-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_16642271-16850005

-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 GlimmerHMM_glimmerT_19167-T1
Valid prediction for Augustus_model.g12961.t1
Valid prediction for GlimmerHMM_glimmerT_19178-T1
Valid prediction for GeneMark_model.32373_t
Valid prediction for snap_scaffold_7-snap.3199-T1
Valid prediction for GeneMark_model.32380_t
Valid prediction for GeneMark_model.32361_t
Valid prediction for snap_scaffold_7-snap.3208-T1
Valid prediction for snap_scaffold_7-snap.3211-T1
Valid prediction for HiQ_model.g12965.t1
Valid prediction for GeneMark_model.32389_t
Valid prediction for GeneMark_model.32354_t
Couldn't classify 171420, 171469
Sorry, prediction pasa_asmbl_51355.p1 fails validation.
(ATG)	 AA	168337-168423	GT	AGG
(GGA)	 AG	168836-168894	GT	AAG
(ACT)	 AG	169065-169125	GC	AGG
(AGA)	 AG	169517-169573	GT	TGG
(GAG)	 AG	169740-169837	GT	AAG
(GCT)	 AG	170415-170511	GT	AGG
(CAT)	 AG	170601-170669	GT	AGG
(AGT)	 AG	171092-171242	GT	CGG
(GGA)	 AG	171420-171469	CT	TGC
-recovered pasa_asmbl_51355.p1, initial, 168337, 168423
-recovered pasa_asmbl_51355.p1, internal, 168836, 168894
-recovered pasa_asmbl_51355.p1, internal, 169065, 169125
-recovered pasa_asmbl_51355.p1, internal, 169517, 169573
-recovered pasa_asmbl_51355.p1, internal, 169740, 169837
-recovered pasa_asmbl_51355.p1, internal, 170415, 170511
-recovered pasa_asmbl_51355.p1, internal, 170601, 170669
-recovered pasa_asmbl_51355.p1, internal, 171092, 171242
Valid prediction for snap_scaffold_7-snap.3217-T1
Valid prediction for GeneMark_model.32357_t
Valid prediction for GeneMark_model.32385_t
Valid prediction for snap_scaffold_7-snap.3191-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.32388_t
Valid prediction for GeneMark_model.32378_t
Valid prediction for snap_scaffold_7-snap.3205-T1
Valid prediction for GeneMark_model.32394_t
Valid prediction for GeneMark_model.32365_t
Valid prediction for Augustus_model.g12967.t1
Valid prediction for GeneMark_model.32377_t
Valid prediction for GlimmerHMM_glimmerT_19166-T1
Valid prediction for snap_scaffold_7-snap.3207-T1
Valid prediction for GeneMark_model.32371_t
Valid prediction for snap_scaffold_7-snap.3182-T1
Valid prediction for snap_scaffold_7-snap.3204-T1
Valid prediction for GlimmerHMM_glimmerT_19163-T1
Valid prediction for Augustus_model.g12960.t1
Valid prediction for snap_scaffold_7-snap.3202-T1
Valid prediction for GlimmerHMM_glimmerT_19176-T1
Valid prediction for snap_scaffold_7-snap.3192-T1
Valid prediction for snap_scaffold_7-snap.3183-T1
Valid prediction for GeneMark_model.32375_t
Valid prediction for GlimmerHMM_glimmerT_19182-T1
Valid prediction for Augustus_model.g12959.t1
Valid prediction for CodingQuarry_transcript_57597-T1
Valid prediction for snap_scaffold_7-snap.3213-T1
Valid prediction for snap_scaffold_7-snap.3215-T1
Valid prediction for GeneMark_model.32356_t
Valid prediction for GlimmerHMM_glimmerT_19169-T1
Valid prediction for snap_scaffold_7-snap.3214-T1
Valid prediction for CodingQuarry_transcript_57592-T1
Valid prediction for GeneMark_model.32396_t
Valid prediction for GlimmerHMM_glimmerT_19168-T1
Valid prediction for GeneMark_model.32392_t
Valid prediction for snap_scaffold_7-snap.3186-T1
Valid prediction for CodingQuarry_transcript_57596-T1
Valid prediction for snap_scaffold_7-snap.3209-T1
Valid prediction for snap_scaffold_7-snap.3181-T1
Valid prediction for snap_scaffold_7-snap.3206-T1
Valid prediction for GeneMark_model.32369_t
Valid prediction for snap_scaffold_7-snap.3197-T1
Valid prediction for pasa_asmbl_51357.p1
Valid prediction for GeneMark_model.32359_t
Valid prediction for GeneMark_model.32399_t
Valid prediction for GeneMark_model.32368_t
Valid prediction for Augustus_model.g12958.t1
Valid prediction for GeneMark_model.32400_t
Valid prediction for GlimmerHMM_glimmerT_19180-T1
Valid prediction for snap_scaffold_7-snap.3188-T1
Valid prediction for GeneMark_model.32360_t
Valid prediction for GlimmerHMM_glimmerT_19164-T1
Valid prediction for snap_scaffold_7-snap.3185-T1
Valid prediction for GlimmerHMM_glimmerT_19161-T1
Valid prediction for GlimmerHMM_glimmerT_19171-T1
Valid prediction for snap_scaffold_7-snap.3187-T1
Valid prediction for GeneMark_model.32398_t
Valid prediction for GeneMark_model.32383_t

-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_7-snap.3193-T1
Valid prediction for Augustus_model.g12966.t1
Valid prediction for snap_scaffold_7-snap.3203-T1
Valid prediction for HiQ_model.g12962.t1
Valid prediction for snap_scaffold_7-snap.3218-T1
Valid prediction for CodingQuarry_transcript_57595-T1
Valid prediction for GeneMark_model.32384_t
Valid prediction for GeneMark_model.32386_t
Valid prediction for GeneMark_model.32370_t
Valid prediction for GlimmerHMM_glimmerT_19165-T1
Valid prediction for HiQ_model.g12963.t1
Valid prediction for GlimmerHMM_glimmerT_19181-T1
Valid prediction for GlimmerHMM_glimmerT_19160-T1
Valid prediction for snap_scaffold_7-snap.3184-T1
Valid prediction for GeneMark_model.32366_t
Couldn't classify 32660, 32770
Sorry, prediction pasa_asmbl_50233.p1 fails validation.
(ACC)	 AG	32660-32770	GT	GGG
(AAA)	 AG	33037-33555	CC	AAC
-recovered pasa_asmbl_50233.p1, terminal, 33037, 33555
-recovered pasa_asmbl_50233.p1, internal, 32660, 32770
Valid prediction for GeneMark_model.32393_t
Valid prediction for GlimmerHMM_glimmerT_19174-T1
Valid prediction for GlimmerHMM_glimmerT_19179-T1
Valid prediction for pasa_asmbl_50231.p1
Valid prediction for GlimmerHMM_glimmerT_19162-T1
Valid prediction for pasa_asmbl_50237.p1
Valid prediction for GeneMark_model.32390_t
Valid prediction for GeneMark_model.32395_t
Valid prediction for GlimmerHMM_glimmerT_19173-T1
Valid prediction for GeneMark_model.32364_t
Valid prediction for GeneMark_model.32391_t
Valid prediction for GlimmerHMM_glimmerT_19170-T1
Valid prediction for snap_scaffold_7-snap.3194-T1
Valid prediction for GeneMark_model.32397_t
Valid prediction for GeneMark_model.32372_t
Valid prediction for GeneMark_model.32353_t
Valid prediction for GeneMark_model.32362_t
Valid prediction for GeneMark_model.32379_t
Valid prediction for snap_scaffold_7-snap.3210-T1
Valid prediction for snap_scaffold_7-snap.3180-T1
Valid prediction for GeneMark_model.32376_t
Valid prediction for snap_scaffold_7-snap.3216-T1
Valid prediction for snap_scaffold_7-snap.3195-T1
Valid prediction for GeneMark_model.32363_t
Valid prediction for snap_scaffold_7-snap.3189-T1
Valid prediction for snap_scaffold_7-snap.3198-T1
Valid prediction for snap_scaffold_7-snap.3190-T1
Valid prediction for GeneMark_model.32382_t
Valid prediction for GlimmerHMM_glimmerT_19177-T1
Valid prediction for CodingQuarry_transcript_57593-T1
Valid prediction for GeneMark_model.32387_t
Valid prediction for GeneMark_model.32367_t
Valid prediction for snap_scaffold_7-snap.3196-T1
Valid prediction for HiQ_model.g12964.t1
Valid prediction for GlimmerHMM_glimmerT_19175-T1
Valid prediction for GeneMark_model.32355_t
Valid prediction for snap_scaffold_7-snap.3212-T1
Valid prediction for GlimmerHMM_glimmerT_19172-T1
Valid prediction for snap_scaffold_7-snap.3201-T1
Valid prediction for GeneMark_model.32374_t
Valid prediction for GeneMark_model.32381_t
Valid prediction for snap_scaffold_7-snap.3200-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31994, rend_intergenic: 6833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42417, rend_intergenic: 32742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54212, rend_intergenic: 43419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75901, rend_intergenic: 65315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85825, rend_intergenic: 78938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97163, rend_intergenic: 94765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105850, rend_intergenic: 97247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154502, rend_intergenic: 144675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177502, rend_intergenic: 174948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180488, rend_intergenic: 178378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207735
-exon list size: 639


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 31994, rend_intergenic: 6833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42417, rend_intergenic: 32742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54212, rend_intergenic: 43419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75901, rend_intergenic: 65315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85825, rend_intergenic: 78938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97163, rend_intergenic: 94765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105850, rend_intergenic: 97247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154502, rend_intergenic: 144675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177502, rend_intergenic: 174948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180488, rend_intergenic: 178378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14193
-exon list size: 49


building trellis

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66.7    
68.6    
70.6    
72.5    
74.5    
76.5    
78.4    
80.4    
82.4    
84.3    
86.3    
88.2    
90.2    
92.2    
94.1    
96.1    
98.0    
-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

-building DP trellis

-building trellis in range 1 - 11047
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-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

-building DP trellis

-building trellis in range 1 - 10985
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-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