-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_7336508-7575619

-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.71411_t
Valid prediction for GeneMark_model.71384_t
Valid prediction for Augustus_model.g27793.t1
Valid prediction for Augustus_model.g27781.t1
Valid prediction for GeneMark_model.71420_t
Couldn't classify 33772, 34067
Sorry, prediction pasa_asmbl_18034.p1 fails validation.
(ATG)	 AC	31599-31607	GT	AGG
(ATC)	 AG	31721-31964	GT	GAG
(AGC)	 AG	33772-34067	CC	TGC
-recovered pasa_asmbl_18034.p1, initial, 31599, 31607
-recovered pasa_asmbl_18034.p1, terminal, 31721, 31964
-recovered pasa_asmbl_18034.p1, internal, 31721, 31964
Valid prediction for snap_scaffold_17-snap.1468-T1
Valid prediction for GeneMark_model.71391_t
Valid prediction for snap_scaffold_17-snap.1451-T1
Valid prediction for GeneMark_model.71381_t
Valid prediction for GeneMark_model.71395_t
Valid prediction for snap_scaffold_17-snap.1453-T1
Valid prediction for snap_scaffold_17-snap.1480-T1
Valid prediction for snap_scaffold_17-snap.1470-T1
Valid prediction for snap_scaffold_17-snap.1467-T1
Couldn't classify 103638, 103988
Sorry, prediction pasa_asmbl_19095.p1 fails validation.
(TCC)	 CC	103638-103988	CC	AAC
Valid prediction for GlimmerHMM_glimmerT_41474-T1
Valid prediction for Augustus_model.g27795.t1
Valid prediction for GlimmerHMM_glimmerT_41469-T1
Valid prediction for snap_scaffold_17-snap.1486-T1
Valid prediction for GeneMark_model.71409_t
Valid prediction for CodingQuarry_transcript_21989-T1
Valid prediction for Augustus_model.g27796.t1
Valid prediction for GeneMark_model.71396_t
Couldn't classify 90523, 90669
Sorry, prediction pasa_asmbl_18036.p1 fails validation.
(GTG)	 GC	90523-90669	GT	AGG
(TTG)	 AG	90818-90907	GT	AGG
(AAG)	 AG	91132-91227	CA	GAC
-recovered pasa_asmbl_18036.p1, terminal, 91132, 91227
-recovered pasa_asmbl_18036.p1, internal, 90818, 90907
Valid prediction for GeneMark_model.71387_t
Valid prediction for Augustus_model.g27784.t1
Valid prediction for GlimmerHMM_glimmerT_41485-T1
Valid prediction for GeneMark_model.71403_t
Valid prediction for GlimmerHMM_glimmerT_41465-T1
Valid prediction for GeneMark_model.71426_t
Valid prediction for snap_scaffold_17-snap.1472-T1
Valid prediction for Augustus_model.g27782.t1
Valid prediction for GeneMark_model.71393_t
Valid prediction for GlimmerHMM_glimmerT_41472-T1
Valid prediction for Augustus_model.g27798.t1
Valid prediction for snap_scaffold_17-snap.1477-T1
Valid prediction for GeneMark_model.71413_t
Valid prediction for Augustus_model.g27794.t1
Valid prediction for GeneMark_model.71398_t
Valid prediction for CodingQuarry_transcript_21988-T1
Valid prediction for GeneMark_model.71394_t
Valid prediction for Augustus_model.g27785.t1
Valid prediction for HiQ_model.g27792.t1
Valid prediction for snap_scaffold_17-snap.1471-T1
Valid prediction for snap_scaffold_17-snap.1456-T1
Valid prediction for snap_scaffold_17-snap.1465-T1
Valid prediction for snap_scaffold_17-snap.1487-T1
Valid prediction for GlimmerHMM_glimmerT_41483-T1
Valid prediction for snap_scaffold_17-snap.1475-T1
Valid prediction for snap_scaffold_17-snap.1484-T1
Valid prediction for snap_scaffold_17-snap.1447-T1
Valid prediction for GlimmerHMM_glimmerT_41493-T1
Valid prediction for GeneMark_model.71385_t
Valid prediction for GlimmerHMM_glimmerT_41482-T1
Valid prediction for snap_scaffold_17-snap.1488-T1
Valid prediction for GlimmerHMM_glimmerT_41476-T1
Valid prediction for pasa_asmbl_18037.p1
Valid prediction for GeneMark_model.71389_t
Valid prediction for snap_scaffold_17-snap.1483-T1
Valid prediction for GeneMark_model.71402_t
Valid prediction for snap_scaffold_17-snap.1473-T1
Valid prediction for GeneMark_model.71430_t
Valid prediction for GlimmerHMM_glimmerT_41478-T1
Valid prediction for GeneMark_model.71424_t
Valid prediction for GlimmerHMM_glimmerT_41470-T1
Valid prediction for snap_scaffold_17-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_41468-T1
Valid prediction for GlimmerHMM_glimmerT_41467-T1
Valid prediction for GeneMark_model.71383_t
Valid prediction for CodingQuarry_transcript_21987-T1
Valid prediction for snap_scaffold_17-snap.1463-T1
Valid prediction for snap_scaffold_17-snap.1490-T1
Valid prediction for GlimmerHMM_glimmerT_41487-T1
Valid prediction for GeneMark_model.71407_t
Valid prediction for Augustus_model.g27789.t1
Valid prediction for GlimmerHMM_glimmerT_41479-T1
Valid prediction for GeneMark_model.71422_t
Valid prediction for GeneMark_model.71416_t
Valid prediction for GeneMark_model.71379_t
Couldn't classify 163716, 163833
Sorry, prediction pasa_asmbl_18557.p1 fails validation.
(ATA)	 AG	163716-163833	GT	AGG
(GCG)	 AG	164061-164227	GT	AGG
(TCC)	 AG	165218-165350	GT	AGG
(CCG)	 AG	166799-166962	AG	AAA
-recovered pasa_asmbl_18557.p1, terminal, 166799, 166962
-recovered pasa_asmbl_18557.p1, internal, 163716, 163833
-recovered pasa_asmbl_18557.p1, internal, 164061, 164227
-recovered pasa_asmbl_18557.p1, internal, 165218, 165350
Valid prediction for Augustus_model.g27780.t1
Valid prediction for GeneMark_model.71418_t
Valid prediction for Augustus_model.g27783.t1
Valid prediction for snap_scaffold_17-snap.1458-T1
Valid prediction for GlimmerHMM_glimmerT_41489-T1
Valid prediction for snap_scaffold_17-snap.1479-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 GeneMark_model.71427_t
Valid prediction for Augustus_model.g27797.t1
Valid prediction for snap_scaffold_17-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_41494-T1
Valid prediction for GeneMark_model.71412_t
Valid prediction for GeneMark_model.71415_t
Valid prediction for GlimmerHMM_glimmerT_41484-T1
Valid prediction for GlimmerHMM_glimmerT_41475-T1
Valid prediction for GlimmerHMM_glimmerT_41488-T1
Valid prediction for Augustus_model.g27788.t1
Valid prediction for GeneMark_model.71401_t
Valid prediction for GlimmerHMM_glimmerT_41492-T1
Valid prediction for GlimmerHMM_glimmerT_41471-T1
Valid prediction for GlimmerHMM_glimmerT_41491-T1
Valid prediction for GeneMark_model.71414_t
Valid prediction for Augustus_model.g27790.t1
Valid prediction for snap_scaffold_17-snap.1454-T1
Valid prediction for GeneMark_model.71408_t
Valid prediction for HiQ_model.g27779.t1
Valid prediction for snap_scaffold_17-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_41480-T1
Valid prediction for snap_scaffold_17-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_41486-T1
Valid prediction for GeneMark_model.71419_t
Valid prediction for Augustus_model.g27786.t1
Valid prediction for GeneMark_model.71392_t
Valid prediction for snap_scaffold_17-snap.1450-T1
Valid prediction for GeneMark_model.71378_t
Valid prediction for GeneMark_model.71423_t
Valid prediction for snap_scaffold_17-snap.1485-T1
Valid prediction for GeneMark_model.71400_t
Valid prediction for GlimmerHMM_glimmerT_41477-T1
Valid prediction for GeneMark_model.71425_t
Valid prediction for snap_scaffold_17-snap.1448-T1
Valid prediction for GeneMark_model.71397_t
Valid prediction for pasa_asmbl_19094.p1
Valid prediction for GeneMark_model.71386_t
Valid prediction for GeneMark_model.71376_t
Valid prediction for snap_scaffold_17-snap.1459-T1
Valid prediction for GeneMark_model.71405_t
Valid prediction for Augustus_model.g27787.t1
Valid prediction for snap_scaffold_17-snap.1469-T1
Valid prediction for snap_scaffold_17-snap.1464-T1
Valid prediction for GeneMark_model.71404_t
Valid prediction for GeneMark_model.71377_t
Valid prediction for GeneMark_model.71380_t
Valid prediction for CodingQuarry_transcript_21986-T1
Valid prediction for snap_scaffold_17-snap.1489-T1
Valid prediction for GlimmerHMM_glimmerT_41490-T1
Valid prediction for GeneMark_model.71390_t
Valid prediction for snap_scaffold_17-snap.1461-T1
Valid prediction for GeneMark_model.71410_t
Valid prediction for snap_scaffold_17-snap.1481-T1
Valid prediction for GeneMark_model.71382_t
Valid prediction for GlimmerHMM_glimmerT_41466-T1
Valid prediction for snap_scaffold_17-snap.1455-T1
Valid prediction for snap_scaffold_17-snap.1474-T1
Valid prediction for snap_scaffold_17-snap.1457-T1
Valid prediction for GlimmerHMM_glimmerT_41481-T1
Valid prediction for GeneMark_model.71429_t
Valid prediction for Augustus_model.g27791.t1
Valid prediction for snap_scaffold_17-snap.1478-T1
Valid prediction for snap_scaffold_17-snap.1466-T1
Valid prediction for snap_scaffold_17-snap.1482-T1
Valid prediction for GeneMark_model.71399_t
Valid prediction for GeneMark_model.71406_t
Valid prediction for snap_scaffold_17-snap.1452-T1
Valid prediction for GlimmerHMM_glimmerT_41473-T1
Valid prediction for GeneMark_model.71421_t
Valid prediction for GeneMark_model.71428_t
Valid prediction for GeneMark_model.71417_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14774, rend_intergenic: 5729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18719, rend_intergenic: 15237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23218, rend_intergenic: 20751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36001, rend_intergenic: 27304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51891, rend_intergenic: 50449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53750, rend_intergenic: 53358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68917, rend_intergenic: 65446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104039, rend_intergenic: 92531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105992, rend_intergenic: 104047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117185, rend_intergenic: 106949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120093, rend_intergenic: 117588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126855, rend_intergenic: 120121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147978, rend_intergenic: 145399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155099, rend_intergenic: 149558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166962, rend_intergenic: 158732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183839, rend_intergenic: 176050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185158, rend_intergenic: 184231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199323, rend_intergenic: 198013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219832, rend_intergenic: 199378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229396, rend_intergenic: 223756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239112
-exon list size: 755


building trellis

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80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 14774, rend_intergenic: 5729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18719, rend_intergenic: 15237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23218, rend_intergenic: 20751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36001, rend_intergenic: 27304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51891, rend_intergenic: 50449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53750, rend_intergenic: 53358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68917, rend_intergenic: 65446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104039, rend_intergenic: 92531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105992, rend_intergenic: 104047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117185, rend_intergenic: 106949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120093, rend_intergenic: 117588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126855, rend_intergenic: 120121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147978, rend_intergenic: 145399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155099, rend_intergenic: 149558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166962, rend_intergenic: 158732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183839, rend_intergenic: 176050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185158, rend_intergenic: 184231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199323, rend_intergenic: 198013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219832, rend_intergenic: 199378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229396, rend_intergenic: 223756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 227981 - 239112
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal

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