-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_7491643-7637823

-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.59847_t
Valid prediction for snap_scaffold_14-snap.1583-T1
Valid prediction for Augustus_model.g23502.t1
Valid prediction for Augustus_model.g23506.t1
Valid prediction for snap_scaffold_14-snap.1566-T1
Valid prediction for snap_scaffold_14-snap.1580-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for HiQ_model.g23497.t1
Valid prediction for snap_scaffold_14-snap.1584-T1
Couldn't classify 88977, 89161
Sorry, prediction pasa_asmbl_12675.p1 fails validation.
(ATG)	 TC	88236-88466	GT	AGG
(GCG)	 AG	88664-88844	GT	AGG
(GCC)	 AG	88977-89161	GA	GGG
-recovered pasa_asmbl_12675.p1, initial, 88236, 88466
-recovered pasa_asmbl_12675.p1, internal, 88664, 88844
Valid prediction for snap_scaffold_14-snap.1577-T1
Valid prediction for snap_scaffold_14-snap.1565-T1
Valid prediction for Augustus_model.g23504.t1
Valid prediction for snap_scaffold_14-snap.1576-T1
Valid prediction for GlimmerHMM_glimmerT_34938-T1
Valid prediction for CodingQuarry_transcript_15672-T1
Valid prediction for snap_scaffold_14-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_34955-T1
Valid prediction for Augustus_model.g23493.t1
Valid prediction for GeneMark_model.59822_t
Valid prediction for GlimmerHMM_glimmerT_34951-T1
Valid prediction for snap_scaffold_14-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_34948-T1
Valid prediction for GlimmerHMM_glimmerT_34945-T1
Valid prediction for GeneMark_model.59839_t
Valid prediction for GlimmerHMM_glimmerT_34943-T1
Couldn't classify 7165, 7324
Sorry, prediction pasa_asmbl_12149.p1 fails validation.
(TGT)	 TG	7165-7324	GT	AGG
(AGC)	 AG	7458-7528	GT	AGG
(GTG)	 AG	7627-7719	GT	AGG
(GAG)	 AG	7836-7928	GT	AGG
(CAG)	 AG	8200-8373	GT	AGG
(GAG)	 AG	8657-8804	GT	AGG
(GTT)	 AG	8941-9134	AC	AAA
-recovered pasa_asmbl_12149.p1, terminal, 8941, 9134
-recovered pasa_asmbl_12149.p1, internal, 7458, 7528
-recovered pasa_asmbl_12149.p1, internal, 7627, 7719
-recovered pasa_asmbl_12149.p1, internal, 7836, 7928
-recovered pasa_asmbl_12149.p1, internal, 8200, 8373
-recovered pasa_asmbl_12149.p1, internal, 8657, 8804
Valid prediction for GlimmerHMM_glimmerT_34950-T1
Valid prediction for snap_scaffold_14-snap.1581-T1
Valid prediction for snap_scaffold_14-snap.1568-T1
Valid prediction for GlimmerHMM_glimmerT_34946-T1
Valid prediction for GeneMark_model.59825_t
Valid prediction for snap_scaffold_14-snap.1578-T1
Valid prediction for CodingQuarry_transcript_15673-T1
Valid prediction for HiQ_model.g23492.t1
Valid prediction for snap_scaffold_14-snap.1573-T1
Valid prediction for snap_scaffold_14-snap.1574-T1
Valid prediction for pasa_asmbl_12152.p1
Valid prediction for Augustus_model.g23505.t1
Valid prediction for GeneMark_model.59830_t
Valid prediction for GlimmerHMM_glimmerT_34953-T1
Valid prediction for GeneMark_model.59833_t
Valid prediction for GeneMark_model.59836_t
Valid prediction for GeneMark_model.59828_t
Valid prediction for GeneMark_model.59841_t
Valid prediction for GeneMark_model.59818_t
Valid prediction for snap_scaffold_14-snap.1588-T1
Valid prediction for snap_scaffold_14-snap.1561-T1
Valid prediction for GeneMark_model.59831_t
Valid prediction for snap_scaffold_14-snap.1571-T1
Valid prediction for GeneMark_model.59844_t
Valid prediction for GeneMark_model.59834_t
Valid prediction for GeneMark_model.59843_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 GlimmerHMM_glimmerT_34952-T1
Valid prediction for snap_scaffold_14-snap.1567-T1
Valid prediction for CodingQuarry_transcript_15677-T1
Valid prediction for snap_scaffold_14-snap.1575-T1
Valid prediction for GlimmerHMM_glimmerT_34939-T1
Valid prediction for snap_scaffold_14-snap.1587-T1
Valid prediction for GeneMark_model.59826_t
Valid prediction for snap_scaffold_14-snap.1585-T1
Valid prediction for GeneMark_model.59829_t
Valid prediction for GeneMark_model.59820_t
Valid prediction for HiQ_model.g23494.t1
Couldn't classify 70629, 70757
Sorry, prediction pasa_asmbl_13211.p1 fails validation.
(CCA)	 AG	70629-70757	GT	AGG
(GAA)	 AG	71128-71277	GT	AGG
(CTC)	 AG	71535-71745	GT	AGG
(GTG)	 AG	73086-73282	AT	AAA
-recovered pasa_asmbl_13211.p1, terminal, 73086, 73282
-recovered pasa_asmbl_13211.p1, internal, 70629, 70757
-recovered pasa_asmbl_13211.p1, internal, 71128, 71277
-recovered pasa_asmbl_13211.p1, internal, 71535, 71745
Valid prediction for snap_scaffold_14-snap.1582-T1
Valid prediction for GeneMark_model.59819_t
Valid prediction for snap_scaffold_14-snap.1579-T1
Valid prediction for GeneMark_model.59835_t
Valid prediction for GlimmerHMM_glimmerT_34954-T1
Valid prediction for GeneMark_model.59842_t
Valid prediction for GeneMark_model.59823_t
Valid prediction for GlimmerHMM_glimmerT_34956-T1
Valid prediction for GeneMark_model.59846_t
Valid prediction for GeneMark_model.59838_t
Valid prediction for Augustus_model.g23495.t1
Valid prediction for GeneMark_model.59832_t
Valid prediction for GlimmerHMM_glimmerT_34944-T1
Valid prediction for snap_scaffold_14-snap.1564-T1
Valid prediction for GeneMark_model.59824_t
Valid prediction for snap_scaffold_14-snap.1559-T1
Valid prediction for GeneMark_model.59849_t
Valid prediction for CodingQuarry_transcript_15675-T1
Valid prediction for GlimmerHMM_glimmerT_34947-T1
Valid prediction for GeneMark_model.59837_t
Valid prediction for CodingQuarry_transcript_15674-T1
Couldn't classify 92159, 92528
Couldn't classify 92668, 92843
Sorry, prediction pasa_asmbl_13210.p1 fails validation.
(CTC)	 AC	92159-92528	GT	GGG
(GCG)	 AG	92668-92843	GC	CAG
-recovered pasa_asmbl_13210.p1, internal, 92668, 92843
Valid prediction for GeneMark_model.59840_t
Valid prediction for Augustus_model.g23503.t1
Valid prediction for GlimmerHMM_glimmerT_34940-T1
Valid prediction for GlimmerHMM_glimmerT_34942-T1
Valid prediction for snap_scaffold_14-snap.1589-T1
Valid prediction for GeneMark_model.59848_t
Valid prediction for GeneMark_model.59845_t
Valid prediction for snap_scaffold_14-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_34957-T1
Couldn't classify 93654, 93743
Sorry, prediction pasa_asmbl_13804.p1 fails validation.
(GCC)	 GG	93654-93743	GT	AGG
(TTG)	 AG	93884-94135	GT	AGG
(GTG)	 AG	94246-94383	GG	AGG
-recovered pasa_asmbl_13804.p1, terminal, 94246, 94383
-recovered pasa_asmbl_13804.p1, internal, 93884, 94135
Couldn't classify 50424, 50535
Sorry, prediction pasa_asmbl_13214.p1 fails validation.
(GGT)	 CA	50424-50535	GT	AGG
(TGG)	 AG	51209-51357	GT	TGG
(ATC)	 AG	51475-51703	GT	CGG
(AGC)	 AG	51830-52000	GT	CTG
(CTG)	 AG	52119-52267	GT	TTG
(GGA)	 AG	52432-52600	GT	AGG
(CCA)	 AG	52813-52952	GT	AGG
(ATG)	 AG	54156-54197	GA	GAG
-recovered pasa_asmbl_13214.p1, terminal, 54156, 54197
-recovered pasa_asmbl_13214.p1, internal, 51209, 51357
-recovered pasa_asmbl_13214.p1, internal, 51475, 51703
-recovered pasa_asmbl_13214.p1, internal, 51830, 52000
-recovered pasa_asmbl_13214.p1, internal, 52119, 52267
-recovered pasa_asmbl_13214.p1, internal, 52432, 52600
-recovered pasa_asmbl_13214.p1, internal, 52813, 52952
Valid prediction for GlimmerHMM_glimmerT_34949-T1
Valid prediction for snap_scaffold_14-snap.1572-T1
Valid prediction for GlimmerHMM_glimmerT_34941-T1
Valid prediction for CodingQuarry_transcript_15676-T1
Valid prediction for Augustus_model.g23501.t1
Valid prediction for snap_scaffold_14-snap.1569-T1
Valid prediction for pasa_asmbl_13203.p1
Valid prediction for Augustus_model.g23498.t1
Couldn't classify 121530, 122054
Sorry, prediction pasa_asmbl_13208.p1 fails validation.
(ATG)	 GA	121530-122054	GG	TAG
Valid prediction for snap_scaffold_14-snap.1570-T1
Valid prediction for GeneMark_model.59850_t
Couldn't classify 68564, 68636
Couldn't classify 69780, 69848
Sorry, prediction pasa_asmbl_13213.p1 fails validation.
(CCC)	 CC	68564-68636	GT	AGG
(GTG)	 AG	68936-69036	GT	AGG
(TGT)	 AG	69398-69655	GT	AGG
(AGT)	 AG	69780-69848	GC	GGG
-recovered pasa_asmbl_13213.p1, internal, 68936, 69036
-recovered pasa_asmbl_13213.p1, internal, 69398, 69655
-recovered pasa_asmbl_13213.p1, internal, 69780, 69848
Valid prediction for GeneMark_model.59827_t
Valid prediction for snap_scaffold_14-snap.1562-T1
Valid prediction for Augustus_model.g23496.t1
Valid prediction for Augustus_model.g23500.t1
Valid prediction for GeneMark_model.59821_t
Valid prediction for Augustus_model.g23499.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9553, rend_intergenic: 4520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12928, rend_intergenic: 10506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24652, rend_intergenic: 20345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33760, rend_intergenic: 30259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47082, rend_intergenic: 42563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70130, rend_intergenic: 55139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83197, rend_intergenic: 73650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98277, rend_intergenic: 91687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110626, rend_intergenic: 102197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119560, rend_intergenic: 116783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120321, rend_intergenic: 119973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130439, rend_intergenic: 120559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146181
-exon list size: 589


building trellis

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-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 9553, rend_intergenic: 4520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12928, rend_intergenic: 10506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24652, rend_intergenic: 20345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33760, rend_intergenic: 30259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47082, rend_intergenic: 42563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70130, rend_intergenic: 55139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83197, rend_intergenic: 73650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98277, rend_intergenic: 91687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110626, rend_intergenic: 102197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119560, rend_intergenic: 116783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120321, rend_intergenic: 119973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130439, rend_intergenic: 120559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 132564 - 146181
-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