-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_9696017-9848378

-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_12-snap.1866-T1
Valid prediction for GeneMark_model.52715_t
Valid prediction for Augustus_model.g20325.t1
Valid prediction for Augustus_model.g20330.t1
Valid prediction for snap_scaffold_12-snap.1873-T1
Valid prediction for snap_scaffold_12-snap.1858-T1
Valid prediction for snap_scaffold_12-snap.1860-T1
Couldn't classify 131087, 131205
Sorry, prediction pasa_asmbl_8847.p1 fails validation.
(GCG)	 TG	131087-131205	GT	GTG
(GTT)	 AG	131814-131868	GT	AGG
(GTG)	 AG	132911-133066	GT	GGG
(ACA)	 AG	133473-133529	GT	AGG
(CTT)	 AG	134087-134146	GT	ACG
(GTC)	 AG	134298-134348	GA	GAG
-recovered pasa_asmbl_8847.p1, terminal, 134298, 134348
-recovered pasa_asmbl_8847.p1, internal, 131814, 131868
-recovered pasa_asmbl_8847.p1, internal, 132911, 133066
-recovered pasa_asmbl_8847.p1, internal, 133473, 133529
-recovered pasa_asmbl_8847.p1, internal, 134087, 134146
Valid prediction for GlimmerHMM_glimmerT_30491-T1
Valid prediction for GeneMark_model.52719_t
Couldn't classify 114842, 114946
Sorry, prediction pasa_asmbl_8845.p1 fails validation.
(TAC)	 GA	114842-114946	GT	AGG
(GAA)	 AG	116362-116483	GT	TGG
(GAA)	 AG	117294-117372	GT	AGG
(GGG)	 AG	117521-117624	GT	GCG
(GAT)	 AG	119469-119655	CA	AAC
-recovered pasa_asmbl_8845.p1, terminal, 119469, 119655
-recovered pasa_asmbl_8845.p1, internal, 116362, 116483
-recovered pasa_asmbl_8845.p1, internal, 117294, 117372
-recovered pasa_asmbl_8845.p1, internal, 117521, 117624
Valid prediction for snap_scaffold_12-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_30518-T1
Valid prediction for GeneMark_model.52706_t
Valid prediction for GeneMark_model.52685_t
Valid prediction for GlimmerHMM_glimmerT_30495-T1
Valid prediction for GeneMark_model.52695_t
Valid prediction for GeneMark_model.52724_t
Valid prediction for GeneMark_model.52699_t
Valid prediction for GeneMark_model.52688_t
Valid prediction for snap_scaffold_12-snap.1850-T1
Valid prediction for snap_scaffold_12-snap.1869-T1
Valid prediction for GeneMark_model.52692_t
Valid prediction for snap_scaffold_12-snap.1879-T1
Valid prediction for snap_scaffold_12-snap.1856-T1
Valid prediction for GeneMark_model.52723_t
Valid prediction for Augustus_model.g20331.t1
Valid prediction for snap_scaffold_12-snap.1876-T1
Valid prediction for GlimmerHMM_glimmerT_30507-T1
Valid prediction for GeneMark_model.52694_t
Valid prediction for GlimmerHMM_glimmerT_30503-T1
Valid prediction for snap_scaffold_12-snap.1853-T1
Valid prediction for snap_scaffold_12-snap.1871-T1
Valid prediction for GeneMark_model.52720_t
Couldn't classify 87459, 87642
Couldn't classify 111728, 111825
Sorry, prediction pasa_asmbl_8843.p1 fails validation.
(AGC)	 GG	87459-87642	GT	AGG
(ATC)	 AG	89706-89833	GT	GGG
(GAA)	 AG	91317-91476	GT	AAG
(CTT)	 AG	91670-91806	GT	CAG
(GCC)	 AG	91905-92076	GT	TGG
(AAC)	 AG	92333-92453	GT	TGG
(GTA)	 AG	92694-92860	GT	TGG
(TGA)	 AG	94344-94500	GT	CAG
(GTG)	 AG	96285-96417	GT	AGG
(ACT)	 AG	99205-99313	GT	CAG
(ATC)	 AG	100653-100931	GT	TGG
(AGA)	 AG	101152-101298	GT	AGG
(GTA)	 AG	101460-101588	GT	AGG
(GGG)	 AG	102617-102723	GT	AGG
(AAT)	 AG	103286-103415	GT	GGG
(GTA)	 AG	104467-104571	GT	AGG
(GCG)	 AG	106664-106777	GT	CGG
(GTC)	 AG	107042-107130	GT	AGG
(AGC)	 AG	107305-107458	GT	AGG
(AGC)	 AG	108453-108550	GT	AGG
(TGC)	 AG	108999-109121	GT	ATG
(GCC)	 AG	109536-109647	GT	GGG
(GTG)	 AG	111728-111825	AT	AGA
add_exon() Sorry, pasa_asmbl_8843.p1 91317-91476-terminal-3 is invalid.
-recovered pasa_asmbl_8843.p1, terminal, 91317, 91476
add_exon() Sorry, pasa_asmbl_8843.p1 101460-101588-terminal-1 is invalid.
-recovered pasa_asmbl_8843.p1, terminal, 101460, 101588
-recovered pasa_asmbl_8843.p1, internal, 89706, 89833
-recovered pasa_asmbl_8843.p1, internal, 91317, 91476
-recovered pasa_asmbl_8843.p1, internal, 91670, 91806
-recovered pasa_asmbl_8843.p1, internal, 91905, 92076
-recovered pasa_asmbl_8843.p1, internal, 92333, 92453
-recovered pasa_asmbl_8843.p1, internal, 92694, 92860
-recovered pasa_asmbl_8843.p1, internal, 94344, 94500
-recovered pasa_asmbl_8843.p1, internal, 96285, 96417
-recovered pasa_asmbl_8843.p1, internal, 99205, 99313
-recovered pasa_asmbl_8843.p1, internal, 100653, 100931
-recovered pasa_asmbl_8843.p1, internal, 101152, 101298
-recovered pasa_asmbl_8843.p1, internal, 101460, 101588
-recovered pasa_asmbl_8843.p1, internal, 102617, 102723
-recovered pasa_asmbl_8843.p1, internal, 103286, 103415
-recovered pasa_asmbl_8843.p1, internal, 104467, 104571
-recovered pasa_asmbl_8843.p1, internal, 106664, 106777
-recovered pasa_asmbl_8843.p1, internal, 107042, 107130
-recovered pasa_asmbl_8843.p1, internal, 107305, 107458
-recovered pasa_asmbl_8843.p1, internal, 108453, 108550
-recovered pasa_asmbl_8843.p1, internal, 108999, 109121
-recovered pasa_asmbl_8843.p1, internal, 109536, 109647
Valid prediction for snap_scaffold_12-snap.1870-T1
Valid prediction for GeneMark_model.52704_t
Valid prediction for GlimmerHMM_glimmerT_30516-T1
Valid prediction for snap_scaffold_12-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_30511-T1
Valid prediction for GlimmerHMM_glimmerT_30520-T1
Valid prediction for GlimmerHMM_glimmerT_30515-T1
Valid prediction for Augustus_model.g20328.t1
Valid prediction for HiQ_model.g20337.t1
Valid prediction for GeneMark_model.52686_t
Valid prediction for GlimmerHMM_glimmerT_30499-T1
Valid prediction for snap_scaffold_12-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_30493-T1
Valid prediction for GlimmerHMM_glimmerT_30504-T1
Valid prediction for GeneMark_model.52713_t
Valid prediction for snap_scaffold_12-snap.1872-T1
Valid prediction for GeneMark_model.52703_t
Valid prediction for GlimmerHMM_glimmerT_30502-T1
Valid prediction for GeneMark_model.52690_t
Valid prediction for Augustus_model.g20335.t1
Valid prediction for GeneMark_model.52701_t
Valid prediction for GeneMark_model.52697_t
Valid prediction for GlimmerHMM_glimmerT_30517-T1
Valid prediction for Augustus_model.g20336.t1
Valid prediction for HiQ_model.g20333.t1
Valid prediction for GeneMark_model.52710_t
Valid prediction for Augustus_model.g20324.t1
Valid prediction for snap_scaffold_12-snap.1851-T1
Valid prediction for GeneMark_model.52708_t
Valid prediction for GeneMark_model.52718_t
Valid prediction for GlimmerHMM_glimmerT_30513-T1
Couldn't classify 58565, 58680
Sorry, prediction pasa_asmbl_8838.p1 fails validation.
(GAG)	 CA	58565-58680	GT	AGG
(AGC)	 AG	60023-60199	GT	AGG
(GGT)	 AG	60354-60429	GT	GGG
(CCA)	 AG	61144-61243	GT	ACG
(AAT)	 AG	62701-62742	GT	AAG
(AGG)	 AG	63030-63080	GT	GAG
(TTC)	 AG	63197-63298	GT	CCG
(ACA)	 AG	63420-63592	GT	GGG
(GGA)	 AG	63825-63934	GT	ATG
(GGA)	 AG	64051-64142	GT	AGG
(CCA)	 AG	64287-64393	GC	GAG
-recovered pasa_asmbl_8838.p1, terminal, 64287, 64393
-recovered pasa_asmbl_8838.p1, internal, 60023, 60199
-recovered pasa_asmbl_8838.p1, internal, 60354, 60429
-recovered pasa_asmbl_8838.p1, internal, 61144, 61243
-recovered pasa_asmbl_8838.p1, internal, 62701, 62742
-recovered pasa_asmbl_8838.p1, internal, 63030, 63080
-recovered pasa_asmbl_8838.p1, internal, 63197, 63298
-recovered pasa_asmbl_8838.p1, internal, 63420, 63592
-recovered pasa_asmbl_8838.p1, internal, 63825, 63934
-recovered pasa_asmbl_8838.p1, internal, 64051, 64142
-recovered pasa_asmbl_8838.p1, internal, 64287, 64393
Valid prediction for GlimmerHMM_glimmerT_30514-T1
Valid prediction for snap_scaffold_12-snap.1863-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_30501-T1
Valid prediction for GlimmerHMM_glimmerT_30498-T1
Valid prediction for GlimmerHMM_glimmerT_30506-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_12-snap.1874-T1
Valid prediction for snap_scaffold_12-snap.1861-T1
Valid prediction for GeneMark_model.52707_t
Valid prediction for GlimmerHMM_glimmerT_30496-T1
Valid prediction for snap_scaffold_12-snap.1877-T1
Valid prediction for GeneMark_model.52714_t
Valid prediction for GeneMark_model.52712_t
Valid prediction for snap_scaffold_12-snap.1859-T1
Valid prediction for GlimmerHMM_glimmerT_30505-T1
Valid prediction for GlimmerHMM_glimmerT_30494-T1
Valid prediction for GeneMark_model.52705_t
Valid prediction for snap_scaffold_12-snap.1854-T1
Valid prediction for GeneMark_model.52722_t
Valid prediction for GeneMark_model.52693_t
Valid prediction for GlimmerHMM_glimmerT_30509-T1
Valid prediction for GeneMark_model.52709_t
Valid prediction for GlimmerHMM_glimmerT_30500-T1
Valid prediction for Augustus_model.g20332.t1
Valid prediction for snap_scaffold_12-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_30521-T1
Valid prediction for GlimmerHMM_glimmerT_30510-T1
Valid prediction for GeneMark_model.52700_t
Valid prediction for GeneMark_model.52691_t
Valid prediction for snap_scaffold_12-snap.1849-T1
Valid prediction for GeneMark_model.52689_t
Valid prediction for GeneMark_model.52711_t
Valid prediction for snap_scaffold_12-snap.1862-T1
Valid prediction for GlimmerHMM_glimmerT_30492-T1
Valid prediction for GeneMark_model.52698_t
Valid prediction for snap_scaffold_12-snap.1868-T1
Valid prediction for GeneMark_model.52717_t
Valid prediction for GlimmerHMM_glimmerT_30519-T1
Valid prediction for GeneMark_model.52696_t
Valid prediction for snap_scaffold_12-snap.1848-T1
Valid prediction for snap_scaffold_12-snap.1847-T1
Valid prediction for GeneMark_model.52702_t
Valid prediction for Augustus_model.g20338.t1
Valid prediction for Augustus_model.g20329.t1
Valid prediction for GeneMark_model.52683_t
Valid prediction for GeneMark_model.52682_t
Valid prediction for GlimmerHMM_glimmerT_30508-T1
Valid prediction for GeneMark_model.52684_t
Valid prediction for snap_scaffold_12-snap.1857-T1
Valid prediction for GlimmerHMM_glimmerT_30497-T1
Valid prediction for snap_scaffold_12-snap.1852-T1
Valid prediction for snap_scaffold_12-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_30512-T1
Valid prediction for GeneMark_model.52721_t
Valid prediction for GeneMark_model.52687_t
Valid prediction for Augustus_model.g20326.t1
Valid prediction for snap_scaffold_12-snap.1878-T1
Valid prediction for Augustus_model.g20334.t1
Valid prediction for GeneMark_model.52716_t
Valid prediction for Augustus_model.g20327.t1
Valid prediction for snap_scaffold_12-snap.1865-T1
Couldn't classify 12861, 12891
Couldn't classify 13506, 13596
Sorry, prediction pasa_asmbl_7825.p2 fails validation.
(TGC)	 GC	12861-12891	GT	TGG
(GAG)	 AG	13040-13283	GT	AGG
(TCA)	 AG	13506-13596	GT	ACG
-recovered pasa_asmbl_7825.p2, internal, 13040, 13283
-recovered pasa_asmbl_7825.p2, internal, 13506, 13596

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14905, rend_intergenic: 11648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26396, rend_intergenic: 26211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30649, rend_intergenic: 26428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37870, rend_intergenic: 31062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49327, rend_intergenic: 40790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49845, rend_intergenic: 49375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61002, rend_intergenic: 55451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73940, rend_intergenic: 67817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87028, rend_intergenic: 82900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94509, rend_intergenic: 89571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148838, rend_intergenic: 142617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152362
-exon list size: 605


building trellis

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79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 14905, rend_intergenic: 11648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26396, rend_intergenic: 26211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30649, rend_intergenic: 26428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37870, rend_intergenic: 31062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49327, rend_intergenic: 40790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49845, rend_intergenic: 49375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61002, rend_intergenic: 55451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73940, rend_intergenic: 67817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87028, rend_intergenic: 82900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94509, rend_intergenic: 89571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148838, rend_intergenic: 142617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support