1, internal, 143834, 143899
-recovered pasa_asmbl_2839.p1, internal, 144057, 144089
-recovered pasa_asmbl_2839.p1, internal, 144240, 144294
-recovered pasa_asmbl_2839.p1, internal, 144372, 144450
-recovered pasa_asmbl_2839.p1, internal, 144581, 144647
-recovered pasa_asmbl_2839.p1, internal, 144737, 144885
Valid prediction for snap_scaffold_1-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_1249-T1
Valid prediction for snap_scaffold_1-snap.1586-T1
Couldn't classify 199100, 200026
Sorry, prediction pasa_asmbl_1950.p1 fails validation.
(ATC)	 CC	199100-200026	GT	AGG
(TTG)	 AG	200116-200242	GT	TGG
(ATG)	 AG	200328-200555	GT	AAG
(GAG)	 AG	200698-200910	GT	GGG
(GTT)	 AG	201038-201155	GT	AGG
(GGG)	 AG	201237-201408	GT	AGG
(ACC)	 AG	201529-201876	GT	AGG
(TTT)	 AG	202012-202233	GT	AGG
(CCC)	 AG	202360-202600	GT	TGG
(GAA)	 AG	202713-202902	GT	AAG
(CTC)	 AG	203008-203191	GT	AGG
(AAG)	 AG	203353-203364	GG	GAG
add_exon() Sorry, pasa_asmbl_1950.p1 200328-200555-initial-1 is invalid.
-recovered pasa_asmbl_1950.p1, initial, 200328, 200555
-recovered pasa_asmbl_1950.p1, terminal, 203353, 203364
-recovered pasa_asmbl_1950.p1, internal, 200116, 200242
-recovered pasa_asmbl_1950.p1, internal, 200328, 200555
-recovered pasa_asmbl_1950.p1, internal, 200698, 200910
-recovered pasa_asmbl_1950.p1, internal, 201038, 201155
-recovered pasa_asmbl_1950.p1, internal, 201237, 201408
-recovered pasa_asmbl_1950.p1, internal, 201529, 201876
-recovered pasa_asmbl_1950.p1, internal, 202012, 202233
-recovered pasa_asmbl_1950.p1, internal, 202360, 202600
-recovered pasa_asmbl_1950.p1, internal, 202713, 202902
-recovered pasa_asmbl_1950.p1, internal, 203008, 203191
Valid prediction for GlimmerHMM_glimmerT_1241-T1
Valid prediction for Augustus_model.g926.t1
Valid prediction for Augustus_model.g924.t1
Valid prediction for Augustus_model.g923.t1
Valid prediction for GlimmerHMM_glimmerT_1247-T1
Couldn't classify 197912, 198033
Couldn't classify 198155, 198695
Sorry, prediction pasa_asmbl_1949.p1 fails validation.
(CCG)	 CG	197912-198033	GT	AGG
(GGA)	 AG	198155-198695	CC	GTC
Valid prediction for GlimmerHMM_glimmerT_1244-T1
Valid prediction for snap_scaffold_1-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_1240-T1
Valid prediction for snap_scaffold_1-snap.1608-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.g917.t1
Valid prediction for snap_scaffold_1-snap.1587-T1
Valid prediction for snap_scaffold_1-snap.1607-T1
Valid prediction for snap_scaffold_1-snap.1601-T1
Valid prediction for snap_scaffold_1-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_1258-T1
Couldn't classify 51618, 51805
Sorry, prediction pasa_asmbl_510.p1 fails validation.
(ATG)	 CC	51058-51349	GT	GGG
(GTA)	 AG	51618-51805	CC	CCC
-recovered pasa_asmbl_510.p1, initial, 51058, 51349
Valid prediction for pasa_asmbl_513.p1
Valid prediction for GlimmerHMM_glimmerT_1234-T1
Valid prediction for GlimmerHMM_glimmerT_1256-T1
Valid prediction for GlimmerHMM_glimmerT_1252-T1
Valid prediction for GlimmerHMM_glimmerT_1260-T1
Valid prediction for GlimmerHMM_glimmerT_1243-T1
Valid prediction for Augustus_model.g915.t1
Valid prediction for snap_scaffold_1-snap.1604-T1
Valid prediction for GlimmerHMM_glimmerT_1259-T1
Couldn't classify 49070, 49304
Sorry, prediction pasa_asmbl_512.p1 fails validation.
(ATG)	 AG	48642-48719	GT	GTG
(AGT)	 AG	48832-48947	GC	AGG
(GGC)	 AG	49070-49304	GA	CGG
-recovered pasa_asmbl_512.p1, initial, 48642, 48719
-recovered pasa_asmbl_512.p1, internal, 48642, 48719
-recovered pasa_asmbl_512.p1, internal, 48832, 48947
Valid prediction for GlimmerHMM_glimmerT_1251-T1
Valid prediction for Augustus_model.g919.t1
Couldn't classify 50240, 50291
Couldn't classify 50819, 50922
Sorry, prediction pasa_asmbl_511.p1 fails validation.
(CCT)	 CA	50240-50291	GT	GGG
(ATC)	 AG	50457-50639	GT	AGG
(GTA)	 AG	50819-50922	GA	AGG
add_exon() Sorry, pasa_asmbl_511.p1 50457-50639-terminal-1 is invalid.
-recovered pasa_asmbl_511.p1, terminal, 50457, 50639
-recovered pasa_asmbl_511.p1, internal, 50457, 50639
Couldn't classify 51989, 52148
Sorry, prediction pasa_asmbl_508.p1 fails validation.
(GCA)	 CT	51989-52148	GT	AGG
(CTG)	 AG	52271-52467	GT	AAG
(ATC)	 AG	52561-52641	GT	AGG
(ATT)	 AG	52732-52810	GT	AGG
(AGT)	 AG	52990-53229	GT	AGG
(CAA)	 AG	53363-53532	CC	AAC
add_exon() Sorry, pasa_asmbl_508.p1 52732-52810-terminal-3 is invalid.
-recovered pasa_asmbl_508.p1, terminal, 52732, 52810
-recovered pasa_asmbl_508.p1, terminal, 53363, 53532
-recovered pasa_asmbl_508.p1, internal, 52271, 52467
-recovered pasa_asmbl_508.p1, internal, 52561, 52641
-recovered pasa_asmbl_508.p1, internal, 52732, 52810
-recovered pasa_asmbl_508.p1, internal, 52990, 53229
Valid prediction for GlimmerHMM_glimmerT_1255-T1
Valid prediction for snap_scaffold_1-snap.1609-T1
Valid prediction for GlimmerHMM_glimmerT_1236-T1
Valid prediction for Augustus_model.g921.t1
Valid prediction for snap_scaffold_1-snap.1582-T1
Valid prediction for snap_scaffold_1-snap.1590-T1
Valid prediction for HiQ_model.g925.t1
Valid prediction for snap_scaffold_1-snap.1603-T1
Valid prediction for snap_scaffold_1-snap.1599-T1
Couldn't classify 59920, 60183
Sorry, prediction pasa_asmbl_506.p1 fails validation.
(CTG)	 CA	59920-60183	GT	AGG
(AAG)	 AG	61379-61663	GT	AGG
-recovered pasa_asmbl_506.p1, terminal, 61379, 61663
-recovered pasa_asmbl_506.p1, internal, 61379, 61663
Valid prediction for GlimmerHMM_glimmerT_1242-T1
Valid prediction for GlimmerHMM_glimmerT_1238-T1
Valid prediction for Augustus_model.g922.t1
Valid prediction for CodingQuarry_transcript_2719-T1
Valid prediction for GlimmerHMM_glimmerT_1266-T1
Valid prediction for snap_scaffold_1-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_1245-T1
Valid prediction for GlimmerHMM_glimmerT_1265-T1
Valid prediction for GlimmerHMM_glimmerT_1250-T1
Valid prediction for GlimmerHMM_glimmerT_1254-T1
Valid prediction for snap_scaffold_1-snap.1594-T1
Valid prediction for snap_scaffold_1-snap.1600-T1
Valid prediction for snap_scaffold_1-snap.1584-T1
Valid prediction for GlimmerHMM_glimmerT_1257-T1
Couldn't classify 67397, 67456
Couldn't classify 68826, 69055
Sorry, prediction pasa_asmbl_502.p1 fails validation.
(CGG)	 GC	67397-67456	GT	AGG
(GAG)	 AG	67546-67741	GT	AGG
(GAC)	 AG	68826-69055	TC	GAT
-recovered pasa_asmbl_502.p1, internal, 67546, 67741
Valid prediction for Augustus_model.g913.t1
Valid prediction for Augustus_model.g918.t1
Valid prediction for GlimmerHMM_glimmerT_1261-T1
Valid prediction for Augustus_model.g914.t1
Couldn't classify 59331, 59670
Sorry, prediction pasa_asmbl_507.p1 fails validation.
(ATG)	 CT	57526-57607	GT	AGG
(CAA)	 AG	57940-58957	GT	CGG
(GTT)	 AG	59331-59670	AT	AGA
-recovered pasa_asmbl_507.p1, initial, 57526, 57607
-recovered pasa_asmbl_507.p1, internal, 57940, 58957
Valid prediction for GlimmerHMM_glimmerT_1253-T1
Valid prediction for snap_scaffold_1-snap.1598-T1
Valid prediction for snap_scaffold_1-snap.1595-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21724, rend_intergenic: 19607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25462, rend_intergenic: 22061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30214, rend_intergenic: 26255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42915, rend_intergenic: 38851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191918, rend_intergenic: 191520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195886, rend_intergenic: 194758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219889
-exon list size: 287


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.8    
5.2    
5.5    
5.9    
6.2    
6.6    
6.9    
7.3    
7.6    
8.0    
8.3    
8.7    
9.0    
9.3    
9.7    
10.0    
10.4    
10.7    
11.1    
11.4    
11.8    
12.1    
12.5    
12.8    
13.1    
13.5    
13.8    
14.2    
14.5    
14.9    
15.2    
15.6    
15.9    
16.3    
16.6    
17.0    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.1    
22.5    
22.8    
23.2    
23.5    
23.9    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.6    
27.0    
27.3    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.8    
30.1    
30.4    
30.8    
31.1    
31.5    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.6    
34.9    
35.3    
35.6    
36.0    
36.3    
36.7    
37.0    
37.4    
37.7    
38.1    
38.4    
38.8    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
42.9    
43.3    
43.6    
43.9    
44.3    
44.6    
45.0    
45.3    
45.7    
46.0    
46.4    
46.7    
47.1    
47.4    
47.8    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.2    
52.6    
52.9    
53.3    
53.6    
54.0    
54.3    
54.7    
55.0    
55.4    
55.7    
56.1    
56.4    
56.7    
57.1    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.2    
61.6    
61.9    
62.3    
62.6    
63.0    
63.3    
63.7    
64.0    
64.4    
64.7    
65.1    
65.4    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.5    
68.9    
69.2    
69.6    
69.9    
70.2    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.7    
73.0    
73.4    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.1    
76.5    
76.8    
77.2    
77.5    
77.9    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.0    
83.4    
83.7    
84.1    
84.4    
84.8    
85.1    
85.5    
85.8    
86.2    
86.5    
86.9    
87.2    
87.5    
87.9    
88.2    
88.6    
88.9    
89.3    
89.6    
90.0    
90.3    
90.7    
91.0    
91.3    
91.7    
92.0    
92.4    
92.7    
93.1    
93.4    
93.8    
94.1    
94.5    
94.8    
95.2    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 21724, rend_intergenic: 19607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25462, rend_intergenic: 22061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30214, rend_intergenic: 26255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42915, rend_intergenic: 38851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191918, rend_intergenic: 191520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195886, rend_intergenic: 194758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support