-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_11504286-11685760

-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_34308-T1
Valid prediction for GlimmerHMM_glimmerT_50285-T1
Valid prediction for GlimmerHMM_glimmerT_50284-T1
Valid prediction for GlimmerHMM_glimmerT_50286-T1
Couldn't classify 44306, 44449
Sorry, prediction pasa_asmbl_30491.p1 fails validation.
(TCA)	 GC	44306-44449	GT	AGG
(GTT)	 AG	45115-45272	GT	AGG
(GTG)	 AG	45416-45620	GT	AGG
(GGT)	 AG	46364-46435	GT	AGG
(TAT)	 AG	48426-48589	GT	AGG
(AGG)	 AG	48964-49038	GT	AGG
(GAT)	 AG	49314-49368	CT	AGC
-recovered pasa_asmbl_30491.p1, terminal, 49314, 49368
-recovered pasa_asmbl_30491.p1, internal, 45115, 45272
-recovered pasa_asmbl_30491.p1, internal, 45416, 45620
-recovered pasa_asmbl_30491.p1, internal, 46364, 46435
-recovered pasa_asmbl_30491.p1, internal, 48426, 48589
-recovered pasa_asmbl_30491.p1, internal, 48964, 49038
Valid prediction for GlimmerHMM_glimmerT_50293-T1
Couldn't classify 14162, 14183
Sorry, prediction pasa_asmbl_30398.p1 fails validation.
(TCT)	 CT	14162-14183	GT	AGG
(GAT)	 AG	14459-14589	GT	CGG
(GCA)	 AG	17017-17197	GT	GGG
(CCC)	 AG	17409-17506	CC	GAC
-recovered pasa_asmbl_30398.p1, terminal, 17409, 17506
-recovered pasa_asmbl_30398.p1, internal, 14459, 14589
-recovered pasa_asmbl_30398.p1, internal, 17017, 17197
Valid prediction for GlimmerHMM_glimmerT_50275-T1
Valid prediction for pasa_asmbl_30399.p1
Valid prediction for GlimmerHMM_glimmerT_50274-T1
Couldn't classify 35907, 36350
Sorry, prediction pasa_asmbl_30453.p1 fails validation.
(ATG)	 GG	35907-36350	CC	ACC
Valid prediction for GlimmerHMM_glimmerT_50277-T1
Couldn't classify 44029, 44141
Sorry, prediction pasa_asmbl_30405.p1 fails validation.
(ATG)	 AG	39941-39959	GT	AGG
(ATA)	 AG	40670-40830	GT	AGG
(TCG)	 AG	42330-42508	GT	AGG
(GAC)	 AG	42804-42882	GT	TGG
(ATG)	 AG	43342-43570	GT	AGG
(GTT)	 AG	44029-44141	TC	CCT
-recovered pasa_asmbl_30405.p1, initial, 39941, 39959
-recovered pasa_asmbl_30405.p1, initial, 43342, 43570
add_exon() Sorry, pasa_asmbl_30405.p1 39941-39959-terminal-3 is invalid.
-recovered pasa_asmbl_30405.p1, terminal, 39941, 39959
-recovered pasa_asmbl_30405.p1, internal, 39941, 39959
-recovered pasa_asmbl_30405.p1, internal, 40670, 40830
-recovered pasa_asmbl_30405.p1, internal, 42330, 42508
-recovered pasa_asmbl_30405.p1, internal, 42804, 42882
-recovered pasa_asmbl_30405.p1, internal, 43342, 43570
Valid prediction for snap_scaffold_22-snap.2363-T1
Valid prediction for snap_scaffold_22-snap.2355-T1
Valid prediction for snap_scaffold_22-snap.2336-T1
Couldn't classify 36414, 36509
Couldn't classify 37005, 37123
Sorry, prediction pasa_asmbl_30404.p1 fails validation.
(TTC)	 CT	36414-36509	GT	AGG
(GGT)	 AG	36673-36799	GT	AGG
(CTC)	 AG	37005-37123	AG	CCA
-recovered pasa_asmbl_30404.p1, internal, 36673, 36799
Valid prediction for snap_scaffold_22-snap.2362-T1
Valid prediction for GlimmerHMM_glimmerT_50289-T1
Valid prediction for CodingQuarry_transcript_34309-T1
Valid prediction for snap_scaffold_22-snap.2352-T1
Valid prediction for CodingQuarry_transcript_34307-T1
Valid prediction for snap_scaffold_22-snap.2350-T1
Valid prediction for snap_scaffold_22-snap.2346-T1
Couldn't classify 124667, 124716
Couldn't classify 127250, 127415
Sorry, prediction pasa_asmbl_30411.p1 fails validation.
(CAG)	 TG	124667-124716	GT	AGG
(GAT)	 AG	126103-126224	GT	TGG
(ACC)	 AG	126883-126961	GT	CGG
(TAT)	 AG	127250-127415	GA	GGG
-recovered pasa_asmbl_30411.p1, internal, 126103, 126224
-recovered pasa_asmbl_30411.p1, internal, 126883, 126961
Valid prediction for GlimmerHMM_glimmerT_50282-T1
Valid prediction for GlimmerHMM_glimmerT_50288-T1
Valid prediction for snap_scaffold_22-snap.2353-T1
Valid prediction for snap_scaffold_22-snap.2359-T1
Valid prediction for snap_scaffold_22-snap.2358-T1
Valid prediction for GlimmerHMM_glimmerT_50273-T1
Valid prediction for snap_scaffold_22-snap.2335-T1
Couldn't classify 35352, 35876
Sorry, prediction pasa_asmbl_30403.p1 fails validation.
(AGA)	 AG	35352-35876	AG	AGA
Valid prediction for snap_scaffold_22-snap.2339-T1
Valid prediction for GlimmerHMM_glimmerT_50290-T1
Couldn't classify 34564, 34997
Sorry, prediction pasa_asmbl_30402.p1 fails validation.
(ATG)	 TG	32273-32306	GT	CGG
(ACT)	 AG	32446-32552	GT	AGG
(GAA)	 AG	32650-32717	GT	AGG
(GCC)	 AG	32802-32937	GT	AGG
(TGT)	 AG	33263-33334	GT	AGG
(AAC)	 AG	33477-33624	GT	GTG
(TCC)	 AG	33719-33838	GT	AGG
(TGT)	 AG	34564-34997	TA	CGT
-recovered pasa_asmbl_30402.p1, initial, 32273, 32306
-recovered pasa_asmbl_30402.p1, internal, 32446, 32552
-recovered pasa_asmbl_30402.p1, internal, 32650, 32717
-recovered pasa_asmbl_30402.p1, internal, 32802, 32937
-recovered pasa_asmbl_30402.p1, internal, 33263, 33334
-recovered pasa_asmbl_30402.p1, internal, 33477, 33624
-recovered pasa_asmbl_30402.p1, internal, 33719, 33838
Valid prediction for Augustus_model.g33554.t1
Couldn't classify 4585, 4790
Couldn't classify 5843, 5943
Sorry, prediction pasa_asmbl_30532.p1 fails validation.
(CTG)	 GC	4585-4790	GT	AGG
(ATT)	 AG	4959-5049	GT	GGG
(GGG)	 AG	5439-5529	GT	AGG
(GGT)	 AG	5843-5943	TG	GGT
-recovered pasa_asmbl_30532.p1, internal, 4959, 5049
-recovered pasa_asmbl_30532.p1, internal, 5439, 5529
Valid prediction for snap_scaffold_22-snap.2341-T1
Valid prediction for GlimmerHMM_glimmerT_50276-T1
Valid prediction for snap_scaffold_22-snap.2333-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_22-snap.2361-T1
Valid prediction for GlimmerHMM_glimmerT_50296-T1
Couldn't classify 91705, 91764
Couldn't classify 93156, 93431
Sorry, prediction pasa_asmbl_29726.p1 fails validation.
(CCC)	 CC	91705-91764	GT	CGG
(GGC)	 AG	93156-93431	TA	TGT
Valid prediction for snap_scaffold_22-snap.2348-T1
Valid prediction for pasa_asmbl_29687.p1
Valid prediction for GlimmerHMM_glimmerT_50283-T1
Valid prediction for snap_scaffold_22-snap.2360-T1
Valid prediction for snap_scaffold_22-snap.2343-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_34311-T1
Valid prediction for snap_scaffold_22-snap.2345-T1
Valid prediction for snap_scaffold_22-snap.2357-T1
Valid prediction for snap_scaffold_22-snap.2344-T1
Valid prediction for snap_scaffold_22-snap.2367-T1
Valid prediction for snap_scaffold_22-snap.2338-T1
Valid prediction for snap_scaffold_22-snap.2332-T1
Valid prediction for CodingQuarry_transcript_34313-T1
Valid prediction for snap_scaffold_22-snap.2351-T1
Valid prediction for snap_scaffold_22-snap.2334-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50295-T1
Valid prediction for GlimmerHMM_glimmerT_50287-T1
Couldn't classify 114818, 114916
Sorry, prediction pasa_asmbl_29683.p1 fails validation.
(ATT)	 AC	114818-114916	GT	TGG
(GGA)	 AG	115554-115703	GT	ACG
(GTG)	 AG	117547-117740	GT	GGG
(GCC)	 AG	117998-118156	GT	GAG
(GGA)	 AG	118358-118463	CC	GAC
-recovered pasa_asmbl_29683.p1, terminal, 118358, 118463
-recovered pasa_asmbl_29683.p1, internal, 115554, 115703
-recovered pasa_asmbl_29683.p1, internal, 117547, 117740
-recovered pasa_asmbl_29683.p1, internal, 117998, 118156
Valid prediction for pasa_asmbl_29684.p1
Couldn't classify 35351, 35749
Couldn't classify 36254, 36391
Sorry, prediction pasa_asmbl_29693.p1 fails validation.
(GAA)	 AG	35351-35749	GT	CGG
(GTA)	 AG	35903-35992	GT	AGG
(GAT)	 AG	36254-36391	GT	AGG
-recovered pasa_asmbl_29693.p1, internal, 35351, 35749
-recovered pasa_asmbl_29693.p1, internal, 35903, 35992
-recovered pasa_asmbl_29693.p1, internal, 36254, 36391
Valid prediction for snap_scaffold_22-snap.2337-T1
Valid prediction for snap_scaffold_22-snap.2364-T1
Valid prediction for snap_scaffold_22-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_50279-T1
Valid prediction for GlimmerHMM_glimmerT_50291-T1
Valid prediction for snap_scaffold_22-snap.2349-T1
Valid prediction for snap_scaffold_22-snap.2368-T1
Valid prediction for snap_scaffold_22-snap.2340-T1
Valid prediction for snap_scaffold_22-snap.2342-T1
Valid prediction for CodingQuarry_transcript_34310-T1
Valid prediction for snap_scaffold_22-snap.2354-T1
Valid prediction for snap_scaffold_22-snap.2369-T1
Valid prediction for snap_scaffold_22-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_50294-T1
Valid prediction for GlimmerHMM_glimmerT_50280-T1
Valid prediction for GlimmerHMM_glimmerT_50292-T1
Valid prediction for CodingQuarry_transcript_34314-T1
Valid prediction for snap_scaffold_22-snap.2347-T1
Valid prediction for GlimmerHMM_glimmerT_50281-T1
Couldn't classify 42055, 42122
Sorry, prediction pasa_asmbl_29691.p1 fails validation.
(CAG)	 TA	42055-42122	GT	AAG
(AGC)	 AG	43079-43229	GT	AGG
(GAC)	 AG	43563-43686	GT	GGG
(ACA)	 AG	43778-43905	AT	AAA
-recovered pasa_asmbl_29691.p1, terminal, 43778, 43905
-recovered pasa_asmbl_29691.p1, internal, 43079, 43229
-recovered pasa_asmbl_29691.p1, internal, 43563, 43686
Valid prediction for GlimmerHMM_glimmerT_50278-T1
Couldn't classify 33608, 33842
Couldn't classify 35140, 35185
Sorry, prediction pasa_asmbl_29737.p1 fails validation.
(TCC)	 GG	33608-33842	GT	AGG
(GCT)	 AG	34083-34197	GT	AGG
(GGT)	 AG	35140-35185	TC	CAT
-recovered pasa_asmbl_29737.p1, internal, 34083, 34197

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18307, rend_intergenic: 2468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26874, rend_intergenic: 19879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31024, rend_intergenic: 30163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39423, rend_intergenic: 31567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50242, rend_intergenic: 39511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63906, rend_intergenic: 57503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71559, rend_intergenic: 65882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81383, rend_intergenic: 71586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82538, rend_intergenic: 81606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85928, rend_intergenic: 84619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91229, rend_intergenic: 86605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104309, rend_intergenic: 94190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107317, rend_intergenic: 105173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126523, rend_intergenic: 110090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133859, rend_intergenic: 126533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135929, rend_intergenic: 133944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153203, rend_intergenic: 137593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181475
-exon list size: 385


building trellis

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33.3    
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35.7    
35.9    
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36.4    
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39.3    
39.5    
39.8    
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40.3    
40.6    
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41.3    
41.6    
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42.9    
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99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 18307, rend_intergenic: 2468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26874, rend_intergenic: 19879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31024, rend_intergenic: 30163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39423, rend_intergenic: 31567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50242, rend_intergenic: 39511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63906, rend_intergenic: 57503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71559, rend_intergenic: 65882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81383, rend_intergenic: 71586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82538, rend_intergenic: 81606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85928, rend_intergenic: 84619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91229, rend_intergenic: 86605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104309, rend_intergenic: 94190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107317, rend_intergenic: 105173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126523, rend_intergenic: 110090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133859, rend_intergenic: 126533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135929, rend_intergenic: 133944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153203, rend_intergenic: 137593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support