-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_5545129-5722233

-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_11-snap.1351-T1
Valid prediction for snap_scaffold_11-snap.1362-T1
Valid prediction for GeneMark_model.47967_t
Valid prediction for GeneMark_model.47963_t
Valid prediction for Augustus_model.g18470.t1
Valid prediction for snap_scaffold_11-snap.1368-T1
Couldn't classify 169852, 169870
Couldn't classify 173154, 173317
Sorry, prediction pasa_asmbl_5546.p1 fails validation.
(AAG)	 AC	169852-169870	GT	GGG
(CCT)	 AG	169988-170061	GT	TGG
(GAT)	 AG	170194-170328	GT	AGG
(GGT)	 AG	170959-171226	GT	AGG
(ATG)	 AG	173154-173317	AG	TGA
-recovered pasa_asmbl_5546.p1, internal, 169988, 170061
-recovered pasa_asmbl_5546.p1, internal, 170194, 170328
-recovered pasa_asmbl_5546.p1, internal, 170959, 171226
Valid prediction for snap_scaffold_11-snap.1345-T1
Valid prediction for GeneMark_model.47917_t
Valid prediction for GeneMark_model.47926_t
Valid prediction for GeneMark_model.47944_t
Couldn't classify 114617, 114624
Couldn't classify 117293, 117370
Sorry, prediction pasa_asmbl_5540.p1 fails validation.
(TCC)	 AC	114617-114624	GT	TTG
(TGT)	 AG	114805-114881	GT	AGG
(GGC)	 AG	115267-115490	GT	AGG
(CCC)	 AG	117293-117370	GA	GTG
-recovered pasa_asmbl_5540.p1, internal, 114805, 114881
-recovered pasa_asmbl_5540.p1, internal, 115267, 115490
Couldn't classify 118098, 118195
Couldn't classify 121658, 121953
Sorry, prediction pasa_asmbl_5541.p1 fails validation.
(ATT)	 AG	118098-118195	GT	AAG
(ATA)	 AG	118429-118672	GT	GGG
(GGG)	 AG	119338-119612	GT	AGG
(GGG)	 AG	119836-119997	GT	AGG
(GTA)	 AG	120487-120571	GT	AGG
(AAC)	 AG	120818-121010	GT	AGG
(GGA)	 AG	121431-121493	GT	CGG
(AAG)	 AG	121658-121953	GC	AGG
-recovered pasa_asmbl_5541.p1, internal, 118098, 118195
-recovered pasa_asmbl_5541.p1, internal, 118429, 118672
-recovered pasa_asmbl_5541.p1, internal, 119338, 119612
-recovered pasa_asmbl_5541.p1, internal, 119836, 119997
-recovered pasa_asmbl_5541.p1, internal, 120487, 120571
-recovered pasa_asmbl_5541.p1, internal, 120818, 121010
-recovered pasa_asmbl_5541.p1, internal, 121431, 121493
-recovered pasa_asmbl_5541.p1, internal, 121658, 121953
Valid prediction for GeneMark_model.47951_t
Valid prediction for snap_scaffold_11-snap.1369-T1
Valid prediction for snap_scaffold_11-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_27722-T1
Valid prediction for GeneMark_model.47969_t
Valid prediction for snap_scaffold_11-snap.1364-T1
Valid prediction for snap_scaffold_11-snap.1339-T1
Valid prediction for HiQ_model.g18477.t1
Valid prediction for GeneMark_model.47930_t
Valid prediction for snap_scaffold_11-snap.1359-T1
Valid prediction for snap_scaffold_11-snap.1379-T1
Valid prediction for GeneMark_model.47916_t
Valid prediction for snap_scaffold_11-snap.1347-T1
Valid prediction for snap_scaffold_11-snap.1375-T1
Valid prediction for GeneMark_model.47948_t
Valid prediction for GlimmerHMM_glimmerT_27713-T1
Valid prediction for snap_scaffold_11-snap.1381-T1
Valid prediction for snap_scaffold_11-snap.1370-T1
Valid prediction for snap_scaffold_11-snap.1340-T1
Valid prediction for GlimmerHMM_glimmerT_27728-T1
Valid prediction for Augustus_model.g18478.t1
Valid prediction for GeneMark_model.47922_t
Valid prediction for Augustus_model.g18480.t1
Valid prediction for GeneMark_model.47958_t
Valid prediction for GlimmerHMM_glimmerT_27724-T1
Valid prediction for GlimmerHMM_glimmerT_27707-T1
Valid prediction for CodingQuarry_transcript_8045-T1
Valid prediction for GeneMark_model.47968_t
Valid prediction for snap_scaffold_11-snap.1355-T1
Valid prediction for snap_scaffold_11-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_27721-T1
Valid prediction for GeneMark_model.47935_t
Valid prediction for GeneMark_model.47940_t
Valid prediction for snap_scaffold_11-snap.1363-T1
Valid prediction for GeneMark_model.47932_t
Couldn't classify 138743, 139576
Sorry, prediction pasa_asmbl_5544.p1 fails validation.
(CCA)	 TC	138743-139576	CA	AGC
Valid prediction for Augustus_model.g18485.t1
Valid prediction for snap_scaffold_11-snap.1367-T1
Valid prediction for snap_scaffold_11-snap.1343-T1
Valid prediction for Augustus_model.g18482.t1
Valid prediction for GeneMark_model.47915_t
Valid prediction for GlimmerHMM_glimmerT_27723-T1
Valid prediction for GlimmerHMM_glimmerT_27715-T1
Valid prediction for GeneMark_model.47924_t
Valid prediction for snap_scaffold_11-snap.1376-T1
Valid prediction for snap_scaffold_11-snap.1349-T1
Valid prediction for snap_scaffold_11-snap.1360-T1
Valid prediction for GeneMark_model.47950_t
Valid prediction for GlimmerHMM_glimmerT_27711-T1
Valid prediction for GlimmerHMM_glimmerT_27726-T1
Couldn't classify 114268, 114346
Sorry, prediction pasa_asmbl_5538.p2 fails validation.
(ATG)	 AG	109849-109854	GT	AGG
(GCA)	 AG	110211-110321	GT	AGG
(GTG)	 AG	111671-111736	GT	GGG
(GTG)	 AG	112155-112245	GT	GGG
(TGT)	 AG	112512-112591	GT	AGG
(ACG)	 AG	112728-112825	GT	GTG
(AGC)	 AG	114268-114346	AA	GGA
-recovered pasa_asmbl_5538.p2, initial, 109849, 109854
-recovered pasa_asmbl_5538.p2, internal, 109849, 109854
-recovered pasa_asmbl_5538.p2, internal, 110211, 110321
-recovered pasa_asmbl_5538.p2, internal, 111671, 111736
-recovered pasa_asmbl_5538.p2, internal, 112155, 112245
-recovered pasa_asmbl_5538.p2, internal, 112512, 112591
-recovered pasa_asmbl_5538.p2, internal, 112728, 112825
Valid prediction for snap_scaffold_11-snap.1366-T1
Valid prediction for GeneMark_model.47942_t
Valid prediction for Augustus_model.g18475.t1
Valid prediction for GeneMark_model.47938_t
Valid prediction for snap_scaffold_11-snap.1383-T1
Valid prediction for Augustus_model.g18484.t1
Valid prediction for GeneMark_model.47937_t
Valid prediction for pasa_asmbl_5535.p1
Valid prediction for GeneMark_model.47947_t
Valid prediction for GeneMark_model.47965_t
Valid prediction for Augustus_model.g18467.t1
Valid prediction for GlimmerHMM_glimmerT_27706-T1
Valid prediction for GeneMark_model.47946_t
Valid prediction for GeneMark_model.47956_t
Valid prediction for snap_scaffold_11-snap.1384-T1
Valid prediction for snap_scaffold_11-snap.1346-T1
Valid prediction for GeneMark_model.47920_t
Valid prediction for GeneMark_model.47954_t
Valid prediction for GeneMark_model.47970_t
Valid prediction for GeneMark_model.47953_t
Valid prediction for GeneMark_model.47933_t
Valid prediction for GlimmerHMM_glimmerT_27717-T1
Valid prediction for snap_scaffold_11-snap.1373-T1
Couldn't classify 124669, 125049
Sorry, prediction pasa_asmbl_5543.p1 fails validation.
(TCT)	 CG	124669-125049	GT	GAG

-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_11-snap.1382-T1
Valid prediction for GlimmerHMM_glimmerT_27725-T1
Valid prediction for snap_scaffold_11-snap.1377-T1
Valid prediction for GlimmerHMM_glimmerT_27712-T1
Valid prediction for GeneMark_model.47925_t
Valid prediction for snap_scaffold_11-snap.1371-T1
Valid prediction for GeneMark_model.47941_t
Valid prediction for snap_scaffold_11-snap.1344-T1
Valid prediction for GeneMark_model.47923_t
Valid prediction for GlimmerHMM_glimmerT_27714-T1
Valid prediction for snap_scaffold_11-snap.1378-T1
Valid prediction for GeneMark_model.47964_t
Valid prediction for GlimmerHMM_glimmerT_27705-T1
Valid prediction for Augustus_model.g18469.t1
Valid prediction for Augustus_model.g18481.t1
Valid prediction for HiQ_model.g18479.t1
Valid prediction for GeneMark_model.47919_t
Valid prediction for GlimmerHMM_glimmerT_27709-T1
Valid prediction for GeneMark_model.47943_t
Valid prediction for Augustus_model.g18468.t1
Valid prediction for GeneMark_model.47914_t
Valid prediction for snap_scaffold_11-snap.1342-T1
Valid prediction for snap_scaffold_11-snap.1358-T1
Valid prediction for GlimmerHMM_glimmerT_27720-T1
Valid prediction for GeneMark_model.47921_t
Valid prediction for snap_scaffold_11-snap.1350-T1
Valid prediction for GeneMark_model.47966_t
Valid prediction for GlimmerHMM_glimmerT_27727-T1
Valid prediction for GeneMark_model.47952_t
Valid prediction for GlimmerHMM_glimmerT_27718-T1
Valid prediction for GlimmerHMM_glimmerT_27719-T1
Valid prediction for snap_scaffold_11-snap.1356-T1
Valid prediction for snap_scaffold_11-snap.1372-T1
Valid prediction for GeneMark_model.47939_t
Valid prediction for Augustus_model.g18472.t1
Valid prediction for snap_scaffold_11-snap.1380-T1
Valid prediction for Augustus_model.g18476.t1
Valid prediction for snap_scaffold_11-snap.1361-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27710-T1
Valid prediction for snap_scaffold_11-snap.1374-T1
Valid prediction for GeneMark_model.47931_t
Valid prediction for GeneMark_model.47955_t
Valid prediction for GlimmerHMM_glimmerT_27716-T1
Valid prediction for snap_scaffold_11-snap.1354-T1
Valid prediction for Augustus_model.g18473.t1
Valid prediction for GeneMark_model.47962_t
Valid prediction for GeneMark_model.47927_t
Valid prediction for GeneMark_model.47945_t
Valid prediction for GeneMark_model.47934_t
Valid prediction for snap_scaffold_11-snap.1338-T1
Valid prediction for CodingQuarry_transcript_8046-T1
Valid prediction for Augustus_model.g18466.t1
Valid prediction for GeneMark_model.47960_t
Valid prediction for GeneMark_model.47957_t
Valid prediction for snap_scaffold_11-snap.1352-T1
Valid prediction for GeneMark_model.47929_t
Valid prediction for Augustus_model.g18471.t1
Valid prediction for GlimmerHMM_glimmerT_27708-T1
Valid prediction for GeneMark_model.47949_t
Couldn't classify 100372, 100542
Sorry, prediction pasa_asmbl_6651.p1 fails validation.
(ATG)	 GC	94636-94704	GT	AGG
(TTG)	 AG	95584-95689	GT	AGG
(TGC)	 AG	97156-97285	GT	GAG
(GAT)	 AG	99793-99826	GT	TGG
(GAC)	 AG	100372-100542	GT	AGG
-recovered pasa_asmbl_6651.p1, initial, 94636, 94704
-recovered pasa_asmbl_6651.p1, internal, 95584, 95689
-recovered pasa_asmbl_6651.p1, internal, 97156, 97285
-recovered pasa_asmbl_6651.p1, internal, 99793, 99826
-recovered pasa_asmbl_6651.p1, internal, 100372, 100542
Valid prediction for Augustus_model.g18483.t1
Valid prediction for GeneMark_model.47959_t
Valid prediction for snap_scaffold_11-snap.1365-T1
Valid prediction for Augustus_model.g18474.t1
Valid prediction for GeneMark_model.47936_t
Valid prediction for snap_scaffold_11-snap.1353-T1
Valid prediction for snap_scaffold_11-snap.1348-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9721, rend_intergenic: 4066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23715, rend_intergenic: 20245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41116, rend_intergenic: 26372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56636, rend_intergenic: 55772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59835, rend_intergenic: 56722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66401, rend_intergenic: 62827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66582, rend_intergenic: 66431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73117, rend_intergenic: 69738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74496, rend_intergenic: 73169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79191, rend_intergenic: 75123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90839, rend_intergenic: 79601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98486, rend_intergenic: 94351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125049, rend_intergenic: 121672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137363, rend_intergenic: 133504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145835, rend_intergenic: 141244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151626, rend_intergenic: 149119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156792, rend_intergenic: 154103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157235, rend_intergenic: 156941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163898, rend_intergenic: 160490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167205, rend_intergenic: 165133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177105
-exon list size: 725


building trellis

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65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 9721, rend_intergenic: 4066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23715, rend_intergenic: 20245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41116, rend_intergenic: 26372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56636, rend_intergenic: 55772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59835, rend_intergenic: 56722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66401, rend_intergenic: 62827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66582, rend_intergenic: 66431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73117, rend_intergenic: 69738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74496, rend_intergenic: 73169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79191, rend_intergenic: 75123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90839, rend_intergenic: 79601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98486, rend_intergenic: 94351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125049, rend_intergenic: 121672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137363, rend_intergenic: 133504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145835, rend_intergenic: 141244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151626, rend_intergenic: 149119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156792, rend_intergenic: 154103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157235, rend_intergenic: 156941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163898, rend_intergenic: 160490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167205, rend_intergenic: 165133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support