-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_137

-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: +)Couldn't classify 12948, 13029
Sorry, prediction snap_scaffold_137-snap.3-T1 fails validation.
(ATG)	 CA	9012-9060	GT	AGG
(CGG)	 AG	9355-9515	GT	AGG
(CAC)	 AG	11770-11875	GT	AGG
(GTA)	 AG	12454-12785	GT	AGG
(GTC)	 AG	12948-13029	GT	GGG
-recovered snap_scaffold_137-snap.3-T1, initial, 9012, 9060
-recovered snap_scaffold_137-snap.3-T1, internal, 9355, 9515
-recovered snap_scaffold_137-snap.3-T1, internal, 11770, 11875
-recovered snap_scaffold_137-snap.3-T1, internal, 12454, 12785
-recovered snap_scaffold_137-snap.3-T1, internal, 12948, 13029
Couldn't classify 12948, 12983
Sorry, prediction pasa_asmbl_11735.p1 fails validation.
(ATG)	 GA	8970-9060	GT	AGG
(CGG)	 AG	9355-9515	GT	AGG
(CAC)	 AG	11770-11875	GT	AGG
(GTA)	 AG	12454-12785	GT	AGG
(GTC)	 AG	12948-12983	GC	GGG
-recovered pasa_asmbl_11735.p1, initial, 8970, 9060
-recovered pasa_asmbl_11735.p1, internal, 9355, 9515
-recovered pasa_asmbl_11735.p1, internal, 11770, 11875
-recovered pasa_asmbl_11735.p1, internal, 12454, 12785
-recovered pasa_asmbl_11735.p1, internal, 12948, 12983
Couldn't classify 960, 1278
Sorry, prediction snap_scaffold_137-snap.2-T1 fails validation.
(AGA)	 AG	960-1278	GT	AGG
(GCC)	 AG	3392-3475	GT	AAG
(GCT)	 AG	3963-4032	GT	AGG
(CCT)	 AG	6350-6499	GT	GTG
(AAG)	 AG	6608-6710	GT	AGG
(TGA)	 AG	6994-7071	GT	AGG
(CCG)	 AG	7788-7930	GA	GAG
add_exon() Sorry, snap_scaffold_137-snap.2-T1 6608-6710-terminal-3 is invalid.
-recovered snap_scaffold_137-snap.2-T1, terminal, 6608, 6710
-recovered snap_scaffold_137-snap.2-T1, terminal, 7788, 7930
-recovered snap_scaffold_137-snap.2-T1, internal, 960, 1278
-recovered snap_scaffold_137-snap.2-T1, internal, 3392, 3475
-recovered snap_scaffold_137-snap.2-T1, internal, 3963, 4032
-recovered snap_scaffold_137-snap.2-T1, internal, 6350, 6499
-recovered snap_scaffold_137-snap.2-T1, internal, 6608, 6710
-recovered snap_scaffold_137-snap.2-T1, internal, 6994, 7071
Couldn't classify 12948, 13010
Sorry, prediction GlimmerHMM_glimmerT_59869-T1 fails validation.
(ATG)	 AC	8796-8823	GT	ACG
(CGG)	 AG	9355-9515	GT	AGG
(CAC)	 AG	11770-11875	GT	AGG
(GTA)	 AG	12454-12785	GT	AGG
(GTC)	 AG	12948-13010	GT	CTG
-recovered GlimmerHMM_glimmerT_59869-T1, initial, 8796, 8823
-recovered GlimmerHMM_glimmerT_59869-T1, internal, 9355, 9515
-recovered GlimmerHMM_glimmerT_59869-T1, internal, 11770, 11875
-recovered GlimmerHMM_glimmerT_59869-T1, internal, 12454, 12785
-recovered GlimmerHMM_glimmerT_59869-T1, internal, 12948, 13010
Couldn't classify 12948, 13029
Sorry, prediction Augustus_model.g39659.t1 fails validation.
(ATG)	 CA	9012-9060	GT	AGG
(CGG)	 AG	9355-9515	GT	AGG
(CAC)	 AG	11770-11875	GT	AGG
(GTA)	 AG	12454-12785	GT	AGG
(GTC)	 AG	12948-13029	GT	GGG
-recovered Augustus_model.g39659.t1, initial, 9012, 9060
-recovered Augustus_model.g39659.t1, internal, 9355, 9515
-recovered Augustus_model.g39659.t1, internal, 11770, 11875
-recovered Augustus_model.g39659.t1, internal, 12454, 12785
-recovered Augustus_model.g39659.t1, internal, 12948, 13029

-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: -)Couldn't classify 7328, 7413
Sorry, prediction pasa_asmbl_11733.p1 fails validation.
(ATG)	 GG	5263-5384	GT	AGG
(GTA)	 AG	6070-6178	GT	AGG
(TTT)	 AG	6569-6761	GT	GGG
(GGT)	 AG	7328-7413	GT	AGG
-recovered pasa_asmbl_11733.p1, initial, 5263, 5384
-recovered pasa_asmbl_11733.p1, internal, 6070, 6178
-recovered pasa_asmbl_11733.p1, internal, 6569, 6761
-recovered pasa_asmbl_11733.p1, internal, 7328, 7413
Couldn't classify 9076, 9166
Couldn't classify 10284, 10315
Sorry, prediction pasa_asmbl_11732.p2 fails validation.
(TGG)	 CC	9076-9166	GT	AGG
(TGC)	 AG	9654-9832	GT	AGG
(GAT)	 AG	9996-10068	GT	CGG
(CCA)	 AG	10284-10315	CA	ACC
-recovered pasa_asmbl_11732.p2, internal, 9654, 9832
-recovered pasa_asmbl_11732.p2, internal, 9996, 10068
Couldn't classify 99, 166
Sorry, prediction snap_scaffold_137-snap.4-T1 fails validation.
(TAG)	 AG	99-166	GT	AGG
(TCC)	 AG	359-441	GT	CGG
(AAA)	 AG	523-548	GT	TCG
(GCG)	 AG	599-894	GT	AGG
(CCG)	 AG	1748-1786	GT	CGG
(CCG)	 AG	1827-1865	GT	CGG
(CCG)	 AG	1906-1944	GT	CGG
(CTT)	 AG	2070-2109	GT	CGG
(CCG)	 AG	2152-2191	GT	TGG
(CTT)	 AG	2238-2279	GT	CGG
(ACC)	 AG	2656-2695	GT	CGG
(CCG)	 AG	2736-2778	GT	CGG
(CCG)	 AG	2893-2934	GT	CGG
(CGT)	 AG	3057-3094	GT	CGG
(CCG)	 AG	3566-3789	CA	GAC
-recovered snap_scaffold_137-snap.4-T1, terminal, 3566, 3789
-recovered snap_scaffold_137-snap.4-T1, internal, 99, 166
-recovered snap_scaffold_137-snap.4-T1, internal, 359, 441
-recovered snap_scaffold_137-snap.4-T1, internal, 523, 548
-recovered snap_scaffold_137-snap.4-T1, internal, 599, 894
-recovered snap_scaffold_137-snap.4-T1, internal, 1748, 1786
-recovered snap_scaffold_137-snap.4-T1, internal, 1827, 1865
-recovered snap_scaffold_137-snap.4-T1, internal, 1906, 1944
-recovered snap_scaffold_137-snap.4-T1, internal, 2070, 2109
-recovered snap_scaffold_137-snap.4-T1, internal, 2152, 2191
-recovered snap_scaffold_137-snap.4-T1, internal, 2238, 2279
-recovered snap_scaffold_137-snap.4-T1, internal, 2656, 2695
-recovered snap_scaffold_137-snap.4-T1, internal, 2736, 2778
-recovered snap_scaffold_137-snap.4-T1, internal, 2893, 2934
-recovered snap_scaffold_137-snap.4-T1, internal, 3057, 3094
Couldn't classify 12021, 12161
Sorry, prediction snap_scaffold_137-snap.1-T1 fails validation.
(ATG)	 AG	4995-5011	GT	ACG
(GAT)	 AG	5262-5384	GT	AGG
(GTA)	 AG	6070-6178	GT	AGG
(TTT)	 AG	6569-6953	GT	AGG
(GGT)	 AG	7328-7413	GT	AGG
(AAT)	 AG	8394-8477	GT	ACG
(GAC)	 AG	8886-8908	GT	AAG
(GAC)	 AG	9021-9166	GT	AGG
(TGC)	 AG	9654-9832	GT	AGG
(GAT)	 AG	9996-10068	GT	CGG
(CCA)	 AG	10284-10394	GT	CAG
(GTG)	 AG	12021-12161	GT	GAG
-recovered snap_scaffold_137-snap.1-T1, initial, 4995, 5011
-recovered snap_scaffold_137-snap.1-T1, terminal, 8886, 8908
-recovered snap_scaffold_137-snap.1-T1, internal, 4995, 5011
-recovered snap_scaffold_137-snap.1-T1, internal, 5262, 5384
-recovered snap_scaffold_137-snap.1-T1, internal, 6070, 6178
-recovered snap_scaffold_137-snap.1-T1, internal, 6569, 6953
-recovered snap_scaffold_137-snap.1-T1, internal, 7328, 7413
-recovered snap_scaffold_137-snap.1-T1, internal, 8394, 8477
-recovered snap_scaffold_137-snap.1-T1, internal, 8886, 8908
-recovered snap_scaffold_137-snap.1-T1, internal, 9021, 9166
-recovered snap_scaffold_137-snap.1-T1, internal, 9654, 9832
-recovered snap_scaffold_137-snap.1-T1, internal, 9996, 10068
-recovered snap_scaffold_137-snap.1-T1, internal, 10284, 10394
-recovered snap_scaffold_137-snap.1-T1, internal, 12021, 12161
Couldn't classify 13084, 13106
Sorry, prediction Augustus_model.g39658.t1 fails validation.
(ATG)	 AC	4270-4283	GT	ACG
(AGA)	 AG	5032-5065	GT	CTG
(CTC)	 AG	5218-5384	GT	AGG
(GTA)	 AG	6070-6178	GT	AGG
(TTT)	 AG	6569-6761	GT	GGG
(GGT)	 AG	7328-7413	GT	AGG
(AAT)	 AG	8394-8477	GT	ACG
(GAC)	 AG	8767-8779	GT	TGG
(GAC)	 AG	8886-8898	GT	TGG
(GAC)	 AG	9021-9166	GT	AGG
(TGC)	 AG	9654-9832	GT	AGG
(GAT)	 AG	9996-10068	GT	CGG
(CCA)	 AG	10284-10360	GT	TCG
(TCT)	 AG	10468-10522	GT	TGG
(TAG)	 AG	10748-10828	GT	CAG
(GTG)	 AG	12021-12161	GT	GAG
(AGC)	 AG	13084-13106		CT
-recovered Augustus_model.g39658.t1, initial, 4270, 4283
-recovered Augustus_model.g39658.t1, internal, 5032, 5065
-recovered Augustus_model.g39658.t1, internal, 5218, 5384
-recovered Augustus_model.g39658.t1, internal, 6070, 6178
-recovered Augustus_model.g39658.t1, internal, 6569, 6761
-recovered Augustus_model.g39658.t1, internal, 7328, 7413
-recovered Augustus_model.g39658.t1, internal, 8394, 8477
-recovered Augustus_model.g39658.t1, internal, 8767, 8779
-recovered Augustus_model.g39658.t1, internal, 8886, 8898
-recovered Augustus_model.g39658.t1, internal, 9021, 9166
-recovered Augustus_model.g39658.t1, internal, 9654, 9832
-recovered Augustus_model.g39658.t1, internal, 9996, 10068
-recovered Augustus_model.g39658.t1, internal, 10284, 10360
-recovered Augustus_model.g39658.t1, internal, 10468, 10522
-recovered Augustus_model.g39658.t1, internal, 10748, 10828
-recovered Augustus_model.g39658.t1, internal, 12021, 12161
Valid prediction for GlimmerHMM_glimmerT_59868-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8112, rend_intergenic: 960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13029, rend_intergenic: 9318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 13106
-exon list size: 97


building trellis

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-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 8112, rend_intergenic: 960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13029, rend_intergenic: 9318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support