-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_15917462-16088476

-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 132021, 132036
Sorry, prediction pasa_asmbl_12666.p1 fails validation.
(GAG)	 GG	132021-132036	GT	AGG
(GTG)	 AG	132207-132256	GT	CTG
(GTG)	 AG	132848-132967	GT	CGG
(GAC)	 AG	133183-133268	GT	AAG
(GGA)	 AG	133363-133407	GT	ATG
(AGT)	 AG	133736-133827	GT	TGG
(TCA)	 AG	134190-134310	GT	AGG
(TGA)	 AG	134584-134665	GT	TGG
(ATG)	 AG	135557-135616	GT	AGG
(CTC)	 AG	135708-135865	GT	AAG
(GTT)	 AG	136266-136327	GT	AGG
(AGC)	 AG	136442-136899	GT	CGG
(TTC)	 AG	138733-138810	GT	AGG
(CAC)	 AG	138934-139059	GT	AGG
(GAA)	 AG	139257-139313	CC	GAC
-recovered pasa_asmbl_12666.p1, initial, 135557, 135616
-recovered pasa_asmbl_12666.p1, terminal, 139257, 139313
-recovered pasa_asmbl_12666.p1, internal, 132207, 132256
-recovered pasa_asmbl_12666.p1, internal, 132848, 132967
-recovered pasa_asmbl_12666.p1, internal, 133183, 133268
-recovered pasa_asmbl_12666.p1, internal, 133363, 133407
-recovered pasa_asmbl_12666.p1, internal, 133736, 133827
-recovered pasa_asmbl_12666.p1, internal, 134190, 134310
-recovered pasa_asmbl_12666.p1, internal, 134584, 134665
-recovered pasa_asmbl_12666.p1, internal, 135557, 135616
-recovered pasa_asmbl_12666.p1, internal, 135708, 135865
-recovered pasa_asmbl_12666.p1, internal, 136266, 136327
-recovered pasa_asmbl_12666.p1, internal, 136442, 136899
-recovered pasa_asmbl_12666.p1, internal, 138733, 138810
-recovered pasa_asmbl_12666.p1, internal, 138934, 139059
Couldn't classify 22944, 23003
Couldn't classify 27438, 27548
Sorry, prediction pasa_asmbl_12651.p1 fails validation.
(GAG)	 CA	22944-23003	GT	AGG
(CGC)	 AG	25251-25315	GT	AGG
(GAA)	 AG	25533-25599	GT	AGG
(GGG)	 AG	25779-25897	GT	AGG
(AGA)	 AG	26580-26660	GT	AGG
(GCA)	 AG	26841-26953	GT	CGG
(ATA)	 AG	27159-27307	GT	GGG
(AAC)	 AG	27438-27548	GG	TAG
-recovered pasa_asmbl_12651.p1, internal, 25251, 25315
-recovered pasa_asmbl_12651.p1, internal, 25533, 25599
-recovered pasa_asmbl_12651.p1, internal, 25779, 25897
-recovered pasa_asmbl_12651.p1, internal, 26580, 26660
-recovered pasa_asmbl_12651.p1, internal, 26841, 26953
-recovered pasa_asmbl_12651.p1, internal, 27159, 27307
Couldn't classify 28499, 28579
Sorry, prediction pasa_asmbl_12656.p2 fails validation.
(TCA)	 CT	28499-28579	GT	CTG
(GAC)	 AG	29237-29308	GT	CTG
(AAC)	 AG	29572-29726	GT	AAG
(AGC)	 AG	30112-30190	GC	AGG
-recovered pasa_asmbl_12656.p2, terminal, 30112, 30190
-recovered pasa_asmbl_12656.p2, internal, 29237, 29308
-recovered pasa_asmbl_12656.p2, internal, 29572, 29726
-recovered pasa_asmbl_12656.p2, internal, 30112, 30190
Valid prediction for Augustus_model.g23643.t1
Valid prediction for Augustus_model.g23648.t1
Valid prediction for CodingQuarry_transcript_15972-T1
Valid prediction for snap_scaffold_14-snap.3345-T1
Valid prediction for GlimmerHMM_glimmerT_35387-T1
Valid prediction for snap_scaffold_14-snap.3336-T1
Couldn't classify 106353, 106436
Sorry, prediction Augustus_model.g23651.t1 fails validation.
(ATG)	 CA	105846-106134	GT	CGG
(AGT)	 AG	106353-106436	GT	GGG
-recovered Augustus_model.g23651.t1, initial, 105846, 106134
-recovered Augustus_model.g23651.t1, internal, 106353, 106436
Valid prediction for GlimmerHMM_glimmerT_35373-T1
Valid prediction for Augustus_model.g23647.t1
Valid prediction for snap_scaffold_14-snap.3355-T1
Valid prediction for snap_scaffold_14-snap.3332-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35367-T1
Valid prediction for Augustus_model.g23646.t1
Valid prediction for GlimmerHMM_glimmerT_35362-T1
Valid prediction for Augustus_model.g23650.t1
Couldn't classify 6646, 6747
Sorry, prediction pasa_asmbl_12650.p2 fails validation.
(GTC)	 CA	6646-6747	GT	AGG
(ATG)	 AG	6940-7048	GT	AGG
(GCA)	 AG	8396-8520	GT	AGG
(ATT)	 AG	8810-9007	TC	AGT
-recovered pasa_asmbl_12650.p2, initial, 6940, 7048
-recovered pasa_asmbl_12650.p2, terminal, 8810, 9007
-recovered pasa_asmbl_12650.p2, internal, 6940, 7048
-recovered pasa_asmbl_12650.p2, internal, 8396, 8520
Valid prediction for snap_scaffold_14-snap.3331-T1
Valid prediction for GlimmerHMM_glimmerT_35368-T1
Valid prediction for snap_scaffold_14-snap.3352-T1
Valid prediction for GlimmerHMM_glimmerT_35382-T1
Valid prediction for GlimmerHMM_glimmerT_35365-T1
Valid prediction for snap_scaffold_14-snap.3344-T1
Valid prediction for GlimmerHMM_glimmerT_35364-T1
Valid prediction for snap_scaffold_14-snap.3348-T1
Valid prediction for snap_scaffold_14-snap.3350-T1
Couldn't classify 108600, 108689
Sorry, prediction pasa_asmbl_12659.p1 fails validation.
(ATG)	 AG	105840-106134	GT	CGG
(AGT)	 AG	106353-106436	GT	GGG
(TGA)	 AG	106633-106721	GT	AGG
(CTA)	 AG	107223-107408	GT	AGG
(GTA)	 AG	107871-108008	GT	AGG
(GGT)	 AG	108600-108689	AT	GGA
-recovered pasa_asmbl_12659.p1, initial, 105840, 106134
-recovered pasa_asmbl_12659.p1, internal, 105840, 106134
-recovered pasa_asmbl_12659.p1, internal, 106353, 106436
-recovered pasa_asmbl_12659.p1, internal, 106633, 106721
-recovered pasa_asmbl_12659.p1, internal, 107223, 107408
-recovered pasa_asmbl_12659.p1, internal, 107871, 108008
Valid prediction for GlimmerHMM_glimmerT_35372-T1
Valid prediction for snap_scaffold_14-snap.3361-T1
Valid prediction for GlimmerHMM_glimmerT_35379-T1
Valid prediction for snap_scaffold_14-snap.3327-T1
Valid prediction for GlimmerHMM_glimmerT_35361-T1
Valid prediction for snap_scaffold_14-snap.3325-T1
Valid prediction for GlimmerHMM_glimmerT_35369-T1
Valid prediction for snap_scaffold_14-snap.3363-T1
Valid prediction for snap_scaffold_14-snap.3359-T1
Valid prediction for snap_scaffold_14-snap.3354-T1
Valid prediction for HiQ_model.g23645.t1
Valid prediction for GlimmerHMM_glimmerT_35381-T1
Valid prediction for snap_scaffold_14-snap.3347-T1
Valid prediction for GlimmerHMM_glimmerT_35375-T1
Valid prediction for GlimmerHMM_glimmerT_35380-T1
Valid prediction for GlimmerHMM_glimmerT_35371-T1
Valid prediction for Augustus_model.g23644.t1
Valid prediction for GlimmerHMM_glimmerT_35383-T1
Valid prediction for snap_scaffold_14-snap.3341-T1
Valid prediction for GlimmerHMM_glimmerT_35377-T1
Valid prediction for pasa_asmbl_12665.p1
Valid prediction for snap_scaffold_14-snap.3362-T1
Valid prediction for snap_scaffold_14-snap.3329-T1
Valid prediction for GlimmerHMM_glimmerT_35378-T1
Valid prediction for snap_scaffold_14-snap.3338-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_14-snap.3364-T1
Valid prediction for snap_scaffold_14-snap.3342-T1
Valid prediction for snap_scaffold_14-snap.3346-T1
Valid prediction for GlimmerHMM_glimmerT_35385-T1
Valid prediction for GlimmerHMM_glimmerT_35374-T1
Valid prediction for snap_scaffold_14-snap.3326-T1
Valid prediction for snap_scaffold_14-snap.3339-T1
Valid prediction for snap_scaffold_14-snap.3351-T1
Valid prediction for GlimmerHMM_glimmerT_35370-T1
Valid prediction for HiQ_model.g23649.t1
Valid prediction for snap_scaffold_14-snap.3330-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35376-T1
Valid prediction for snap_scaffold_14-snap.3357-T1
Valid prediction for snap_scaffold_14-snap.3353-T1
Valid prediction for GlimmerHMM_glimmerT_35386-T1
Valid prediction for snap_scaffold_14-snap.3349-T1
Valid prediction for snap_scaffold_14-snap.3358-T1
Valid prediction for snap_scaffold_14-snap.3328-T1
Valid prediction for snap_scaffold_14-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_35363-T1
Valid prediction for snap_scaffold_14-snap.3334-T1
Valid prediction for snap_scaffold_14-snap.3356-T1
Valid prediction for snap_scaffold_14-snap.3360-T1
Valid prediction for snap_scaffold_14-snap.3335-T1
Valid prediction for snap_scaffold_14-snap.3343-T1
Valid prediction for GlimmerHMM_glimmerT_35366-T1
Valid prediction for GlimmerHMM_glimmerT_35384-T1
Valid prediction for snap_scaffold_14-snap.3340-T1
Valid prediction for snap_scaffold_14-snap.3337-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 88984, rend_intergenic: 88981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5367, rend_intergenic: 4064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9297, rend_intergenic: 5397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17947, rend_intergenic: 14738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21511, rend_intergenic: 19223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30385, rend_intergenic: 21921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57911, rend_intergenic: 36226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58529, rend_intergenic: 58271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59652, rend_intergenic: 58788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60235, rend_intergenic: 59679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71820, rend_intergenic: 60245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77523, rend_intergenic: 72652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81249, rend_intergenic: 77827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87989, rend_intergenic: 84761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89274, rend_intergenic: 88981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106169, rend_intergenic: 89844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110332, rend_intergenic: 106270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120894, rend_intergenic: 118371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139313, rend_intergenic: 130594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156688, rend_intergenic: 153593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158478, rend_intergenic: 157455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168976, rend_intergenic: 164610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171015
-exon list size: 509


building trellis

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32.3    
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33.1    
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92.8    
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98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 88984, rend_intergenic: 88981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5367, rend_intergenic: 4064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9297, rend_intergenic: 5397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17947, rend_intergenic: 14738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21511, rend_intergenic: 19223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30385, rend_intergenic: 21921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57911, rend_intergenic: 36226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58529, rend_intergenic: 58271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59652, rend_intergenic: 58788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60235, rend_intergenic: 59679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71820, rend_intergenic: 60245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77523, rend_intergenic: 72652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81249, rend_intergenic: 77827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87989, rend_intergenic: 84761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89274, rend_intergenic: 88981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106169, rend_intergenic: 89844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110332, rend_intergenic: 106270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120894, rend_intergenic: 118371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139313, rend_intergenic: 130594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156688, rend_intergenic: 153593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158478, rend_intergenic: 157455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168976, rend_intergenic: 164610  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