-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_2377658-2526227

-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 snap_scaffold_24-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_52156-T1
Valid prediction for snap_scaffold_24-snap.559-T1
Couldn't classify 132040, 132082
Sorry, prediction pasa_asmbl_32103.p1 fails validation.
(AAG)	 CG	132040-132082	GT	GGG
(GCT)	 AG	132704-132906	GT	TGG
(GGT)	 AG	133530-133751	GT	TGG
(AGT)	 AG	133882-133993	GT	TGG
(ATG)	 AG	134223-134304	GT	AGG
(GGA)	 AG	134613-134709	GT	TGG
(GAC)	 AG	135031-135103	GT	ACG
(TGC)	 AG	135473-135549	GT	AGG
(ATC)	 AG	135834-136002	GT	TGG
(GCC)	 AG	136189-136259	GT	AGG
(CAA)	 AG	136415-136504	GT	TGG
(ATG)	 AG	137018-137110	GT	AGG
(GGC)	 AG	137410-137496	GA	GAG
add_exon() Sorry, pasa_asmbl_32103.p1 134223-134304-initial-1 is invalid.
-recovered pasa_asmbl_32103.p1, initial, 134223, 134304
-recovered pasa_asmbl_32103.p1, initial, 137018, 137110
-recovered pasa_asmbl_32103.p1, terminal, 137410, 137496
-recovered pasa_asmbl_32103.p1, internal, 132704, 132906
-recovered pasa_asmbl_32103.p1, internal, 133530, 133751
-recovered pasa_asmbl_32103.p1, internal, 133882, 133993
-recovered pasa_asmbl_32103.p1, internal, 134223, 134304
-recovered pasa_asmbl_32103.p1, internal, 134613, 134709
-recovered pasa_asmbl_32103.p1, internal, 135031, 135103
-recovered pasa_asmbl_32103.p1, internal, 135473, 135549
-recovered pasa_asmbl_32103.p1, internal, 135834, 136002
-recovered pasa_asmbl_32103.p1, internal, 136189, 136259
-recovered pasa_asmbl_32103.p1, internal, 136415, 136504
-recovered pasa_asmbl_32103.p1, internal, 137018, 137110
Valid prediction for snap_scaffold_24-snap.550-T1
Valid prediction for GlimmerHMM_glimmerT_52154-T1
Valid prediction for snap_scaffold_24-snap.543-T1
Valid prediction for snap_scaffold_24-snap.546-T1
Valid prediction for snap_scaffold_24-snap.556-T1
Valid prediction for snap_scaffold_24-snap.549-T1
Valid prediction for HiQ_model.g34754.t1
Valid prediction for CodingQuarry_transcript_37250-T1
Couldn't classify 20096, 20299
Sorry, prediction pasa_asmbl_32095.p1 fails validation.
(TGT)	 GC	20096-20299	GT	TTG
(GAT)	 AG	21019-21069	GT	AGG
(CAA)	 AG	21411-21472	GT	AGG
(GCC)	 AG	21727-21808	GT	ACG
(TCC)	 AG	24253-24325	GT	AGG
(TGA)	 AG	24710-24789	TT	GAT
-recovered pasa_asmbl_32095.p1, terminal, 24710, 24789
-recovered pasa_asmbl_32095.p1, internal, 21019, 21069
-recovered pasa_asmbl_32095.p1, internal, 21411, 21472
-recovered pasa_asmbl_32095.p1, internal, 21727, 21808
-recovered pasa_asmbl_32095.p1, internal, 24253, 24325
Valid prediction for HiQ_model.g34748.t1
Valid prediction for snap_scaffold_24-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_52149-T1
Valid prediction for Augustus_model.g34749.t1
Valid prediction for GlimmerHMM_glimmerT_52150-T1
Valid prediction for CodingQuarry_transcript_37251-T1
Valid prediction for snap_scaffold_24-snap.562-T1
Valid prediction for GlimmerHMM_glimmerT_52148-T1
Valid prediction for snap_scaffold_24-snap.575-T1
Valid prediction for Augustus_model.g34750.t1
Valid prediction for snap_scaffold_24-snap.572-T1
Valid prediction for snap_scaffold_24-snap.554-T1
Valid prediction for snap_scaffold_24-snap.569-T1
Valid prediction for snap_scaffold_24-snap.555-T1
Valid prediction for GlimmerHMM_glimmerT_52140-T1
Valid prediction for snap_scaffold_24-snap.561-T1
Valid prediction for pasa_asmbl_32096.p1
Valid prediction for snap_scaffold_24-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_52145-T1
Valid prediction for snap_scaffold_24-snap.563-T1
Valid prediction for HiQ_model.g34745.t1
Valid prediction for snap_scaffold_24-snap.542-T1
Valid prediction for snap_scaffold_24-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_52146-T1
Valid prediction for CodingQuarry_transcript_37249-T1
Valid prediction for snap_scaffold_24-snap.558-T1
Valid prediction for GlimmerHMM_glimmerT_52152-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_24-snap.551-T1
Couldn't classify 142219, 142530
Couldn't classify 144327, 144407
Sorry, prediction pasa_asmbl_33241.p1 fails validation.
(GCC)	 TC	142219-142530	GT	AGG
(AAG)	 AG	143147-143299	GT	TGG
(TTC)	 AG	143612-143734	GT	AGG
(AAA)	 AG	144125-144214	GT	AGG
(GTT)	 AG	144327-144407	GG	CAG
-recovered pasa_asmbl_33241.p1, internal, 143147, 143299
-recovered pasa_asmbl_33241.p1, internal, 143612, 143734
-recovered pasa_asmbl_33241.p1, internal, 144125, 144214
Couldn't classify 2127, 2186
Sorry, prediction pasa_asmbl_32792.p1 fails validation.
(GAG)	 GT	2127-2186	GT	GGG
(AAG)	 AG	2703-2775	GT	AGG
(CCT)	 AG	3223-3366	GT	TGG
(GTG)	 AG	3696-3829	GT	AGG
(CAT)	 AG	4109-4267	GT	ACG
(ATT)	 AG	4520-4623	GT	AGG
(GAT)	 AG	4964-5097	GT	AGG
(AAC)	 AG	5374-5421	GT	GCG
(CCT)	 AG	6825-7018	AG	AGA
-recovered pasa_asmbl_32792.p1, terminal, 6825, 7018
-recovered pasa_asmbl_32792.p1, internal, 2703, 2775
-recovered pasa_asmbl_32792.p1, internal, 3223, 3366
-recovered pasa_asmbl_32792.p1, internal, 3696, 3829
-recovered pasa_asmbl_32792.p1, internal, 4109, 4267
-recovered pasa_asmbl_32792.p1, internal, 4520, 4623
-recovered pasa_asmbl_32792.p1, internal, 4964, 5097
-recovered pasa_asmbl_32792.p1, internal, 5374, 5421
Valid prediction for HiQ_model.g34747.t1
Valid prediction for snap_scaffold_24-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_52139-T1
Valid prediction for HiQ_model.g34751.t1
Valid prediction for CodingQuarry_transcript_37255-T1
Couldn't classify 131052, 131071
Couldn't classify 135737, 135784
Sorry, prediction pasa_asmbl_32780.p1 fails validation.
(AGT)	 AC	131052-131071	GT	AAG
(GAA)	 AG	131236-131329	GT	TGG
(TGT)	 AG	131696-131787	GT	CAG
(TGT)	 AG	131920-131974	GT	AGG
(GCT)	 AG	132327-132454	GT	AGG
(GTT)	 AG	133344-133425	GT	AAG
(GCA)	 AG	134270-134418	GT	ATG
(GAC)	 AG	134988-135150	GT	TGG
(GAC)	 AG	135737-135784	AC	CCA
-recovered pasa_asmbl_32780.p1, internal, 131236, 131329
-recovered pasa_asmbl_32780.p1, internal, 131696, 131787
-recovered pasa_asmbl_32780.p1, internal, 131920, 131974
-recovered pasa_asmbl_32780.p1, internal, 132327, 132454
-recovered pasa_asmbl_32780.p1, internal, 133344, 133425
-recovered pasa_asmbl_32780.p1, internal, 134270, 134418
-recovered pasa_asmbl_32780.p1, internal, 134988, 135150
Valid prediction for Augustus_model.g34744.t1
Valid prediction for snap_scaffold_24-snap.552-T1
Valid prediction for GlimmerHMM_glimmerT_52144-T1
Valid prediction for snap_scaffold_24-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_52151-T1
Valid prediction for GlimmerHMM_glimmerT_52142-T1
Valid prediction for CodingQuarry_transcript_37248-T1
Valid prediction for snap_scaffold_24-snap.574-T1
Valid prediction for CodingQuarry_transcript_37253-T1
Valid prediction for CodingQuarry_transcript_37254-T1
Valid prediction for GlimmerHMM_glimmerT_52147-T1
Valid prediction for snap_scaffold_24-snap.553-T1
Couldn't classify 142186, 142215
Sorry, prediction pasa_asmbl_33288.p1 fails validation.
(ATG)	 TA	140347-140454	GT	AGG
(GTG)	 AG	141393-141499	GT	AGG
(CAT)	 AG	141597-141750	GT	AGG
(GTG)	 AG	142186-142215	AT	CCA
-recovered pasa_asmbl_33288.p1, initial, 140347, 140454
-recovered pasa_asmbl_33288.p1, internal, 141393, 141499
-recovered pasa_asmbl_33288.p1, internal, 141597, 141750
Valid prediction for Augustus_model.g34752.t1
Valid prediction for GlimmerHMM_glimmerT_52143-T1
Valid prediction for snap_scaffold_24-snap.544-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52155-T1
Valid prediction for CodingQuarry_transcript_37252-T1
Couldn't classify 22201, 22539
Sorry, prediction pasa_asmbl_33285.p1 fails validation.
(CTC)	 CG	22201-22539	CT	GTC
Valid prediction for Augustus_model.g34746.t1
Valid prediction for snap_scaffold_24-snap.547-T1
Couldn't classify 136603, 136674
Sorry, prediction pasa_asmbl_32779.p1 fails validation.
(CTG)	 GG	136603-136674	GT	AGG
(GCT)	 AG	137598-137736	GT	CGG
(CCT)	 AG	138149-138281	GT	TGG
(GTG)	 AG	138930-139032	TG	GAT
-recovered pasa_asmbl_32779.p1, terminal, 138930, 139032
-recovered pasa_asmbl_32779.p1, internal, 137598, 137736
-recovered pasa_asmbl_32779.p1, internal, 138149, 138281
Valid prediction for snap_scaffold_24-snap.565-T1
Valid prediction for snap_scaffold_24-snap.573-T1
Valid prediction for snap_scaffold_24-snap.566-T1
Valid prediction for GlimmerHMM_glimmerT_52137-T1
Couldn't classify 104963, 105201
Sorry, prediction pasa_asmbl_32784.p1 fails validation.
(CAG)	 TA	104963-105201	GT	AGG
(GAA)	 AG	105578-105866	CT	GAC
-recovered pasa_asmbl_32784.p1, terminal, 105578, 105866
Valid prediction for GlimmerHMM_glimmerT_52141-T1
Couldn't classify 130912, 130940
Sorry, prediction pasa_asmbl_32782.p1 fails validation.
(ATG)	 GA	129107-129204	GT	ACG
(GTT)	 AG	129355-129417	GC	AGG
(GAA)	 AG	129558-129590	GT	TGG
(GTA)	 AG	129739-129763	GT	AGG
(CTG)	 AG	130561-130693	GT	AGG
(AGC)	 AG	130912-130940	GT	GGG
-recovered pasa_asmbl_32782.p1, initial, 129107, 129204
-recovered pasa_asmbl_32782.p1, internal, 129355, 129417
-recovered pasa_asmbl_32782.p1, internal, 129558, 129590
-recovered pasa_asmbl_32782.p1, internal, 129739, 129763
-recovered pasa_asmbl_32782.p1, internal, 130561, 130693
-recovered pasa_asmbl_32782.p1, internal, 130912, 130940
Valid prediction for GlimmerHMM_glimmerT_52153-T1
Valid prediction for Augustus_model.g34753.t1
Valid prediction for snap_scaffold_24-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_52138-T1
Valid prediction for HiQ_model.g34755.t1
Valid prediction for snap_scaffold_24-snap.557-T1
Valid prediction for snap_scaffold_24-snap.560-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18861, rend_intergenic: 9539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32126, rend_intergenic: 26478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38595, rend_intergenic: 32206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46812, rend_intergenic: 42234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62711, rend_intergenic: 59458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81613, rend_intergenic: 63193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93780, rend_intergenic: 86810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118696, rend_intergenic: 101838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125809, rend_intergenic: 118750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126254, rend_intergenic: 125996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130284, rend_intergenic: 126771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137875, rend_intergenic: 132721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141925, rend_intergenic: 139048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148570
-exon list size: 334


building trellis

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31.8    
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32.4    
32.7    
33.0    
33.3    
33.6    
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34.8    
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35.4    
35.7    
36.0    
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38.1    
38.4    
38.7    
39.0    
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39.6    
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40.8    
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42.6    
42.9    
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44.3    
44.6    
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48.2    
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97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 18861, rend_intergenic: 9539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32126, rend_intergenic: 26478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38595, rend_intergenic: 32206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46812, rend_intergenic: 42234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62711, rend_intergenic: 59458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81613, rend_intergenic: 63193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93780, rend_intergenic: 86810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118696, rend_intergenic: 101838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125809, rend_intergenic: 118750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126254, rend_intergenic: 125996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130284, rend_intergenic: 126771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137875, rend_intergenic: 132721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141925, rend_intergenic: 139048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support