-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_6402629-6640205

-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_26-snap.1466-T1
Valid prediction for GlimmerHMM_glimmerT_55890-T1
Valid prediction for snap_scaffold_26-snap.1480-T1
Valid prediction for snap_scaffold_26-snap.1479-T1
Valid prediction for GlimmerHMM_glimmerT_55912-T1
Valid prediction for snap_scaffold_26-snap.1489-T1
Valid prediction for GlimmerHMM_glimmerT_55895-T1
Valid prediction for snap_scaffold_26-snap.1469-T1
Valid prediction for snap_scaffold_26-snap.1464-T1
Valid prediction for snap_scaffold_26-snap.1491-T1
Valid prediction for snap_scaffold_26-snap.1473-T1
Valid prediction for Augustus_model.g37060.t1
Valid prediction for GlimmerHMM_glimmerT_55893-T1
Valid prediction for snap_scaffold_26-snap.1477-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g37058.t1
Valid prediction for GlimmerHMM_glimmerT_55920-T1
Valid prediction for Augustus_model.g37050.t1
Valid prediction for snap_scaffold_26-snap.1502-T1
Valid prediction for Augustus_model.g37064.t1
Valid prediction for snap_scaffold_26-snap.1485-T1
Valid prediction for snap_scaffold_26-snap.1512-T1
Valid prediction for snap_scaffold_26-snap.1497-T1
Valid prediction for Augustus_model.g37063.t1
Valid prediction for Augustus_model.g37047.t1
Valid prediction for snap_scaffold_26-snap.1499-T1
Valid prediction for Augustus_model.g37053.t1
Valid prediction for snap_scaffold_26-snap.1495-T1
Valid prediction for snap_scaffold_26-snap.1508-T1
Valid prediction for snap_scaffold_26-snap.1481-T1
Valid prediction for Augustus_model.g37065.t1
Valid prediction for snap_scaffold_26-snap.1478-T1
Valid prediction for GlimmerHMM_glimmerT_55905-T1
Valid prediction for GlimmerHMM_glimmerT_55901-T1
Valid prediction for snap_scaffold_26-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_55898-T1
Valid prediction for GlimmerHMM_glimmerT_55922-T1
Valid prediction for Augustus_model.g37054.t1
Couldn't classify 170086, 170154
Sorry, prediction pasa_asmbl_35089.p2 fails validation.
(ATG)	 AC	166224-166247	GT	AGG
(ATC)	 AG	167678-167782	GT	TGG
(ATC)	 AG	167917-168079	GT	AGG
(CGG)	 AG	168751-168938	GT	AGG
(CAC)	 AG	169145-169300	GC	AGG
(CAA)	 AG	170086-170154	GG	ACG
-recovered pasa_asmbl_35089.p2, initial, 166224, 166247
-recovered pasa_asmbl_35089.p2, internal, 167678, 167782
-recovered pasa_asmbl_35089.p2, internal, 167917, 168079
-recovered pasa_asmbl_35089.p2, internal, 168751, 168938
-recovered pasa_asmbl_35089.p2, internal, 169145, 169300
Valid prediction for GlimmerHMM_glimmerT_55918-T1
Valid prediction for Augustus_model.g37061.t1
Valid prediction for snap_scaffold_26-snap.1503-T1
Couldn't classify 82943, 82951
Couldn't classify 84133, 84267
Sorry, prediction pasa_asmbl_35083.p1 fails validation.
(GGA)	 GA	82943-82951	GT	CTG
(GGG)	 AG	83064-83126	GT	GGG
(GAT)	 AG	83225-83390	GT	CGG
(GGA)	 AG	83499-83605	GT	AGG
(GTG)	 AG	83686-83766	GT	AGG
(TTT)	 AG	83856-84038	GT	TGG
(CCC)	 AG	84133-84267	GG	TGG
-recovered pasa_asmbl_35083.p1, internal, 83064, 83126
-recovered pasa_asmbl_35083.p1, internal, 83225, 83390
-recovered pasa_asmbl_35083.p1, internal, 83499, 83605
-recovered pasa_asmbl_35083.p1, internal, 83686, 83766
-recovered pasa_asmbl_35083.p1, internal, 83856, 84038
Valid prediction for snap_scaffold_26-snap.1474-T1
Valid prediction for GlimmerHMM_glimmerT_55921-T1
Valid prediction for GlimmerHMM_glimmerT_55892-T1
Valid prediction for GlimmerHMM_glimmerT_55887-T1
Valid prediction for Augustus_model.g37049.t1
Valid prediction for Augustus_model.g37059.t1
Couldn't classify 91214, 91270
Couldn't classify 94711, 94869
Sorry, prediction pasa_asmbl_35316.p1 fails validation.
(GTT)	 AG	91214-91270	GT	AGG
(AAG)	 AG	91362-91540	GT	AAG
(ATG)	 AG	91640-91740	GT	AGG
(CCA)	 AG	91942-92118	GT	AGG
(AGT)	 AG	92217-92365	GT	CTG
(AAA)	 AG	92587-92775	GT	AGG
(GCT)	 AG	92995-93185	GT	GAG
(GCT)	 AG	93907-94027	GT	TGG
(GAC)	 AG	94198-94392	GT	AGG
(CTT)	 AG	94482-94613	GT	AGG
(GTG)	 AG	94711-94869	TT	TGT
add_exon() Sorry, pasa_asmbl_35316.p1 91640-91740-initial-1 is invalid.
-recovered pasa_asmbl_35316.p1, initial, 91640, 91740
-recovered pasa_asmbl_35316.p1, internal, 91214, 91270
-recovered pasa_asmbl_35316.p1, internal, 91362, 91540
-recovered pasa_asmbl_35316.p1, internal, 91640, 91740
-recovered pasa_asmbl_35316.p1, internal, 91942, 92118
-recovered pasa_asmbl_35316.p1, internal, 92217, 92365
-recovered pasa_asmbl_35316.p1, internal, 92587, 92775
-recovered pasa_asmbl_35316.p1, internal, 92995, 93185
-recovered pasa_asmbl_35316.p1, internal, 93907, 94027
-recovered pasa_asmbl_35316.p1, internal, 94198, 94392
-recovered pasa_asmbl_35316.p1, internal, 94482, 94613
Valid prediction for snap_scaffold_26-snap.1515-T1
Valid prediction for snap_scaffold_26-snap.1484-T1
Valid prediction for snap_scaffold_26-snap.1483-T1
Valid prediction for GlimmerHMM_glimmerT_55903-T1
Valid prediction for GlimmerHMM_glimmerT_55899-T1
Valid prediction for Augustus_model.g37048.t1
Valid prediction for GlimmerHMM_glimmerT_55916-T1
Valid prediction for GlimmerHMM_glimmerT_55889-T1
Valid prediction for snap_scaffold_26-snap.1475-T1
Valid prediction for GlimmerHMM_glimmerT_55911-T1
Valid prediction for snap_scaffold_26-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_55923-T1
Valid prediction for GlimmerHMM_glimmerT_55909-T1
Valid prediction for snap_scaffold_26-snap.1490-T1
Valid prediction for snap_scaffold_26-snap.1513-T1
Valid prediction for snap_scaffold_26-snap.1487-T1
Valid prediction for snap_scaffold_26-snap.1505-T1
Valid prediction for pasa_asmbl_35090.p1
Valid prediction for GlimmerHMM_glimmerT_55914-T1
Valid prediction for Augustus_model.g37068.t1
Valid prediction for Augustus_model.g37056.t1
Couldn't classify 159221, 159349
Couldn't classify 161238, 161278
Sorry, prediction pasa_asmbl_35088.p1 fails validation.
(AGG)	 CG	159221-159349	GT	AGG
(GTT)	 AG	160426-160554	GT	TGG
(TCC)	 AG	160957-161062	GT	TGG
(GTG)	 AG	161238-161278	GC	GCG
-recovered pasa_asmbl_35088.p1, internal, 160426, 160554
-recovered pasa_asmbl_35088.p1, internal, 160957, 161062
-recovered pasa_asmbl_35088.p1, internal, 161238, 161278
Valid prediction for GlimmerHMM_glimmerT_55919-T1
Valid prediction for Augustus_model.g37057.t1
Couldn't classify 79808, 79891
Sorry, prediction pasa_asmbl_35303.p2 fails validation.
(ATG)	 GC	79188-79283	GT	CAG
(GGT)	 AG	79365-79418	GT	AGG
(GGA)	 AG	79511-79564	GT	AGG
(GGT)	 AG	79651-79704	GT	AGG
(GGA)	 AG	79808-79891	GA	GTG
-recovered pasa_asmbl_35303.p2, initial, 79188, 79283
-recovered pasa_asmbl_35303.p2, internal, 79365, 79418
-recovered pasa_asmbl_35303.p2, internal, 79511, 79564
-recovered pasa_asmbl_35303.p2, internal, 79651, 79704
Valid prediction for Augustus_model.g37051.t1
Valid prediction for snap_scaffold_26-snap.1462-T1
Valid prediction for snap_scaffold_26-snap.1470-T1
Valid prediction for snap_scaffold_26-snap.1494-T1
Valid prediction for snap_scaffold_26-snap.1516-T1
Valid prediction for GlimmerHMM_glimmerT_55902-T1
Valid prediction for snap_scaffold_26-snap.1472-T1
Valid prediction for GlimmerHMM_glimmerT_55891-T1
Valid prediction for snap_scaffold_26-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_55897-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 pasa_asmbl_35689.p1
Valid prediction for snap_scaffold_26-snap.1468-T1
Valid prediction for snap_scaffold_26-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_55908-T1
Valid prediction for GlimmerHMM_glimmerT_55910-T1
Valid prediction for snap_scaffold_26-snap.1488-T1
Valid prediction for snap_scaffold_26-snap.1507-T1
Valid prediction for GlimmerHMM_glimmerT_55894-T1
Valid prediction for snap_scaffold_26-snap.1500-T1
Valid prediction for CodingQuarry_transcript_40395-T1
Valid prediction for snap_scaffold_26-snap.1465-T1
Valid prediction for Augustus_model.g37069.t1
Valid prediction for Augustus_model.g37062.t1
Valid prediction for HiQ_model.g37055.t1
Valid prediction for snap_scaffold_26-snap.1493-T1
Valid prediction for GlimmerHMM_glimmerT_55917-T1
Valid prediction for GlimmerHMM_glimmerT_55915-T1
Valid prediction for Augustus_model.g37052.t1
Valid prediction for snap_scaffold_26-snap.1496-T1
Valid prediction for Augustus_model.g37066.t1
Valid prediction for snap_scaffold_26-snap.1486-T1
Valid prediction for snap_scaffold_26-snap.1514-T1
Valid prediction for snap_scaffold_26-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_55900-T1
Valid prediction for snap_scaffold_26-snap.1517-T1
Valid prediction for snap_scaffold_26-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_55888-T1
Valid prediction for GlimmerHMM_glimmerT_55904-T1
Valid prediction for CodingQuarry_transcript_40393-T1
Valid prediction for snap_scaffold_26-snap.1467-T1
Valid prediction for GlimmerHMM_glimmerT_55906-T1
Couldn't classify 2194, 2288
Sorry, prediction pasa_asmbl_35690.p1 fails validation.
(GGA)	 AT	2194-2288	GT	GGG
(TTT)	 AG	2510-2570	GT	TTG
(AGA)	 AG	2690-2739	GT	AGG
(GTC)	 AG	2854-3038	GT	CGG
(GTT)	 AG	3209-3256	GT	AGG
(GGT)	 AG	3363-3456	GT	AGG
(AAA)	 AG	3586-3634	AG	AAA
-recovered pasa_asmbl_35690.p1, terminal, 3586, 3634
-recovered pasa_asmbl_35690.p1, internal, 2510, 2570
-recovered pasa_asmbl_35690.p1, internal, 2690, 2739
-recovered pasa_asmbl_35690.p1, internal, 2854, 3038
-recovered pasa_asmbl_35690.p1, internal, 3209, 3256
-recovered pasa_asmbl_35690.p1, internal, 3363, 3456
Valid prediction for snap_scaffold_26-snap.1471-T1
Valid prediction for snap_scaffold_26-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_55896-T1
Valid prediction for snap_scaffold_26-snap.1510-T1
Valid prediction for snap_scaffold_26-snap.1476-T1
Valid prediction for snap_scaffold_26-snap.1482-T1
Valid prediction for snap_scaffold_26-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_55913-T1
Valid prediction for GlimmerHMM_glimmerT_55907-T1
Valid prediction for Augustus_model.g37067.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 173689, rend_intergenic: 173686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18425, rend_intergenic: 12602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26516, rend_intergenic: 25414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52427, rend_intergenic: 44446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84288, rend_intergenic: 78179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106976, rend_intergenic: 103459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125582, rend_intergenic: 123170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137637, rend_intergenic: 134806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147468, rend_intergenic: 142080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159976, rend_intergenic: 152970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171818, rend_intergenic: 164096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184760, rend_intergenic: 182492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208291, rend_intergenic: 196516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217706, rend_intergenic: 211471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237577
-exon list size: 666


building trellis

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74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 173689, rend_intergenic: 173686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18425, rend_intergenic: 12602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26516, rend_intergenic: 25414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52427, rend_intergenic: 44446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84288, rend_intergenic: 78179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106976, rend_intergenic: 103459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125582, rend_intergenic: 123170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137637, rend_intergenic: 134806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147468, rend_intergenic: 142080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159976, rend_intergenic: 152970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171818, rend_intergenic: 164096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184760, rend_intergenic: 182492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208291, rend_intergenic: 196516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217706, rend_intergenic: 211471  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