-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_13817260-13988975

-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.45078_t
Valid prediction for Augustus_model.g17668.t1
Valid prediction for GeneMark_model.45104_t
Valid prediction for snap_scaffold_10-snap.2781-T1
Valid prediction for snap_scaffold_10-snap.2765-T1
Valid prediction for GeneMark_model.45075_t
Valid prediction for CodingQuarry_transcript_5631-T1
Valid prediction for GlimmerHMM_glimmerT_26314-T1
Valid prediction for CodingQuarry_transcript_5634-T1
Valid prediction for GeneMark_model.45111_t
Valid prediction for snap_scaffold_10-snap.2769-T1
Valid prediction for GlimmerHMM_glimmerT_26305-T1
Valid prediction for snap_scaffold_10-snap.2754-T1
Valid prediction for GlimmerHMM_glimmerT_26307-T1
Valid prediction for GeneMark_model.45089_t
Valid prediction for GeneMark_model.45113_t
Valid prediction for GeneMark_model.45091_t
Valid prediction for snap_scaffold_10-snap.2768-T1
Valid prediction for snap_scaffold_10-snap.2752-T1
Valid prediction for GeneMark_model.45086_t
Valid prediction for GlimmerHMM_glimmerT_26306-T1
Valid prediction for snap_scaffold_10-snap.2756-T1
Valid prediction for GeneMark_model.45073_t
Valid prediction for pasa_asmbl_4898.p1
Valid prediction for GeneMark_model.45099_t
Valid prediction for GeneMark_model.45109_t
Valid prediction for GeneMark_model.45082_t
Valid prediction for GeneMark_model.45105_t
Valid prediction for snap_scaffold_10-snap.2776-T1
Valid prediction for GlimmerHMM_glimmerT_26310-T1
Valid prediction for GlimmerHMM_glimmerT_26318-T1
Valid prediction for GeneMark_model.45088_t
Valid prediction for Augustus_model.g17670.t1
Valid prediction for GeneMark_model.45102_t
Valid prediction for snap_scaffold_10-snap.2763-T1
Valid prediction for HiQ_model.g17666.t1
Valid prediction for snap_scaffold_10-snap.2760-T1
Valid prediction for snap_scaffold_10-snap.2767-T1
Valid prediction for GlimmerHMM_glimmerT_26316-T1
Valid prediction for snap_scaffold_10-snap.2758-T1
Valid prediction for GlimmerHMM_glimmerT_26313-T1
Valid prediction for Augustus_model.g17656.t1
Valid prediction for GeneMark_model.45097_t
Valid prediction for Augustus_model.g17661.t1
Valid prediction for GeneMark_model.45081_t
Couldn't classify 166171, 166264
Couldn't classify 167717, 167759
Sorry, prediction pasa_asmbl_5158.p1 fails validation.
(GTC)	 TA	166171-166264	GT	AGG
(AGT)	 AG	167166-167199	GT	AGG
(GTG)	 AG	167500-167631	GT	AGG
(CAA)	 AG	167717-167759	GC	GAG
-recovered pasa_asmbl_5158.p1, terminal, 167166, 167199
-recovered pasa_asmbl_5158.p1, internal, 167166, 167199
-recovered pasa_asmbl_5158.p1, internal, 167500, 167631
-recovered pasa_asmbl_5158.p1, internal, 167717, 167759
Valid prediction for CodingQuarry_transcript_5633-T1
Valid prediction for pasa_asmbl_4908.p1
Valid prediction for snap_scaffold_10-snap.2771-T1
Valid prediction for snap_scaffold_10-snap.2751-T1
Valid prediction for GlimmerHMM_glimmerT_26297-T1
Valid prediction for GlimmerHMM_glimmerT_26301-T1
Valid prediction for HiQ_model.g17659.t1
Valid prediction for GeneMark_model.45083_t
Valid prediction for GlimmerHMM_glimmerT_26319-T1
Valid prediction for GeneMark_model.45072_t
Valid prediction for snap_scaffold_10-snap.2777-T1
Valid prediction for GlimmerHMM_glimmerT_26299-T1
Valid prediction for GeneMark_model.45085_t
Valid prediction for GeneMark_model.45093_t
Valid prediction for pasa_asmbl_4903.p1
Valid prediction for pasa_asmbl_4904.p2
Valid prediction for GlimmerHMM_glimmerT_26320-T1
Valid prediction for snap_scaffold_10-snap.2773-T1
Valid prediction for HiQ_model.g17662.t1
Valid prediction for GlimmerHMM_glimmerT_26298-T1
Valid prediction for CodingQuarry_transcript_5632-T1
Couldn't classify 88030, 88122
Sorry, prediction pasa_asmbl_4902.p1 fails validation.
(GAC)	 GT	88030-88122	GT	AGG
(ATG)	 AG	88255-88367	GT	CAG
(CCC)	 AG	88633-88738	GT	AGG
(CAA)	 AG	89023-89109	GT	CAG
(GAG)	 AG	89842-89972	GT	AGG
(ACA)	 AG	90385-90479	GT	AGG
(ACC)	 AG	90577-90622	GT	AGG
(CAG)	 AG	91006-91057	GT	CTG
(CTC)	 AG	91229-91301	GT	AGG
(TGT)	 AG	91543-91640	GT	AGG
(GGC)	 AG	91994-92105	GT	AGG
(ATG)	 AG	92214-92365	GT	AGG
(AGC)	 AG	92679-92831	GT	AGG
(CTG)	 AG	95097-95303	GT	ACG
(ATT)	 AG	95588-95677	GT	GGG
(GGC)	 AG	96664-96746	GT	GGG
(CGT)	 AG	97263-97469	GT	AGG
(CTT)	 AG	98647-98710	GT	AGG
(AGA)	 AG	99259-99468	TT	GAT
-recovered pasa_asmbl_4902.p1, initial, 88255, 88367
add_exon() Sorry, pasa_asmbl_4902.p1 92214-92365-initial-1 is invalid.
-recovered pasa_asmbl_4902.p1, initial, 92214, 92365
-recovered pasa_asmbl_4902.p1, terminal, 99259, 99468
-recovered pasa_asmbl_4902.p1, internal, 88255, 88367
-recovered pasa_asmbl_4902.p1, internal, 88633, 88738
-recovered pasa_asmbl_4902.p1, internal, 89023, 89109
-recovered pasa_asmbl_4902.p1, internal, 89842, 89972
-recovered pasa_asmbl_4902.p1, internal, 90385, 90479
-recovered pasa_asmbl_4902.p1, internal, 90577, 90622
-recovered pasa_asmbl_4902.p1, internal, 91006, 91057
-recovered pasa_asmbl_4902.p1, internal, 91229, 91301
-recovered pasa_asmbl_4902.p1, internal, 91543, 91640
-recovered pasa_asmbl_4902.p1, internal, 91994, 92105
-recovered pasa_asmbl_4902.p1, internal, 92214, 92365
-recovered pasa_asmbl_4902.p1, internal, 92679, 92831
-recovered pasa_asmbl_4902.p1, internal, 95097, 95303
-recovered pasa_asmbl_4902.p1, internal, 95588, 95677
-recovered pasa_asmbl_4902.p1, internal, 96664, 96746
-recovered pasa_asmbl_4902.p1, internal, 97263, 97469
-recovered pasa_asmbl_4902.p1, internal, 98647, 98710
Valid prediction for snap_scaffold_10-snap.2779-T1
Valid prediction for GlimmerHMM_glimmerT_26294-T1
Valid prediction for GeneMark_model.45115_t
Valid prediction for GeneMark_model.45107_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_10-snap.2759-T1
Valid prediction for GeneMark_model.45112_t
Valid prediction for CodingQuarry_transcript_5635-T1
Valid prediction for GeneMark_model.45076_t
Valid prediction for GeneMark_model.45098_t
Valid prediction for GeneMark_model.45108_t
Valid prediction for snap_scaffold_10-snap.2761-T1
Valid prediction for GlimmerHMM_glimmerT_26311-T1
Valid prediction for GeneMark_model.45096_t
Valid prediction for snap_scaffold_10-snap.2778-T1
Valid prediction for Augustus_model.g17657.t1
Valid prediction for GeneMark_model.45110_t
Valid prediction for GlimmerHMM_glimmerT_26300-T1
Valid prediction for Augustus_model.g17669.t1
Valid prediction for snap_scaffold_10-snap.2783-T1
Valid prediction for Augustus_model.g17658.t1
Valid prediction for GlimmerHMM_glimmerT_26295-T1
Valid prediction for snap_scaffold_10-snap.2774-T1
Valid prediction for GeneMark_model.45074_t
Valid prediction for GeneMark_model.45100_t
Valid prediction for pasa_asmbl_3843.p1
Valid prediction for GlimmerHMM_glimmerT_26312-T1
Valid prediction for GeneMark_model.45114_t
Valid prediction for snap_scaffold_10-snap.2770-T1
Valid prediction for snap_scaffold_10-snap.2753-T1
Valid prediction for GeneMark_model.45090_t
Valid prediction for GlimmerHMM_glimmerT_26309-T1
Valid prediction for Augustus_model.g17660.t1
Valid prediction for GeneMark_model.45094_t
Valid prediction for GeneMark_model.45080_t
Valid prediction for GeneMark_model.45116_t
Valid prediction for GlimmerHMM_glimmerT_26302-T1
Valid prediction for GeneMark_model.45092_t
Valid prediction for snap_scaffold_10-snap.2762-T1
Valid prediction for snap_scaffold_10-snap.2764-T1
Valid prediction for GeneMark_model.45087_t
Valid prediction for GeneMark_model.45106_t
Valid prediction for snap_scaffold_10-snap.2775-T1
Valid prediction for GlimmerHMM_glimmerT_26304-T1
Valid prediction for CodingQuarry_transcript_5636-T1
Couldn't classify 95201, 95344
Sorry, prediction pasa_asmbl_3840.p1 fails validation.
(CTT)	 GG	95201-95344	GT	CCG
(GCC)	 AG	95918-96046	GT	AGG
(GTG)	 AG	96567-96740	GT	ATG
(AGC)	 AG	96958-97017	GT	AGG
(GTA)	 AG	97124-98524	GT	CGG
(CAA)	 AG	98757-98881	GT	AGG
(TTA)	 AG	98995-99077	GT	CGG
(AGG)	 AG	99203-99312	GT	AGG
(ATC)	 AG	99473-99569	GT	AGG
(AGA)	 AG	99739-99906	GT	CGG
(AAA)	 AG	100266-100354	TC	GAT
-recovered pasa_asmbl_3840.p1, terminal, 100266, 100354
-recovered pasa_asmbl_3840.p1, internal, 95918, 96046
-recovered pasa_asmbl_3840.p1, internal, 96567, 96740
-recovered pasa_asmbl_3840.p1, internal, 96958, 97017
-recovered pasa_asmbl_3840.p1, internal, 97124, 98524
-recovered pasa_asmbl_3840.p1, internal, 98757, 98881
-recovered pasa_asmbl_3840.p1, internal, 98995, 99077
-recovered pasa_asmbl_3840.p1, internal, 99203, 99312
-recovered pasa_asmbl_3840.p1, internal, 99473, 99569
-recovered pasa_asmbl_3840.p1, internal, 99739, 99906
Valid prediction for GlimmerHMM_glimmerT_26308-T1
Valid prediction for snap_scaffold_10-snap.2772-T1
Valid prediction for GlimmerHMM_glimmerT_26296-T1
Valid prediction for GlimmerHMM_glimmerT_26303-T1
Valid prediction for GeneMark_model.45103_t
Valid prediction for snap_scaffold_10-snap.2755-T1
Valid prediction for GeneMark_model.45077_t
Valid prediction for GlimmerHMM_glimmerT_26317-T1
Valid prediction for HiQ_model.g17667.t1
Valid prediction for snap_scaffold_10-snap.2780-T1
Valid prediction for GeneMark_model.45079_t
Valid prediction for snap_scaffold_10-snap.2750-T1
Valid prediction for snap_scaffold_10-snap.2782-T1
Valid prediction for Augustus_model.g17664.t1
Valid prediction for GeneMark_model.45101_t
Valid prediction for Augustus_model.g17663.t1
Valid prediction for GlimmerHMM_glimmerT_26315-T1
Valid prediction for snap_scaffold_10-snap.2766-T1
Valid prediction for snap_scaffold_10-snap.2757-T1
Valid prediction for Augustus_model.g17665.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10606, rend_intergenic: 6567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33519, rend_intergenic: 29600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37011, rend_intergenic: 35744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38292, rend_intergenic: 37506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81284, rend_intergenic: 79969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97965, rend_intergenic: 88948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120629, rend_intergenic: 113434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121233, rend_intergenic: 121041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124396, rend_intergenic: 123843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147417, rend_intergenic: 145751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150186, rend_intergenic: 149762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170237, rend_intergenic: 152933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171716
-exon list size: 623


building trellis

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90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 10606, rend_intergenic: 6567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33519, rend_intergenic: 29600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37011, rend_intergenic: 35744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38292, rend_intergenic: 37506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81284, rend_intergenic: 79969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97965, rend_intergenic: 88948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120629, rend_intergenic: 113434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121233, rend_intergenic: 121041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124396, rend_intergenic: 123843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147417, rend_intergenic: 145751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150186, rend_intergenic: 149762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170237, rend_intergenic: 152933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 29629
-exon list size: 51


building trellis

1.9    
3.8    
5.7    
7.5    
9.4    
11.3    
13.2    
15.1    
17.0    
18.9    
20.8    
22.6    
24.5    
26.4    
28.3    
30.2    
32.1    
34.0    
35.8    
37.7    
39.6    
41.5    
43.4    
45.3    
47.2    
49.1    
50.9    
52.8    
54.7    
56.6    
58.5    
60.4    
62.3    
64.2    
66.0    
67.9    
69.8    
71.7    
73.6    
75.5    
77.4    
79.2    
81.1    
83.0    
84.9    
86.8    
88.7    
90.6    
92.5    
94.3    
96.2    
98.1    
-found 4 predictions from path traversal
GOT 5prime partial gene.

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