-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_9659739-9850254

-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.44012_t
Valid prediction for GeneMark_model.44032_t
Valid prediction for GlimmerHMM_glimmerT_25741-T1
Valid prediction for snap_scaffold_10-snap.1894-T1
Valid prediction for snap_scaffold_10-snap.1878-T1
Valid prediction for snap_scaffold_10-snap.1895-T1
Valid prediction for GeneMark_model.44026_t
Valid prediction for snap_scaffold_10-snap.1877-T1
Valid prediction for GeneMark_model.44022_t
Valid prediction for Augustus_model.g17277.t1
Valid prediction for snap_scaffold_10-snap.1886-T1
Valid prediction for snap_scaffold_10-snap.1899-T1
Valid prediction for GlimmerHMM_glimmerT_25733-T1
Valid prediction for GlimmerHMM_glimmerT_25742-T1
Valid prediction for GlimmerHMM_glimmerT_25736-T1
Valid prediction for snap_scaffold_10-snap.1903-T1
Valid prediction for GeneMark_model.44011_t
Valid prediction for snap_scaffold_10-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_25735-T1
Valid prediction for snap_scaffold_10-snap.1879-T1
Valid prediction for snap_scaffold_10-snap.1884-T1
Couldn't classify 137194, 137724
Sorry, prediction pasa_asmbl_5133.p1 fails validation.
(ATG)	 AG	136534-136545	GT	GGG
(GTA)	 AG	137194-137724	CT	TCC
-recovered pasa_asmbl_5133.p1, initial, 136534, 136545
-recovered pasa_asmbl_5133.p1, internal, 136534, 136545
Valid prediction for GeneMark_model.44000_t
Valid prediction for snap_scaffold_10-snap.1902-T1
Valid prediction for snap_scaffold_10-snap.1888-T1
Valid prediction for GeneMark_model.44033_t
Valid prediction for GeneMark_model.44034_t
Valid prediction for snap_scaffold_10-snap.1905-T1
Valid prediction for GeneMark_model.44014_t
Valid prediction for snap_scaffold_10-snap.1875-T1
Valid prediction for GeneMark_model.44037_t
Valid prediction for GeneMark_model.44002_t
Valid prediction for GlimmerHMM_glimmerT_25732-T1
Valid prediction for GeneMark_model.44043_t
Valid prediction for GeneMark_model.44025_t
Valid prediction for GeneMark_model.44007_t
Valid prediction for Augustus_model.g17280.t1
Valid prediction for GeneMark_model.44040_t
Valid prediction for GlimmerHMM_glimmerT_25738-T1
Valid prediction for Augustus_model.g17281.t1
Valid prediction for GeneMark_model.44023_t
Valid prediction for Augustus_model.g17275.t1
Valid prediction for GeneMark_model.44019_t
Valid prediction for Augustus_model.g17276.t1
Valid prediction for snap_scaffold_10-snap.1897-T1
Valid prediction for snap_scaffold_10-snap.1898-T1
Valid prediction for GeneMark_model.44018_t
Valid prediction for GlimmerHMM_glimmerT_25739-T1
Valid prediction for snap_scaffold_10-snap.1893-T1
Valid prediction for GeneMark_model.44004_t
Valid prediction for GlimmerHMM_glimmerT_25743-T1
Valid prediction for GlimmerHMM_glimmerT_25730-T1
Valid prediction for snap_scaffold_10-snap.1887-T1
Valid prediction for GeneMark_model.44024_t
Valid prediction for Augustus_model.g17274.t1
Valid prediction for GeneMark_model.44030_t
Valid prediction for Augustus_model.g17278.t1
Valid prediction for GeneMark_model.44009_t
Valid prediction for snap_scaffold_10-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_25728-T1
Valid prediction for GeneMark_model.44016_t
Valid prediction for snap_scaffold_10-snap.1890-T1
Valid prediction for GeneMark_model.44038_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 GeneMark_model.44036_t
Valid prediction for GlimmerHMM_glimmerT_25740-T1
Valid prediction for HiQ_model.g17273.t1
Valid prediction for snap_scaffold_10-snap.1901-T1
Valid prediction for GeneMark_model.44020_t
Couldn't classify 3313, 3477
Couldn't classify 4423, 4488
Sorry, prediction pasa_asmbl_3611.p1 fails validation.
(TCC)	 CC	3313-3477	GT	AGG
(GCC)	 AG	3633-3731	GC	AGG
(GTG)	 AG	4244-4315	GT	TGG
(GAG)	 AG	4423-4488	CT	AGC
-recovered pasa_asmbl_3611.p1, internal, 3633, 3731
-recovered pasa_asmbl_3611.p1, internal, 4244, 4315
Valid prediction for GeneMark_model.44039_t
Valid prediction for GeneMark_model.44008_t
Valid prediction for snap_scaffold_10-snap.1873-T1
Valid prediction for GeneMark_model.44028_t
Valid prediction for snap_scaffold_10-snap.1907-T1
Valid prediction for GlimmerHMM_glimmerT_25725-T1
Couldn't classify 4623, 4744
Sorry, prediction pasa_asmbl_3610.p1 fails validation.
(GAG)	 GA	4623-4744	GT	GAG
(GTA)	 AG	4989-5181	GT	AGG
(GTG)	 AG	5292-5488	GT	AGG
(GGC)	 AG	5696-5774	GT	AGG
(TAC)	 AG	5943-6038	GT	AAG
(TTG)	 AG	6193-6255	CC	GAC
-recovered pasa_asmbl_3610.p1, terminal, 6193, 6255
-recovered pasa_asmbl_3610.p1, internal, 4989, 5181
-recovered pasa_asmbl_3610.p1, internal, 5292, 5488
-recovered pasa_asmbl_3610.p1, internal, 5696, 5774
-recovered pasa_asmbl_3610.p1, internal, 5943, 6038
Valid prediction for Augustus_model.g17272.t1
Valid prediction for snap_scaffold_10-snap.1892-T1
Valid prediction for snap_scaffold_10-snap.1885-T1
Valid prediction for GeneMark_model.44029_t
Valid prediction for CodingQuarry_transcript_5528-T1
Valid prediction for GeneMark_model.44035_t
Valid prediction for GeneMark_model.44027_t
Valid prediction for snap_scaffold_10-snap.1906-T1
Valid prediction for snap_scaffold_10-snap.1889-T1
Valid prediction for snap_scaffold_10-snap.1891-T1
Valid prediction for GeneMark_model.44041_t
Valid prediction for snap_scaffold_10-snap.1883-T1
Valid prediction for snap_scaffold_10-snap.1904-T1
Couldn't classify 164780, 164842
Couldn't classify 165221, 165255
Sorry, prediction CodingQuarry_transcript_5530-T1 fails validation.
(ATG)	 CA	160630-160981	GT	AGG
(GTA)	 AG	162916-163067	GT	GGG
(AAA)	 AG	163259-163339	GT	AGG
(CTT)	 AG	163555-163674	GT	AGG
(GTG)	 AG	163766-163897	GT	AGG
(GTG)	 AG	164093-164246	GT	AGG
(ACC)	 AG	164780-164842	TG	GGT
(ACA)	 AC	165221-165255	AA	AGA
-recovered CodingQuarry_transcript_5530-T1, initial, 160630, 160981
-recovered CodingQuarry_transcript_5530-T1, internal, 162916, 163067
-recovered CodingQuarry_transcript_5530-T1, internal, 163259, 163339
-recovered CodingQuarry_transcript_5530-T1, internal, 163555, 163674
-recovered CodingQuarry_transcript_5530-T1, internal, 163766, 163897
-recovered CodingQuarry_transcript_5530-T1, internal, 164093, 164246
Valid prediction for GlimmerHMM_glimmerT_25745-T1
Valid prediction for snap_scaffold_10-snap.1876-T1
Valid prediction for GlimmerHMM_glimmerT_25731-T1
Valid prediction for GlimmerHMM_glimmerT_25729-T1
Valid prediction for GlimmerHMM_glimmerT_25726-T1
Valid prediction for snap_scaffold_10-snap.1880-T1
Valid prediction for snap_scaffold_10-snap.1872-T1
Valid prediction for GeneMark_model.44001_t
Valid prediction for GeneMark_model.44013_t
Valid prediction for snap_scaffold_10-snap.1896-T1
Valid prediction for GeneMark_model.44017_t
Valid prediction for GeneMark_model.44006_t
Valid prediction for GlimmerHMM_glimmerT_25727-T1
Valid prediction for GeneMark_model.44010_t
Couldn't classify 166341, 166511
Sorry, prediction pasa_asmbl_3605.p1 fails validation.
(ATG)	 CA	160630-160981	GT	AGG
(GTA)	 AG	162916-163067	GT	GGG
(AAA)	 AG	163259-163339	GT	AGG
(CTT)	 AG	163555-163674	GT	AGG
(GTG)	 AG	163766-163897	GT	AGG
(GTG)	 AG	164093-164246	GT	AGG
(ACC)	 AG	164780-164841	GT	AGG
(GAC)	 AG	165218-165317	GT	CTG
(ACC)	 AG	165559-165692	GT	AGG
(ACT)	 AG	166026-166085	GT	AGG
(ATC)	 AG	166341-166511	TG	TGT
-recovered pasa_asmbl_3605.p1, initial, 160630, 160981
-recovered pasa_asmbl_3605.p1, internal, 162916, 163067
-recovered pasa_asmbl_3605.p1, internal, 163259, 163339
-recovered pasa_asmbl_3605.p1, internal, 163555, 163674
-recovered pasa_asmbl_3605.p1, internal, 163766, 163897
-recovered pasa_asmbl_3605.p1, internal, 164093, 164246
-recovered pasa_asmbl_3605.p1, internal, 164780, 164841
-recovered pasa_asmbl_3605.p1, internal, 165218, 165317
-recovered pasa_asmbl_3605.p1, internal, 165559, 165692
-recovered pasa_asmbl_3605.p1, internal, 166026, 166085
Valid prediction for Augustus_model.g17279.t1
Valid prediction for GeneMark_model.44031_t
Valid prediction for GeneMark_model.44042_t
Valid prediction for GlimmerHMM_glimmerT_25734-T1
Valid prediction for GlimmerHMM_glimmerT_25746-T1
Valid prediction for snap_scaffold_10-snap.1874-T1
Valid prediction for GeneMark_model.44003_t
Valid prediction for Augustus_model.g17283.t1
Valid prediction for pasa_asmbl_3603.p1
Valid prediction for Augustus_model.g17282.t1
Valid prediction for GeneMark_model.43999_t
Valid prediction for GlimmerHMM_glimmerT_25724-T1
Valid prediction for GlimmerHMM_glimmerT_25744-T1
Valid prediction for snap_scaffold_10-snap.1882-T1
Valid prediction for GeneMark_model.44021_t
Valid prediction for GeneMark_model.44044_t
Valid prediction for Augustus_model.g17271.t1
Valid prediction for GlimmerHMM_glimmerT_25737-T1
Valid prediction for GlimmerHMM_glimmerT_25747-T1
Valid prediction for GeneMark_model.44015_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21691, rend_intergenic: 16479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29887, rend_intergenic: 27576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45965, rend_intergenic: 45805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52641, rend_intergenic: 47435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57904, rend_intergenic: 53408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75105, rend_intergenic: 69792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104876, rend_intergenic: 99273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124132, rend_intergenic: 119311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156624, rend_intergenic: 143514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161006, rend_intergenic: 156773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170784, rend_intergenic: 162095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175948, rend_intergenic: 171163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183323, rend_intergenic: 176180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190516
-exon list size: 688


building trellis

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90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 21691, rend_intergenic: 16479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29887, rend_intergenic: 27576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45965, rend_intergenic: 45805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52641, rend_intergenic: 47435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57904, rend_intergenic: 53408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75105, rend_intergenic: 69792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104876, rend_intergenic: 99273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124132, rend_intergenic: 119311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156624, rend_intergenic: 143514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161006, rend_intergenic: 156773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170784, rend_intergenic: 162095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175948, rend_intergenic: 171163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183323, rend_intergenic: 176180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support