-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_8402925-8577638

-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.83104_t
Valid prediction for GeneMark_model.83126_t
Valid prediction for snap_scaffold_20-snap.1863-T1
Valid prediction for GeneMark_model.83100_t
Valid prediction for GeneMark_model.83131_t
Valid prediction for snap_scaffold_20-snap.1856-T1
Valid prediction for GeneMark_model.83134_t
Valid prediction for snap_scaffold_20-snap.1857-T1
Valid prediction for GeneMark_model.83115_t
Valid prediction for snap_scaffold_20-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_47619-T1
Valid prediction for Augustus_model.g31772.t1
Valid prediction for GeneMark_model.83113_t
Valid prediction for snap_scaffold_20-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_47625-T1
Valid prediction for GlimmerHMM_glimmerT_47618-T1
Valid prediction for GlimmerHMM_glimmerT_47608-T1
Valid prediction for GlimmerHMM_glimmerT_47624-T1
Valid prediction for pasa_asmbl_25937.p1
Valid prediction for GeneMark_model.83109_t
Valid prediction for GlimmerHMM_glimmerT_47615-T1
Valid prediction for GlimmerHMM_glimmerT_47616-T1
Valid prediction for snap_scaffold_20-snap.1874-T1
Couldn't classify 146245, 146278
Couldn't classify 147562, 147644
Sorry, prediction pasa_asmbl_25942.p1 fails validation.
(GAC)	 TG	146245-146278	GT	CAG
(CTC)	 AG	146454-146576	GT	TGG
(ATA)	 AG	146713-146835	GT	TGG
(GCA)	 AG	147188-147310	GT	AGG
(ACA)	 AG	147562-147644	GG	AAG
-recovered pasa_asmbl_25942.p1, internal, 146454, 146576
-recovered pasa_asmbl_25942.p1, internal, 146713, 146835
-recovered pasa_asmbl_25942.p1, internal, 147188, 147310
Valid prediction for GlimmerHMM_glimmerT_47607-T1
Valid prediction for Augustus_model.g31763.t1
Valid prediction for snap_scaffold_20-snap.1871-T1
Valid prediction for GeneMark_model.83133_t
Couldn't classify 148290, 148510
Couldn't classify 149551, 149577
Sorry, prediction pasa_asmbl_25943.p1 fails validation.
(TTG)	 AG	148290-148510	GT	AAG
(CTT)	 AG	148689-148807	GT	GGG
(ACA)	 AG	148914-149053	GT	AGG
(GAC)	 AG	149551-149577	AC	GCA
-recovered pasa_asmbl_25943.p1, internal, 148290, 148510
-recovered pasa_asmbl_25943.p1, internal, 148689, 148807
-recovered pasa_asmbl_25943.p1, internal, 148914, 149053
Valid prediction for GeneMark_model.83117_t
Valid prediction for GeneMark_model.83124_t
Valid prediction for GeneMark_model.83111_t
Valid prediction for GeneMark_model.83129_t
Valid prediction for GeneMark_model.83098_t
Valid prediction for snap_scaffold_20-snap.1878-T1
Valid prediction for GeneMark_model.83119_t
Valid prediction for GlimmerHMM_glimmerT_47613-T1
Valid prediction for GeneMark_model.83097_t
Valid prediction for Augustus_model.g31766.t1
Valid prediction for snap_scaffold_20-snap.1873-T1
Couldn't classify 110928, 111025
Sorry, prediction pasa_asmbl_26272.p1 fails validation.
(ATG)	 CC	109583-109790	GT	TGG
(GAT)	 AG	110100-110183	GT	AGG
(ACG)	 AG	110928-111025	TG	ACT
-recovered pasa_asmbl_26272.p1, initial, 109583, 109790
-recovered pasa_asmbl_26272.p1, internal, 110100, 110183
Couldn't classify 112524, 112661
Couldn't classify 113995, 114096
Sorry, prediction pasa_asmbl_25939.p1 fails validation.
(GAT)	 AA	112524-112661	GT	AGG
(AAA)	 AG	112849-112927	GT	AGG
(ATG)	 AG	113017-113093	GT	AGG
(TCC)	 AG	113402-113521	GT	AGG
(GCC)	 AG	113995-114096	CC	CCC
add_exon() Sorry, pasa_asmbl_25939.p1 113017-113093-initial-1 is invalid.
-recovered pasa_asmbl_25939.p1, initial, 113017, 113093
-recovered pasa_asmbl_25939.p1, internal, 112849, 112927
-recovered pasa_asmbl_25939.p1, internal, 113017, 113093
-recovered pasa_asmbl_25939.p1, internal, 113402, 113521
Valid prediction for Augustus_model.g31756.t1
Valid prediction for snap_scaffold_20-snap.1869-T1
Valid prediction for Augustus_model.g31768.t1
Valid prediction for GeneMark_model.83123_t
Valid prediction for Augustus_model.g31769.t1
Valid prediction for Augustus_model.g31773.t1
Valid prediction for Augustus_model.g31770.t1
Valid prediction for snap_scaffold_20-snap.1886-T1
Valid prediction for Augustus_model.g31757.t1
Valid prediction for snap_scaffold_20-snap.1860-T1
Valid prediction for GeneMark_model.83110_t
Valid prediction for GlimmerHMM_glimmerT_47622-T1
Valid prediction for GeneMark_model.83121_t
Valid prediction for snap_scaffold_20-snap.1880-T1
Couldn't classify 111701, 112044
Couldn't classify 112242, 112275
Sorry, prediction pasa_asmbl_25938.p2 fails validation.
(TGG)	 CG	111701-112044	GT	AGG
(GAA)	 AG	112242-112275	CT	ACC
Valid prediction for Augustus_model.g31774.t1
Valid prediction for GeneMark_model.83102_t
Valid prediction for GeneMark_model.83106_t
Valid prediction for GeneMark_model.83107_t
Valid prediction for GlimmerHMM_glimmerT_47611-T1
Valid prediction for GeneMark_model.83128_t
Couldn't classify 28207, 28242
Sorry, prediction pasa_asmbl_25934.p1 fails validation.
(CCC)	 AC	28207-28242	GT	CTG
(TGC)	 AG	28446-28543	GT	AAG
(GCT)	 AG	28904-29087	GT	AGG
(GTG)	 AG	29730-29860	GT	CAG
(GAT)	 AG	30027-30182	GT	TGG
(CCT)	 AG	30424-30502	GT	TGG
(GAG)	 AG	30742-30939	AC	AAA
-recovered pasa_asmbl_25934.p1, terminal, 30742, 30939
-recovered pasa_asmbl_25934.p1, internal, 28446, 28543
-recovered pasa_asmbl_25934.p1, internal, 28904, 29087
-recovered pasa_asmbl_25934.p1, internal, 29730, 29860
-recovered pasa_asmbl_25934.p1, internal, 30027, 30182
-recovered pasa_asmbl_25934.p1, internal, 30424, 30502
Valid prediction for snap_scaffold_20-snap.1885-T1
Valid prediction for snap_scaffold_20-snap.1882-T1
Valid prediction for GlimmerHMM_glimmerT_47628-T1
Valid prediction for pasa_asmbl_25941.p1
Valid prediction for snap_scaffold_20-snap.1868-T1
Valid prediction for snap_scaffold_20-snap.1859-T1
Valid prediction for snap_scaffold_20-snap.1850-T1
Valid prediction for GlimmerHMM_glimmerT_47626-T1
Valid prediction for Augustus_model.g31761.t1
Valid prediction for Augustus_model.g31771.t1
Couldn't classify 25636, 25736
Sorry, prediction pasa_asmbl_25932.p1 fails validation.
(ATG)	 AA	23054-23069	GT	AGG
(TGT)	 AG	23481-23745	GT	AAG
(GGA)	 AG	24231-24379	GT	GGG
(GGA)	 AG	25636-25736	CC	TGC
-recovered pasa_asmbl_25932.p1, initial, 23054, 23069
-recovered pasa_asmbl_25932.p1, internal, 23481, 23745
-recovered pasa_asmbl_25932.p1, internal, 24231, 24379
Valid prediction for GlimmerHMM_glimmerT_47621-T1
Valid prediction for snap_scaffold_20-snap.1854-T1
Valid prediction for snap_scaffold_20-snap.1887-T1
Valid prediction for Augustus_model.g31760.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_20-snap.1858-T1
Valid prediction for GlimmerHMM_glimmerT_47614-T1
Valid prediction for Augustus_model.g31759.t1
Valid prediction for GeneMark_model.83108_t
Valid prediction for GlimmerHMM_glimmerT_47617-T1
Valid prediction for snap_scaffold_20-snap.1862-T1
Valid prediction for snap_scaffold_20-snap.1866-T1
Valid prediction for GlimmerHMM_glimmerT_47627-T1
Valid prediction for snap_scaffold_20-snap.1865-T1
Valid prediction for snap_scaffold_20-snap.1853-T1
Valid prediction for GeneMark_model.83135_t
Valid prediction for GlimmerHMM_glimmerT_47610-T1
Valid prediction for GlimmerHMM_glimmerT_47623-T1
Valid prediction for GeneMark_model.83127_t
Valid prediction for snap_scaffold_20-snap.1875-T1
Valid prediction for Augustus_model.g31764.t1
Valid prediction for GlimmerHMM_glimmerT_47629-T1
Valid prediction for snap_scaffold_20-snap.1851-T1
Valid prediction for snap_scaffold_20-snap.1855-T1
Valid prediction for Augustus_model.g31765.t1
Valid prediction for GlimmerHMM_glimmerT_47612-T1
Valid prediction for snap_scaffold_20-snap.1888-T1
Valid prediction for GeneMark_model.83125_t
Valid prediction for GeneMark_model.83122_t
Valid prediction for snap_scaffold_20-snap.1872-T1
Valid prediction for GeneMark_model.83101_t
Valid prediction for GeneMark_model.83103_t
Valid prediction for Augustus_model.g31767.t1
Valid prediction for snap_scaffold_20-snap.1876-T1
Valid prediction for snap_scaffold_20-snap.1861-T1
Valid prediction for GlimmerHMM_glimmerT_47620-T1
Valid prediction for GeneMark_model.83099_t
Valid prediction for GeneMark_model.83116_t
Valid prediction for snap_scaffold_20-snap.1881-T1
Valid prediction for Augustus_model.g31775.t1
Valid prediction for GlimmerHMM_glimmerT_47609-T1
Valid prediction for snap_scaffold_20-snap.1884-T1
Valid prediction for GeneMark_model.83114_t
Valid prediction for GeneMark_model.83120_t
Valid prediction for snap_scaffold_20-snap.1864-T1
Valid prediction for GeneMark_model.83118_t
Valid prediction for snap_scaffold_20-snap.1879-T1
Valid prediction for Augustus_model.g31758.t1
Valid prediction for GeneMark_model.83112_t
Valid prediction for snap_scaffold_20-snap.1883-T1
Valid prediction for GeneMark_model.83105_t
Valid prediction for snap_scaffold_20-snap.1870-T1
Valid prediction for snap_scaffold_20-snap.1852-T1
Valid prediction for GeneMark_model.83130_t
Valid prediction for Augustus_model.g31762.t1
Valid prediction for GeneMark_model.83132_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30939, rend_intergenic: 23539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65597, rend_intergenic: 60360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81397, rend_intergenic: 74045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84768, rend_intergenic: 83021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91815, rend_intergenic: 86097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105134, rend_intergenic: 95100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123398, rend_intergenic: 118593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125138, rend_intergenic: 123483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128747, rend_intergenic: 125711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129855, rend_intergenic: 128861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134829, rend_intergenic: 132527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174714
-exon list size: 608


building trellis

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99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 30939, rend_intergenic: 23539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65597, rend_intergenic: 60360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81397, rend_intergenic: 74045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84768, rend_intergenic: 83021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91815, rend_intergenic: 86097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105134, rend_intergenic: 95100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123398, rend_intergenic: 118593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125138, rend_intergenic: 123483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128747, rend_intergenic: 125711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129855, rend_intergenic: 128861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134829, rend_intergenic: 132527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support