-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_4068033-4267242

-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 Augustus_model.g7696.t1
Valid prediction for snap_scaffold_5-snap.792-T1
Valid prediction for GlimmerHMM_glimmerT_11776-T1
Valid prediction for snap_scaffold_5-snap.817-T1
Valid prediction for GlimmerHMM_glimmerT_11775-T1
Valid prediction for snap_scaffold_5-snap.815-T1
Valid prediction for snap_scaffold_5-snap.816-T1
Valid prediction for GlimmerHMM_glimmerT_11761-T1
Valid prediction for snap_scaffold_5-snap.796-T1
Valid prediction for Augustus_model.g7688.t1
Valid prediction for snap_scaffold_5-snap.805-T1
Valid prediction for snap_scaffold_5-snap.827-T1
Valid prediction for snap_scaffold_5-snap.787-T1
Valid prediction for snap_scaffold_5-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_11763-T1
Valid prediction for Augustus_model.g7690.t1
Valid prediction for GlimmerHMM_glimmerT_11760-T1
Valid prediction for snap_scaffold_5-snap.801-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11769-T1
Valid prediction for snap_scaffold_5-snap.812-T1
Valid prediction for Augustus_model.g7693.t1
Valid prediction for snap_scaffold_5-snap.823-T1
Valid prediction for snap_scaffold_5-snap.808-T1
Valid prediction for snap_scaffold_5-snap.802-T1
Valid prediction for snap_scaffold_5-snap.825-T1
Valid prediction for snap_scaffold_5-snap.811-T1
Valid prediction for Augustus_model.g7695.t1
Valid prediction for snap_scaffold_5-snap.790-T1
Valid prediction for snap_scaffold_5-snap.828-T1
Valid prediction for snap_scaffold_5-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_11758-T1
Valid prediction for snap_scaffold_5-snap.813-T1
Valid prediction for Augustus_model.g7689.t1
Valid prediction for GlimmerHMM_glimmerT_11771-T1
Valid prediction for GlimmerHMM_glimmerT_11777-T1
Valid prediction for snap_scaffold_5-snap.798-T1
Valid prediction for GlimmerHMM_glimmerT_11773-T1
Valid prediction for snap_scaffold_5-snap.810-T1
Valid prediction for snap_scaffold_5-snap.791-T1
Valid prediction for snap_scaffold_5-snap.819-T1
Valid prediction for Augustus_model.g7691.t1
Valid prediction for GlimmerHMM_glimmerT_11768-T1
Valid prediction for snap_scaffold_5-snap.799-T1
Valid prediction for snap_scaffold_5-snap.794-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_5-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_11766-T1
Valid prediction for snap_scaffold_5-snap.795-T1
Valid prediction for snap_scaffold_5-snap.803-T1
Valid prediction for GlimmerHMM_glimmerT_11765-T1
Valid prediction for snap_scaffold_5-snap.800-T1
Couldn't classify 152229, 152328
Couldn't classify 157554, 157604
Sorry, prediction pasa_asmbl_45059.p1 fails validation.
(GAG)	 GT	152229-152328	GT	TGG
(TGT)	 AG	154662-154765	GT	AGG
(GGG)	 AG	155005-155054	GT	AAG
(GGA)	 AG	156849-156924	GT	AGG
(GGC)	 AG	157554-157604	AA	GCA
-recovered pasa_asmbl_45059.p1, internal, 154662, 154765
-recovered pasa_asmbl_45059.p1, internal, 155005, 155054
-recovered pasa_asmbl_45059.p1, internal, 156849, 156924
Valid prediction for Augustus_model.g7686.t1
Valid prediction for Augustus_model.g7682.t1
Valid prediction for snap_scaffold_5-snap.821-T1
Valid prediction for snap_scaffold_5-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_11754-T1
Valid prediction for Augustus_model.g7687.t1
Valid prediction for GlimmerHMM_glimmerT_11755-T1
Valid prediction for Augustus_model.g7698.t1
Valid prediction for snap_scaffold_5-snap.809-T1
Valid prediction for GlimmerHMM_glimmerT_11770-T1
Valid prediction for Augustus_model.g7683.t1
Valid prediction for GlimmerHMM_glimmerT_11767-T1
Valid prediction for Augustus_model.g7684.t1
Couldn't classify 94679, 94789
Sorry, prediction pasa_asmbl_43955.p1 fails validation.
(TCC)	 CC	94679-94789	GT	AGG
(ATC)	 AG	94905-95073	GT	AGG
(AGG)	 AG	95396-95518	GT	AGG
(AAG)	 AG	95770-95906	GT	AGG
(CTC)	 AG	96324-96432	GT	CGG
(AGA)	 AG	96685-96757	GT	AGG
(GTC)	 AG	97134-97279	GT	AGG
(GGT)	 AG	97772-97965	CC	GAC
add_exon() Sorry, pasa_asmbl_43955.p1 97134-97279-terminal-2 is invalid.
-recovered pasa_asmbl_43955.p1, terminal, 97134, 97279
-recovered pasa_asmbl_43955.p1, terminal, 97772, 97965
-recovered pasa_asmbl_43955.p1, internal, 94905, 95073
-recovered pasa_asmbl_43955.p1, internal, 95396, 95518
-recovered pasa_asmbl_43955.p1, internal, 95770, 95906
-recovered pasa_asmbl_43955.p1, internal, 96324, 96432
-recovered pasa_asmbl_43955.p1, internal, 96685, 96757
-recovered pasa_asmbl_43955.p1, internal, 97134, 97279
Couldn't classify 161616, 161759
Couldn't classify 166580, 166690
Sorry, prediction pasa_asmbl_43951.p1 fails validation.
(GTC)	 CA	161616-161759	GT	TGG
(ATT)	 AG	164377-164469	GT	AGG
(ATG)	 AG	166580-166690	CG	GAC
-recovered pasa_asmbl_43951.p1, internal, 164377, 164469
Valid prediction for Augustus_model.g7694.t1
Couldn't classify 140685, 140800
Couldn't classify 142958, 143193
Sorry, prediction pasa_asmbl_43952.p1 fails validation.
(ATC)	 AC	140685-140800	GT	AGG
(GGT)	 AG	141131-141246	GT	AGG
(CGG)	 AG	142958-143193	GA	GCG
-recovered pasa_asmbl_43952.p1, internal, 141131, 141246
Valid prediction for snap_scaffold_5-snap.818-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g7692.t1
Valid prediction for snap_scaffold_5-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_11759-T1
Valid prediction for GlimmerHMM_glimmerT_11762-T1
Valid prediction for snap_scaffold_5-snap.807-T1
Valid prediction for Augustus_model.g7701.t1
Valid prediction for snap_scaffold_5-snap.820-T1
Valid prediction for Augustus_model.g7700.t1
Valid prediction for CodingQuarry_transcript_52016-T1
Valid prediction for GlimmerHMM_glimmerT_11757-T1
Valid prediction for GlimmerHMM_glimmerT_11778-T1
Valid prediction for GlimmerHMM_glimmerT_11774-T1
Valid prediction for CodingQuarry_transcript_52017-T1
Couldn't classify 184915, 184962
Sorry, prediction pasa_asmbl_43946.p1 fails validation.
(TCA)	 AG	184915-184962	GT	AGG
(CTG)	 AG	185692-185867	GT	AGG
(GTG)	 AG	186214-186316	GT	AGG
(GGA)	 AG	186960-187027	GT	AGG
(GCT)	 AG	187569-187611	AA	AGA
-recovered pasa_asmbl_43946.p1, terminal, 187569, 187611
-recovered pasa_asmbl_43946.p1, internal, 184915, 184962
-recovered pasa_asmbl_43946.p1, internal, 185692, 185867
-recovered pasa_asmbl_43946.p1, internal, 186214, 186316
-recovered pasa_asmbl_43946.p1, internal, 186960, 187027
Couldn't classify 60278, 60364
Sorry, prediction pasa_asmbl_43957.p1 fails validation.
(AAC)	 AG	60278-60364	GT	GGG
(AAC)	 AG	60866-60997	GT	GGG
(AGG)	 AG	61270-61424	GT	AGG
(TGC)	 AG	61752-61819	GT	AGG
(GAC)	 AG	62242-62393	GT	AGG
(AGG)	 AG	62969-63069	GT	GTG
(GAT)	 AG	63658-63745	AT	AAA
-recovered pasa_asmbl_43957.p1, terminal, 63658, 63745
-recovered pasa_asmbl_43957.p1, internal, 60278, 60364
-recovered pasa_asmbl_43957.p1, internal, 60866, 60997
-recovered pasa_asmbl_43957.p1, internal, 61270, 61424
-recovered pasa_asmbl_43957.p1, internal, 61752, 61819
-recovered pasa_asmbl_43957.p1, internal, 62242, 62393
-recovered pasa_asmbl_43957.p1, internal, 62969, 63069
Valid prediction for GlimmerHMM_glimmerT_11764-T1
Valid prediction for snap_scaffold_5-snap.829-T1
Valid prediction for snap_scaffold_5-snap.793-T1
Valid prediction for Augustus_model.g7699.t1
Couldn't classify 169799, 169877
Couldn't classify 170860, 170976
Sorry, prediction pasa_asmbl_43949.p1 fails validation.
(GGG)	 AG	169799-169877	GT	AGG
(ACT)	 AG	170286-170464	GT	AGG
(ATC)	 AG	170860-170976	AC	ACA
-recovered pasa_asmbl_43949.p1, internal, 169799, 169877
-recovered pasa_asmbl_43949.p1, internal, 170286, 170464
Valid prediction for GlimmerHMM_glimmerT_11756-T1
Valid prediction for Augustus_model.g7697.t1
Couldn't classify 181380, 181475
Couldn't classify 184578, 184690
Sorry, prediction pasa_asmbl_43947.p2 fails validation.
(GAG)	 AC	181380-181475	GT	TGG
(AAA)	 AG	182206-182308	GT	CAG
(ACA)	 AG	183404-183547	GT	GGG
(CCT)	 AG	184578-184690	AG	TCA
-recovered pasa_asmbl_43947.p2, internal, 182206, 182308
-recovered pasa_asmbl_43947.p2, internal, 183404, 183547
Valid prediction for Augustus_model.g7685.t1
Valid prediction for snap_scaffold_5-snap.814-T1
Valid prediction for snap_scaffold_5-snap.797-T1
Valid prediction for snap_scaffold_5-snap.822-T1
Valid prediction for snap_scaffold_5-snap.806-T1
Valid prediction for snap_scaffold_5-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_11772-T1
Valid prediction for snap_scaffold_5-snap.826-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22806, rend_intergenic: 15270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26433, rend_intergenic: 23297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47699, rend_intergenic: 28628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52439, rend_intergenic: 47963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64385, rend_intergenic: 59999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65415, rend_intergenic: 65000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73601, rend_intergenic: 66136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76879, rend_intergenic: 76780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80137, rend_intergenic: 78023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85626, rend_intergenic: 81546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88700, rend_intergenic: 86688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95896, rend_intergenic: 93447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121160, rend_intergenic: 105043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148553, rend_intergenic: 141147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172321, rend_intergenic: 165748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188255, rend_intergenic: 179172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188501, rend_intergenic: 188399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195867, rend_intergenic: 189851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 185792, rend_intergenic: 185789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199210
-exon list size: 435


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 22806, rend_intergenic: 15270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26433, rend_intergenic: 23297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47699, rend_intergenic: 28628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52439, rend_intergenic: 47963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64385, rend_intergenic: 59999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65415, rend_intergenic: 65000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73601, rend_intergenic: 66136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76879, rend_intergenic: 76780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80137, rend_intergenic: 78023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85626, rend_intergenic: 81546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88700, rend_intergenic: 86688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95896, rend_intergenic: 93447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121160, rend_intergenic: 105043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148553, rend_intergenic: 141147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172321, rend_intergenic: 165748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188255, rend_intergenic: 179172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188501, rend_intergenic: 188399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195867, rend_intergenic: 189851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 185792, rend_intergenic: 185789  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