-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_4970551-5161899

-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 CodingQuarry_transcript_46041-T1
Valid prediction for GlimmerHMM_glimmerT_6642-T1
Valid prediction for GeneMark_model.10987_t
Valid prediction for GlimmerHMM_glimmerT_6639-T1
Valid prediction for GlimmerHMM_glimmerT_6648-T1
Valid prediction for snap_scaffold_3-snap.1091-T1
Valid prediction for Augustus_model.g4347.t1
Valid prediction for GlimmerHMM_glimmerT_6650-T1
Valid prediction for GeneMark_model.11009_t
Valid prediction for GlimmerHMM_glimmerT_6641-T1
Valid prediction for Augustus_model.g4346.t1
Valid prediction for GeneMark_model.11020_t
Valid prediction for GeneMark_model.10993_t
Valid prediction for HiQ_model.g4342.t1
Valid prediction for GeneMark_model.10996_t
Valid prediction for snap_scaffold_3-snap.1108-T1
Valid prediction for GeneMark_model.10989_t
Valid prediction for snap_scaffold_3-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_6638-T1
Valid prediction for GlimmerHMM_glimmerT_6643-T1
Valid prediction for GeneMark_model.11001_t
Valid prediction for snap_scaffold_3-snap.1078-T1
Valid prediction for GlimmerHMM_glimmerT_6655-T1
Valid prediction for snap_scaffold_3-snap.1103-T1
Valid prediction for HiQ_model.g4340.t1
Valid prediction for snap_scaffold_3-snap.1098-T1
Valid prediction for snap_scaffold_3-snap.1081-T1
Valid prediction for snap_scaffold_3-snap.1085-T1
Valid prediction for GeneMark_model.11030_t
Valid prediction for GlimmerHMM_glimmerT_6649-T1
Valid prediction for GeneMark_model.10992_t
Valid prediction for CodingQuarry_transcript_46043-T1
Valid prediction for GeneMark_model.10997_t
Valid prediction for GeneMark_model.11004_t
Valid prediction for pasa_asmbl_40017.p1
Valid prediction for GeneMark_model.11017_t
Valid prediction for snap_scaffold_3-snap.1094-T1
Valid prediction for CodingQuarry_transcript_46046-T1
Valid prediction for snap_scaffold_3-snap.1096-T1
Valid prediction for Augustus_model.g4344.t1
Valid prediction for GeneMark_model.11025_t
Valid prediction for snap_scaffold_3-snap.1093-T1
Valid prediction for HiQ_model.g4335.t1
Valid prediction for GeneMark_model.11027_t
Valid prediction for Augustus_model.g4339.t1
Valid prediction for snap_scaffold_3-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_6646-T1
Valid prediction for GeneMark_model.11015_t
Valid prediction for CodingQuarry_transcript_46044-T1
Valid prediction for GlimmerHMM_glimmerT_6657-T1
Valid prediction for GeneMark_model.11013_t
Valid prediction for GeneMark_model.10986_t
Valid prediction for GlimmerHMM_glimmerT_6637-T1
Valid prediction for snap_scaffold_3-snap.1097-T1
Valid prediction for CodingQuarry_transcript_46045-T1
Valid prediction for pasa_asmbl_40011.p1
Valid prediction for pasa_asmbl_40022.p2
Valid prediction for pasa_asmbl_40009.p1
Valid prediction for GeneMark_model.11006_t
Valid prediction for GeneMark_model.11018_t
Couldn't classify 69221, 69278
Sorry, prediction pasa_asmbl_40020.p1 fails validation.
(GGC)	 CA	69221-69278	GT	AGG
(GGA)	 AG	70978-71169	GT	GGG
(AGA)	 AG	71530-71706	GT	GGG
(ATA)	 AG	72983-73109	GT	GAG
(TGT)	 AG	73266-73387	GT	AGG
(TTC)	 AG	73852-74031	GT	ACG
(CTA)	 AG	74932-75065	GT	AGG
(CAT)	 AG	75721-75842	GT	AGG
(GTT)	 AG	76162-76342	CC	GAC
-recovered pasa_asmbl_40020.p1, terminal, 76162, 76342
-recovered pasa_asmbl_40020.p1, internal, 70978, 71169
-recovered pasa_asmbl_40020.p1, internal, 71530, 71706
-recovered pasa_asmbl_40020.p1, internal, 72983, 73109
-recovered pasa_asmbl_40020.p1, internal, 73266, 73387
-recovered pasa_asmbl_40020.p1, internal, 73852, 74031
-recovered pasa_asmbl_40020.p1, internal, 74932, 75065
-recovered pasa_asmbl_40020.p1, internal, 75721, 75842
Valid prediction for GlimmerHMM_glimmerT_6631-T1
Valid prediction for GeneMark_model.11023_t
Valid prediction for GeneMark_model.11011_t
Valid prediction for GlimmerHMM_glimmerT_6634-T1
Valid prediction for GeneMark_model.11021_t
Valid prediction for GeneMark_model.11029_t
Valid prediction for snap_scaffold_3-snap.1100-T1
Valid prediction for Augustus_model.g4337.t1
Valid prediction for GlimmerHMM_glimmerT_6633-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 Augustus_model.g4338.t1
Valid prediction for GlimmerHMM_glimmerT_6645-T1
Valid prediction for GeneMark_model.11014_t
Valid prediction for snap_scaffold_3-snap.1090-T1
Valid prediction for snap_scaffold_3-snap.1101-T1
Couldn't classify 13144, 13455
Sorry, prediction pasa_asmbl_38791.p3 fails validation.
(ATG)	 CG	13144-13455	AG	AAA
Valid prediction for GeneMark_model.10991_t
Valid prediction for GlimmerHMM_glimmerT_6656-T1
Valid prediction for pasa_asmbl_38792.p1
Valid prediction for snap_scaffold_3-snap.1075-T1
Valid prediction for GeneMark_model.11033_t
Valid prediction for GlimmerHMM_glimmerT_6654-T1
Valid prediction for GlimmerHMM_glimmerT_6636-T1
Valid prediction for HiQ_model.g4348.t1
Couldn't classify 180167, 180205
Couldn't classify 181098, 181128
Sorry, prediction pasa_asmbl_38783.p1 fails validation.
(CTC)	 TC	180167-180205	GT	AGG
(GTC)	 AG	180316-180482	GT	GGG
(TTT)	 AG	180725-180889	GT	AAG
(GCT)	 AG	181098-181128	CA	CCC
-recovered pasa_asmbl_38783.p1, internal, 180316, 180482
-recovered pasa_asmbl_38783.p1, internal, 180725, 180889
Valid prediction for snap_scaffold_3-snap.1086-T1
Valid prediction for snap_scaffold_3-snap.1082-T1
Valid prediction for snap_scaffold_3-snap.1077-T1
Valid prediction for GeneMark_model.10985_t
Valid prediction for GlimmerHMM_glimmerT_6640-T1
Valid prediction for snap_scaffold_3-snap.1092-T1
Valid prediction for GeneMark_model.11034_t
Valid prediction for snap_scaffold_3-snap.1080-T1
Valid prediction for snap_scaffold_3-snap.1106-T1
Valid prediction for GeneMark_model.11000_t
Valid prediction for Augustus_model.g4333.t1
Valid prediction for GeneMark_model.11022_t
Valid prediction for pasa_asmbl_38785.p1
Valid prediction for Augustus_model.g4349.t1
Valid prediction for GeneMark_model.10994_t
Valid prediction for CodingQuarry_transcript_46042-T1
Valid prediction for pasa_asmbl_38787.p1
Valid prediction for GeneMark_model.11002_t
Couldn't classify 187087, 187389
Sorry, prediction pasa_asmbl_38781.p1 fails validation.
(TGC)	 GC	187087-187389	GT	GGG
Valid prediction for GeneMark_model.11019_t
Valid prediction for GlimmerHMM_glimmerT_6644-T1
Valid prediction for HiQ_model.g4336.t1
Valid prediction for snap_scaffold_3-snap.1105-T1
Valid prediction for snap_scaffold_3-snap.1076-T1
Valid prediction for GeneMark_model.11008_t
Valid prediction for Augustus_model.g4351.t1
Valid prediction for GeneMark_model.10990_t
Valid prediction for GeneMark_model.11005_t
Valid prediction for GlimmerHMM_glimmerT_6651-T1
Valid prediction for snap_scaffold_3-snap.1084-T1
Valid prediction for snap_scaffold_3-snap.1111-T1
Valid prediction for Augustus_model.g4350.t1
Valid prediction for GlimmerHMM_glimmerT_6629-T1
Valid prediction for GeneMark_model.11010_t
Valid prediction for snap_scaffold_3-snap.1109-T1
Valid prediction for snap_scaffold_3-snap.1102-T1
Couldn't classify 179780, 179833
Sorry, prediction pasa_asmbl_38784.p1 fails validation.
(ATG)	 AG	178505-178541	GT	CGG
(GTC)	 AG	179137-179279	GT	AGG
(CTA)	 AG	179484-179642	GT	AGG
(GTC)	 AG	179780-179833	AA	ACA
-recovered pasa_asmbl_38784.p1, initial, 178505, 178541
-recovered pasa_asmbl_38784.p1, internal, 178505, 178541
-recovered pasa_asmbl_38784.p1, internal, 179137, 179279
-recovered pasa_asmbl_38784.p1, internal, 179484, 179642
Valid prediction for GeneMark_model.11031_t
Valid prediction for Augustus_model.g4334.t1
Valid prediction for GeneMark_model.11032_t
Valid prediction for snap_scaffold_3-snap.1110-T1
Valid prediction for snap_scaffold_3-snap.1095-T1
Valid prediction for Augustus_model.g4341.t1
Valid prediction for GeneMark_model.11003_t
Valid prediction for snap_scaffold_3-snap.1083-T1
Valid prediction for snap_scaffold_3-snap.1088-T1
Valid prediction for GeneMark_model.11007_t
Valid prediction for GeneMark_model.11026_t
Valid prediction for CodingQuarry_transcript_46047-T1
Valid prediction for GeneMark_model.10999_t
Valid prediction for snap_scaffold_3-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_6635-T1
Valid prediction for GeneMark_model.10998_t
Valid prediction for GlimmerHMM_glimmerT_6652-T1
Valid prediction for snap_scaffold_3-snap.1089-T1
Valid prediction for snap_scaffold_3-snap.1079-T1
Valid prediction for GeneMark_model.10988_t
Valid prediction for GlimmerHMM_glimmerT_6653-T1
Valid prediction for Augustus_model.g4343.t1
Valid prediction for GeneMark_model.11024_t
Valid prediction for snap_scaffold_3-snap.1099-T1
Valid prediction for GeneMark_model.11028_t
Valid prediction for GeneMark_model.10984_t
Valid prediction for GeneMark_model.11016_t
Valid prediction for GlimmerHMM_glimmerT_6630-T1
Valid prediction for GeneMark_model.10995_t
Valid prediction for GlimmerHMM_glimmerT_6647-T1
Valid prediction for GlimmerHMM_glimmerT_6632-T1
Couldn't classify 182645, 183088
Sorry, prediction pasa_asmbl_38782.p1 fails validation.
(TCC)	 CC	182645-183088	AT	GAA
Valid prediction for Augustus_model.g4345.t1
Valid prediction for GlimmerHMM_glimmerT_6658-T1
Valid prediction for Augustus_model.g4332.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32227, rend_intergenic: 25372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38577, rend_intergenic: 33245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62227, rend_intergenic: 57562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74522, rend_intergenic: 65311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76788, rend_intergenic: 75044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89641, rend_intergenic: 80175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99411, rend_intergenic: 91921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109385, rend_intergenic: 107367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155946, rend_intergenic: 150018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191349
-exon list size: 629


building trellis

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92.9    
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98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 32227, rend_intergenic: 25372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38577, rend_intergenic: 33245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62227, rend_intergenic: 57562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74522, rend_intergenic: 65311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76788, rend_intergenic: 75044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89641, rend_intergenic: 80175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99411, rend_intergenic: 91921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109385, rend_intergenic: 107367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155946, rend_intergenic: 150018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support