-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_6024944-6165883

-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_9-snap.1292-T1
Valid prediction for Augustus_model.g15228.t1
Valid prediction for GlimmerHMM_glimmerT_22753-T1
Valid prediction for GeneMark_model.39094_t
Valid prediction for GeneMark_model.39063_t
Valid prediction for GeneMark_model.39087_t
Valid prediction for snap_scaffold_9-snap.1302-T1
Valid prediction for Augustus_model.g15218.t1
Couldn't classify 123791, 123943
Couldn't classify 131548, 131649
Sorry, prediction pasa_asmbl_54064.p1 fails validation.
(CCC)	 TC	123791-123943	GT	AGG
(GCG)	 AG	125277-125398	GT	ATG
(ATA)	 AG	127949-128017	GT	AGG
(GTA)	 AG	128609-128765	GT	AGG
(CAC)	 AG	131548-131649	TG	CGT
-recovered pasa_asmbl_54064.p1, internal, 125277, 125398
-recovered pasa_asmbl_54064.p1, internal, 127949, 128017
-recovered pasa_asmbl_54064.p1, internal, 128609, 128765
Valid prediction for snap_scaffold_9-snap.1299-T1
Valid prediction for Augustus_model.g15219.t1
Valid prediction for GeneMark_model.39086_t
Valid prediction for GeneMark_model.39084_t
Valid prediction for GeneMark_model.39069_t
Valid prediction for GlimmerHMM_glimmerT_22760-T1
Valid prediction for GeneMark_model.39071_t
Valid prediction for GeneMark_model.39077_t
Valid prediction for snap_scaffold_9-snap.1285-T1
Valid prediction for snap_scaffold_9-snap.1313-T1
Valid prediction for snap_scaffold_9-snap.1301-T1
Valid prediction for GlimmerHMM_glimmerT_22762-T1
Valid prediction for GeneMark_model.39096_t
Valid prediction for GlimmerHMM_glimmerT_22771-T1
Valid prediction for Augustus_model.g15215.t1
Valid prediction for snap_scaffold_9-snap.1304-T1
Valid prediction for GeneMark_model.39105_t
Valid prediction for Augustus_model.g15216.t1
Valid prediction for snap_scaffold_9-snap.1295-T1
Valid prediction for GlimmerHMM_glimmerT_22768-T1
Valid prediction for snap_scaffold_9-snap.1306-T1
Valid prediction for GlimmerHMM_glimmerT_22751-T1
Valid prediction for GeneMark_model.39067_t
Valid prediction for GeneMark_model.39106_t
Valid prediction for GeneMark_model.39102_t
Valid prediction for HiQ_model.g15224.t1
Valid prediction for GeneMark_model.39100_t
Valid prediction for snap_scaffold_9-snap.1284-T1
Valid prediction for GeneMark_model.39108_t
Valid prediction for GlimmerHMM_glimmerT_22759-T1
Valid prediction for Augustus_model.g15226.t1
Valid prediction for Augustus_model.g15217.t1
Valid prediction for Augustus_model.g15220.t1
Valid prediction for GeneMark_model.39079_t
Valid prediction for GeneMark_model.39093_t
Valid prediction for snap_scaffold_9-snap.1291-T1
Valid prediction for GlimmerHMM_glimmerT_22770-T1
Valid prediction for GlimmerHMM_glimmerT_22752-T1
Valid prediction for GeneMark_model.39103_t
Valid prediction for GeneMark_model.39090_t
Valid prediction for snap_scaffold_9-snap.1317-T1
Valid prediction for GlimmerHMM_glimmerT_22754-T1
Valid prediction for GeneMark_model.39088_t
Valid prediction for snap_scaffold_9-snap.1309-T1
Valid prediction for snap_scaffold_9-snap.1293-T1
Valid prediction for snap_scaffold_9-snap.1308-T1
Valid prediction for snap_scaffold_9-snap.1289-T1
Valid prediction for Augustus_model.g15225.t1
Valid prediction for Augustus_model.g15214.t1
Valid prediction for GeneMark_model.39075_t
Valid prediction for GeneMark_model.39098_t
Valid prediction for snap_scaffold_9-snap.1297-T1
Valid prediction for GlimmerHMM_glimmerT_22764-T1
Valid prediction for GeneMark_model.39065_t
Valid prediction for CodingQuarry_transcript_62034-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_9-snap.1296-T1
Valid prediction for GeneMark_model.39091_t
Valid prediction for GeneMark_model.39076_t
Valid prediction for GeneMark_model.39104_t
Valid prediction for GlimmerHMM_glimmerT_22766-T1
Valid prediction for GlimmerHMM_glimmerT_22757-T1
Valid prediction for snap_scaffold_9-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_22772-T1
Valid prediction for GeneMark_model.39064_t
Valid prediction for GeneMark_model.39070_t
Valid prediction for snap_scaffold_9-snap.1310-T1
Valid prediction for snap_scaffold_9-snap.1287-T1
Valid prediction for Augustus_model.g15223.t1
Valid prediction for snap_scaffold_9-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_22769-T1
Valid prediction for GeneMark_model.39072_t
Valid prediction for GeneMark_model.39074_t
Valid prediction for GeneMark_model.39095_t
Valid prediction for snap_scaffold_9-snap.1288-T1
Valid prediction for snap_scaffold_9-snap.1290-T1
Valid prediction for snap_scaffold_9-snap.1307-T1
Valid prediction for snap_scaffold_9-snap.1318-T1
Valid prediction for GeneMark_model.39066_t
Valid prediction for GlimmerHMM_glimmerT_22765-T1
Valid prediction for GeneMark_model.39097_t
Valid prediction for snap_scaffold_9-snap.1315-T1
Valid prediction for GeneMark_model.39080_t
Valid prediction for GlimmerHMM_glimmerT_22761-T1
Valid prediction for Augustus_model.g15221.t1
Valid prediction for snap_scaffold_9-snap.1300-T1
Valid prediction for snap_scaffold_9-snap.1311-T1
Valid prediction for snap_scaffold_9-snap.1298-T1
Valid prediction for GeneMark_model.39068_t
Valid prediction for GeneMark_model.39082_t
Valid prediction for GeneMark_model.39107_t
Valid prediction for GlimmerHMM_glimmerT_22763-T1
Valid prediction for GlimmerHMM_glimmerT_22756-T1
Valid prediction for GeneMark_model.39099_t
Valid prediction for GlimmerHMM_glimmerT_22750-T1
Valid prediction for snap_scaffold_9-snap.1314-T1
Valid prediction for GeneMark_model.39089_t
Valid prediction for snap_scaffold_9-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_22767-T1
Valid prediction for GeneMark_model.39081_t
Valid prediction for GlimmerHMM_glimmerT_22755-T1
Valid prediction for GeneMark_model.39078_t
Valid prediction for Augustus_model.g15222.t1
Valid prediction for GeneMark_model.39083_t
Valid prediction for Augustus_model.g15227.t1
Valid prediction for snap_scaffold_9-snap.1283-T1
Valid prediction for snap_scaffold_9-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_22758-T1
Valid prediction for GeneMark_model.39085_t
Valid prediction for Augustus_model.g15213.t1
Valid prediction for GeneMark_model.39101_t
Valid prediction for GeneMark_model.39073_t
Valid prediction for snap_scaffold_9-snap.1312-T1
Valid prediction for snap_scaffold_9-snap.1286-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19291, rend_intergenic: 17756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26968, rend_intergenic: 25256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28660, rend_intergenic: 27134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30821, rend_intergenic: 29513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48831, rend_intergenic: 46393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59644, rend_intergenic: 56773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67346, rend_intergenic: 64085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84931, rend_intergenic: 70693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94143, rend_intergenic: 92857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95136, rend_intergenic: 94358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112056, rend_intergenic: 108243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115942, rend_intergenic: 114400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128072, rend_intergenic: 116875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130688, rend_intergenic: 128444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132430, rend_intergenic: 130951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140940
-exon list size: 668


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 19291, rend_intergenic: 17756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26968, rend_intergenic: 25256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28660, rend_intergenic: 27134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30821, rend_intergenic: 29513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48831, rend_intergenic: 46393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59644, rend_intergenic: 56773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67346, rend_intergenic: 64085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84931, rend_intergenic: 70693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94143, rend_intergenic: 92857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95136, rend_intergenic: 94358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112056, rend_intergenic: 108243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115942, rend_intergenic: 114400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128072, rend_intergenic: 116875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130688, rend_intergenic: 128444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132430, rend_intergenic: 130951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15629
-exon list size: 45


building trellis

2.1    
4.3    
6.4    
8.5    
10.6    
12.8    
14.9    
17.0    
19.1    
21.3    
23.4    
25.5    
27.7    
29.8    
31.9    
34.0    
36.2    
38.3    
40.4    
42.6    
44.7    
46.8    
48.9    
51.1    
53.2    
55.3    
57.4    
59.6    
61.7    
63.8    
66.0    
68.1    
70.2    
72.3    
74.5    
76.6    
78.7    
80.9    
83.0    
85.1    
87.2    
89.4    
91.5    
93.6    
95.7    
97.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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