-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_20225391-20493986

-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 Augustus_model.g1931.t1
Valid prediction for GlimmerHMM_glimmerT_2722-T1
Valid prediction for GlimmerHMM_glimmerT_2719-T1
Valid prediction for snap_scaffold_1-snap.3759-T1
Valid prediction for GlimmerHMM_glimmerT_2729-T1
Valid prediction for snap_scaffold_1-snap.3790-T1
Valid prediction for snap_scaffold_1-snap.3751-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3798-T1
Valid prediction for snap_scaffold_1-snap.3783-T1
Couldn't classify 253188, 253250
Couldn't classify 254415, 254599
Sorry, prediction pasa_asmbl_2696.p2 fails validation.
(AAG)	 AG	253188-253250	GT	TAG
(GTG)	 AG	253725-253878	GT	CGG
(CTC)	 AG	254415-254599	AG	ACA
-recovered pasa_asmbl_2696.p2, internal, 253188, 253250
-recovered pasa_asmbl_2696.p2, internal, 253725, 253878
Valid prediction for GlimmerHMM_glimmerT_2730-T1
Valid prediction for CodingQuarry_transcript_3025-T1
Valid prediction for snap_scaffold_1-snap.3765-T1
Valid prediction for snap_scaffold_1-snap.3803-T1
Valid prediction for Augustus_model.g1943.t1
Couldn't classify 160230, 160281
Couldn't classify 162758, 163050
Sorry, prediction pasa_asmbl_2627.p1 fails validation.
(TCA)	 CG	160230-160281	GT	TGG
(CGT)	 AG	161295-161410	GT	AGG
(CTC)	 AG	162439-162580	GT	AGG
(ACA)	 AG	162758-163050	GG	TTG
-recovered pasa_asmbl_2627.p1, internal, 161295, 161410
-recovered pasa_asmbl_2627.p1, internal, 162439, 162580
Valid prediction for CodingQuarry_transcript_3030-T1
Valid prediction for snap_scaffold_1-snap.3782-T1
Valid prediction for GlimmerHMM_glimmerT_2727-T1
Valid prediction for GlimmerHMM_glimmerT_2717-T1
Valid prediction for snap_scaffold_1-snap.3776-T1
Valid prediction for Augustus_model.g1934.t1
Valid prediction for GlimmerHMM_glimmerT_2716-T1
Couldn't classify 120160, 120443
Sorry, prediction pasa_asmbl_2625.p1 fails validation.
(ATG)	 GA	113504-113552	GT	AGG
(TAG)	 AG	114332-114367	GT	AGG
(GCA)	 AG	115313-115432	GT	GGG
(GTA)	 AG	117190-117329	GT	AGG
(ATC)	 AG	117841-117940	GT	AGG
(TTG)	 AG	118049-118087	GT	AGG
(CTG)	 AG	118228-118273	GT	AGG
(GGA)	 AG	118482-118659	GT	AGG
(TTT)	 AG	118912-119025	GT	AGG
(GAT)	 AG	119362-119530	GT	AAG
(TTC)	 AG	119738-120010	GT	AGG
(CTG)	 AG	120160-120443	GC	GGG
-recovered pasa_asmbl_2625.p1, initial, 113504, 113552
-recovered pasa_asmbl_2625.p1, internal, 114332, 114367
-recovered pasa_asmbl_2625.p1, internal, 115313, 115432
-recovered pasa_asmbl_2625.p1, internal, 117190, 117329
-recovered pasa_asmbl_2625.p1, internal, 117841, 117940
-recovered pasa_asmbl_2625.p1, internal, 118049, 118087
-recovered pasa_asmbl_2625.p1, internal, 118228, 118273
-recovered pasa_asmbl_2625.p1, internal, 118482, 118659
-recovered pasa_asmbl_2625.p1, internal, 118912, 119025
-recovered pasa_asmbl_2625.p1, internal, 119362, 119530
-recovered pasa_asmbl_2625.p1, internal, 119738, 120010
-recovered pasa_asmbl_2625.p1, internal, 120160, 120443
Valid prediction for Augustus_model.g1933.t1
Valid prediction for CodingQuarry_transcript_3027-T1
Valid prediction for GlimmerHMM_glimmerT_2715-T1
Valid prediction for CodingQuarry_transcript_3031-T1
Valid prediction for GlimmerHMM_glimmerT_2734-T1
Valid prediction for GlimmerHMM_glimmerT_2737-T1
Valid prediction for Augustus_model.g1938.t1
Valid prediction for snap_scaffold_1-snap.3796-T1
Valid prediction for snap_scaffold_1-snap.3785-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2731-T1
Valid prediction for snap_scaffold_1-snap.3768-T1
Valid prediction for Augustus_model.g1939.t1
Valid prediction for snap_scaffold_1-snap.3766-T1
Valid prediction for snap_scaffold_1-snap.3792-T1
Valid prediction for GlimmerHMM_glimmerT_2723-T1
Valid prediction for snap_scaffold_1-snap.3753-T1
Valid prediction for HiQ_model.g1935.t1
Valid prediction for CodingQuarry_transcript_3029-T1
Couldn't classify 249082, 249142
Couldn't classify 251927, 252070
Sorry, prediction pasa_asmbl_2640.p1 fails validation.
(AGC)	 TC	249082-249142	GT	AGG
(GCC)	 AG	250886-251048	GT	AGG
(GAA)	 AG	251524-251641	GT	AGG
(TCA)	 AG	251927-252070	TT	GCT
add_exon() Sorry, pasa_asmbl_2640.p1 250886-251048-terminal-3 is invalid.
-recovered pasa_asmbl_2640.p1, terminal, 250886, 251048
-recovered pasa_asmbl_2640.p1, internal, 250886, 251048
-recovered pasa_asmbl_2640.p1, internal, 251524, 251641
Valid prediction for GlimmerHMM_glimmerT_2736-T1
Valid prediction for snap_scaffold_1-snap.3789-T1
Valid prediction for Augustus_model.g1944.t1
Valid prediction for Augustus_model.g1942.t1
Valid prediction for snap_scaffold_1-snap.3773-T1
Valid prediction for snap_scaffold_1-snap.3774-T1
Valid prediction for CodingQuarry_transcript_3028-T1
Valid prediction for Augustus_model.g1932.t1
Valid prediction for snap_scaffold_1-snap.3758-T1
Valid prediction for snap_scaffold_1-snap.3775-T1
Valid prediction for GlimmerHMM_glimmerT_2721-T1
Valid prediction for snap_scaffold_1-snap.3772-T1
Couldn't classify 122889, 123043
Sorry, prediction pasa_asmbl_2621.p1 fails validation.
(ATG)	 GA	120096-120774	GT	AGG
(GAG)	 AG	121672-121776	GT	TGG
(CAG)	 AG	122889-123043	AG	GGA
-recovered pasa_asmbl_2621.p1, initial, 120096, 120774
-recovered pasa_asmbl_2621.p1, internal, 121672, 121776
Valid prediction for pasa_asmbl_2622.p1
Valid prediction for GlimmerHMM_glimmerT_2735-T1
Valid prediction for Augustus_model.g1930.t1
Valid prediction for snap_scaffold_1-snap.3770-T1
Valid prediction for GlimmerHMM_glimmerT_2738-T1
Valid prediction for snap_scaffold_1-snap.3781-T1
Valid prediction for snap_scaffold_1-snap.3761-T1
Couldn't classify 230987, 231091
Sorry, prediction pasa_asmbl_2635.p1 fails validation.
(GCG)	 CG	230987-231091	GT	ACG
(TAC)	 AG	231438-231611	GT	GGG
(GCG)	 AG	232032-232175	GT	AGG
(ACG)	 AG	232582-232734	GT	AGG
(GTG)	 AG	233351-233464	CA	AAC
-recovered pasa_asmbl_2635.p1, terminal, 233351, 233464
-recovered pasa_asmbl_2635.p1, internal, 231438, 231611
-recovered pasa_asmbl_2635.p1, internal, 232032, 232175
-recovered pasa_asmbl_2635.p1, internal, 232582, 232734
Valid prediction for snap_scaffold_1-snap.3779-T1
Valid prediction for GlimmerHMM_glimmerT_2726-T1
Valid prediction for snap_scaffold_1-snap.3777-T1
Valid prediction for pasa_asmbl_2628.p1
Valid prediction for Augustus_model.g1941.t1
Valid prediction for Augustus_model.g1937.t1
Valid prediction for snap_scaffold_1-snap.3755-T1
Valid prediction for GlimmerHMM_glimmerT_2728-T1
Valid prediction for Augustus_model.g1936.t1
Couldn't classify 141408, 141710
Sorry, prediction pasa_asmbl_2766.p1 fails validation.
(CCC)	 AG	141408-141710	CC	CTC
Valid prediction for snap_scaffold_1-snap.3778-T1
Valid prediction for snap_scaffold_1-snap.3771-T1
Valid prediction for snap_scaffold_1-snap.3754-T1
Valid prediction for Augustus_model.g1940.t1
Valid prediction for snap_scaffold_1-snap.3799-T1
Valid prediction for snap_scaffold_1-snap.3793-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_1-snap.3794-T1
Valid prediction for snap_scaffold_1-snap.3764-T1
Valid prediction for GlimmerHMM_glimmerT_2732-T1
Valid prediction for snap_scaffold_1-snap.3780-T1
Valid prediction for snap_scaffold_1-snap.3791-T1
Valid prediction for snap_scaffold_1-snap.3784-T1
Valid prediction for snap_scaffold_1-snap.3795-T1
Valid prediction for snap_scaffold_1-snap.3763-T1
Valid prediction for snap_scaffold_1-snap.3749-T1
Valid prediction for snap_scaffold_1-snap.3797-T1
Valid prediction for snap_scaffold_1-snap.3760-T1
Valid prediction for snap_scaffold_1-snap.3756-T1
Valid prediction for GlimmerHMM_glimmerT_2720-T1
Valid prediction for snap_scaffold_1-snap.3769-T1
Valid prediction for snap_scaffold_1-snap.3767-T1
Valid prediction for snap_scaffold_1-snap.3800-T1
Valid prediction for GlimmerHMM_glimmerT_2724-T1
Valid prediction for GlimmerHMM_glimmerT_2718-T1
Valid prediction for snap_scaffold_1-snap.3750-T1
Couldn't classify 166674, 166991
Sorry, prediction pasa_asmbl_2611.p1 fails validation.
(ATG)	 GT	166674-166991	AC	CGA
Valid prediction for GlimmerHMM_glimmerT_2725-T1
Valid prediction for snap_scaffold_1-snap.3762-T1
Valid prediction for snap_scaffold_1-snap.3757-T1
Valid prediction for GlimmerHMM_glimmerT_2739-T1
Valid prediction for CodingQuarry_transcript_3032-T1
Valid prediction for snap_scaffold_1-snap.3801-T1
Valid prediction for Augustus_model.g1945.t1
Valid prediction for snap_scaffold_1-snap.3752-T1
Valid prediction for GlimmerHMM_glimmerT_2733-T1
Valid prediction for snap_scaffold_1-snap.3786-T1
Valid prediction for snap_scaffold_1-snap.3787-T1
Valid prediction for snap_scaffold_1-snap.3788-T1
Valid prediction for snap_scaffold_1-snap.3802-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 92719, rend_intergenic: 92716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22749, rend_intergenic: 18925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39944, rend_intergenic: 32047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47673, rend_intergenic: 41898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58444, rend_intergenic: 57186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71595, rend_intergenic: 59841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101864, rend_intergenic: 94006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118024, rend_intergenic: 117113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165534, rend_intergenic: 162394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193567, rend_intergenic: 185946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204089, rend_intergenic: 201009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209538, rend_intergenic: 205323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228209, rend_intergenic: 216211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232785, rend_intergenic: 229094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254605, rend_intergenic: 247653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265692, rend_intergenic: 259401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 268596
-exon list size: 469


building trellis

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32.3    
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33.3    
33.5    
33.8    
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34.6    
34.8    
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35.7    
35.9    
36.1    
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37.8    
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99.6    
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-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 92719, rend_intergenic: 92716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22749, rend_intergenic: 18925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39944, rend_intergenic: 32047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47673, rend_intergenic: 41898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58444, rend_intergenic: 57186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71595, rend_intergenic: 59841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101864, rend_intergenic: 94006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118024, rend_intergenic: 117113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165534, rend_intergenic: 162394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193567, rend_intergenic: 185946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204089, rend_intergenic: 201009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209538, rend_intergenic: 205323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228209, rend_intergenic: 216211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232785, rend_intergenic: 229094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254605, rend_intergenic: 247653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265692, rend_intergenic: 259401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 12842
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 2 predictions from path traversal

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