-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_11986388-12275991

-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_10-snap.2396-T1
Valid prediction for snap_scaffold_10-snap.2350-T1
Valid prediction for GlimmerHMM_glimmerT_25550-T1
Valid prediction for snap_scaffold_10-snap.2342-T1
Valid prediction for Augustus_model.g16981.t1
Valid prediction for GlimmerHMM_glimmerT_25528-T1
Valid prediction for snap_scaffold_10-snap.2391-T1
Valid prediction for snap_scaffold_10-snap.2379-T1
Valid prediction for GlimmerHMM_glimmerT_25537-T1
Valid prediction for GlimmerHMM_glimmerT_25541-T1
Valid prediction for GlimmerHMM_glimmerT_25530-T1
Valid prediction for snap_scaffold_10-snap.2355-T1
Valid prediction for snap_scaffold_10-snap.2390-T1
Valid prediction for GlimmerHMM_glimmerT_25525-T1
Valid prediction for GlimmerHMM_glimmerT_25535-T1
Valid prediction for GlimmerHMM_glimmerT_25523-T1
Valid prediction for snap_scaffold_10-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_25560-T1
Valid prediction for GlimmerHMM_glimmerT_25532-T1
Valid prediction for HiQ_model.g16978.t1
Valid prediction for snap_scaffold_10-snap.2361-T1
Valid prediction for snap_scaffold_10-snap.2357-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25527-T1
Valid prediction for GlimmerHMM_glimmerT_25552-T1
Valid prediction for snap_scaffold_10-snap.2382-T1
Valid prediction for snap_scaffold_10-snap.2387-T1
Valid prediction for GlimmerHMM_glimmerT_25524-T1
Valid prediction for snap_scaffold_10-snap.2359-T1
Couldn't classify 69890, 69985
Sorry, prediction pasa_asmbl_3525.p1 fails validation.
(ATG)	 GG	67868-67960	GT	AGG
(GTC)	 AG	68198-68321	GT	AGG
(ACG)	 AG	69386-69492	GT	TTG
(ACA)	 AG	69890-69985	GG	CAG
-recovered pasa_asmbl_3525.p1, initial, 67868, 67960
-recovered pasa_asmbl_3525.p1, internal, 68198, 68321
-recovered pasa_asmbl_3525.p1, internal, 69386, 69492
Valid prediction for pasa_asmbl_3527.p1
Valid prediction for Augustus_model.g16976.t1
Couldn't classify 66956, 67120
Sorry, prediction pasa_asmbl_3523.p1 fails validation.
(ATG)	 GG	63396-63488	GT	AGG
(GTC)	 AG	63709-63832	GT	AGG
(ACG)	 AG	64898-65004	GT	TTG
(ACA)	 AG	65399-65495	GT	AGG
(CTT)	 AG	66773-66849	GT	CGG
(GAC)	 AG	66956-67120	TA	AGT
-recovered pasa_asmbl_3523.p1, initial, 63396, 63488
-recovered pasa_asmbl_3523.p1, internal, 63709, 63832
-recovered pasa_asmbl_3523.p1, internal, 64898, 65004
-recovered pasa_asmbl_3523.p1, internal, 65399, 65495
-recovered pasa_asmbl_3523.p1, internal, 66773, 66849
Couldn't classify 71344, 71358
Couldn't classify 71481, 71635
Sorry, prediction CodingQuarry_transcript_5593-T1 fails validation.
(ATG)	 CA	71344-71358	TT	CAT
(CAA)	 AC	71481-71635	GT	AAG
(GCC)	 AG	71773-71896	AC	GAA
-recovered CodingQuarry_transcript_5593-T1, terminal, 71773, 71896
Valid prediction for snap_scaffold_10-snap.2380-T1
Valid prediction for GlimmerHMM_glimmerT_25520-T1
Valid prediction for snap_scaffold_10-snap.2369-T1
Valid prediction for snap_scaffold_10-snap.2354-T1
Valid prediction for Augustus_model.g16989.t1
Valid prediction for snap_scaffold_10-snap.2349-T1
Couldn't classify 235988, 236013
Couldn't classify 237050, 237127
Sorry, prediction pasa_asmbl_3530.p1 fails validation.
(GTG)	 TA	235988-236013	GT	AGG
(AGC)	 AG	236300-236731	GT	AGG
(TGA)	 AG	236821-236947	GT	AGG
(GAG)	 AG	237050-237127	AT	GCA
-recovered pasa_asmbl_3530.p1, internal, 236300, 236731
-recovered pasa_asmbl_3530.p1, internal, 236821, 236947
Valid prediction for snap_scaffold_10-snap.2377-T1
Valid prediction for Augustus_model.g16985.t1
Valid prediction for GlimmerHMM_glimmerT_25533-T1
Valid prediction for HiQ_model.g16983.t1
Valid prediction for snap_scaffold_10-snap.2375-T1
Valid prediction for GlimmerHMM_glimmerT_25536-T1
Valid prediction for snap_scaffold_10-snap.2345-T1
Valid prediction for snap_scaffold_10-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_25555-T1
Valid prediction for GlimmerHMM_glimmerT_25521-T1
Valid prediction for CodingQuarry_transcript_5595-T1
Valid prediction for Augustus_model.g16984.t1
Valid prediction for pasa_asmbl_3528.p1
Valid prediction for snap_scaffold_10-snap.2386-T1
Valid prediction for Augustus_model.g16979.t1
Valid prediction for snap_scaffold_10-snap.2353-T1
Valid prediction for snap_scaffold_10-snap.2368-T1
Valid prediction for snap_scaffold_10-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_25546-T1
Valid prediction for GlimmerHMM_glimmerT_25558-T1
Valid prediction for CodingQuarry_transcript_5592-T1
Valid prediction for GlimmerHMM_glimmerT_25543-T1
Valid prediction for Augustus_model.g16977.t1
Valid prediction for snap_scaffold_10-snap.2364-T1
Couldn't classify 12769, 12821
Sorry, prediction pasa_asmbl_3520.p1 fails validation.
(AAC)	 AG	12769-12821	GT	ATG
(CAT)	 AG	13451-13607	GT	GGG
(TTC)	 AG	13896-14049	GT	TGG
(GTT)	 AG	14329-14405	GT	AGG
(CTG)	 AG	14627-14692	GT	TGG
(GTT)	 AG	16386-16460	CC	GAC
-recovered pasa_asmbl_3520.p1, terminal, 16386, 16460
-recovered pasa_asmbl_3520.p1, internal, 12769, 12821
-recovered pasa_asmbl_3520.p1, internal, 13451, 13607
-recovered pasa_asmbl_3520.p1, internal, 13896, 14049
-recovered pasa_asmbl_3520.p1, internal, 14329, 14405
-recovered pasa_asmbl_3520.p1, internal, 14627, 14692
Valid prediction for snap_scaffold_10-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_25553-T1
Valid prediction for snap_scaffold_10-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_25542-T1
Valid prediction for snap_scaffold_10-snap.2370-T1
Valid prediction for GlimmerHMM_glimmerT_25519-T1
Valid prediction for CodingQuarry_transcript_5594-T1
Valid prediction for snap_scaffold_10-snap.2384-T1
Valid prediction for snap_scaffold_10-snap.2365-T1
Valid prediction for GlimmerHMM_glimmerT_25526-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_10-snap.2371-T1
Valid prediction for snap_scaffold_10-snap.2347-T1
Valid prediction for Augustus_model.g16982.t1
Valid prediction for Augustus_model.g16980.t1
Valid prediction for snap_scaffold_10-snap.2373-T1
Valid prediction for Augustus_model.g16987.t1
Valid prediction for snap_scaffold_10-snap.2367-T1
Valid prediction for GlimmerHMM_glimmerT_25529-T1
Valid prediction for snap_scaffold_10-snap.2346-T1
Valid prediction for snap_scaffold_10-snap.2344-T1
Valid prediction for GlimmerHMM_glimmerT_25551-T1
Valid prediction for snap_scaffold_10-snap.2381-T1
Valid prediction for snap_scaffold_10-snap.2351-T1
Valid prediction for GlimmerHMM_glimmerT_25557-T1
Valid prediction for GlimmerHMM_glimmerT_25538-T1
Valid prediction for GlimmerHMM_glimmerT_25548-T1
Valid prediction for GlimmerHMM_glimmerT_25540-T1
Valid prediction for GlimmerHMM_glimmerT_25544-T1
Valid prediction for snap_scaffold_10-snap.2363-T1
Valid prediction for Augustus_model.g16986.t1
Valid prediction for snap_scaffold_10-snap.2352-T1
Valid prediction for snap_scaffold_10-snap.2393-T1
Valid prediction for snap_scaffold_10-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_25547-T1
Valid prediction for Augustus_model.g16990.t1
Valid prediction for snap_scaffold_10-snap.2395-T1
Couldn't classify 141966, 142079
Sorry, prediction pasa_asmbl_4808.p1 fails validation.
(AAG)	 TG	141966-142079	GT	AGG
(ATC)	 AG	142815-142913	GT	AGG
(TTG)	 AG	143089-143217	GT	AGG
(GAC)	 AG	143400-143537	AC	AGA
-recovered pasa_asmbl_4808.p1, terminal, 143400, 143537
-recovered pasa_asmbl_4808.p1, internal, 142815, 142913
-recovered pasa_asmbl_4808.p1, internal, 143089, 143217
Valid prediction for GlimmerHMM_glimmerT_25522-T1
Valid prediction for GlimmerHMM_glimmerT_25531-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.2358-T1
Valid prediction for snap_scaffold_10-snap.2383-T1
Couldn't classify 139009, 139088
Sorry, prediction pasa_asmbl_4809.p1 fails validation.
(ATG)	 CA	135618-135740	GT	GGG
(GAG)	 AG	136411-136590	GT	AGG
(GTC)	 AG	136686-136954	GT	GAG
(GTG)	 AG	138557-138723	GT	GGG
(CCC)	 AG	139009-139088	GG	AGG
-recovered pasa_asmbl_4809.p1, initial, 135618, 135740
-recovered pasa_asmbl_4809.p1, internal, 136411, 136590
-recovered pasa_asmbl_4809.p1, internal, 136686, 136954
-recovered pasa_asmbl_4809.p1, internal, 138557, 138723
Valid prediction for snap_scaffold_10-snap.2366-T1
Valid prediction for Augustus_model.g16991.t1
Valid prediction for Augustus_model.g16992.t1
Valid prediction for snap_scaffold_10-snap.2343-T1
Valid prediction for GlimmerHMM_glimmerT_25534-T1
Valid prediction for GlimmerHMM_glimmerT_25554-T1
Valid prediction for GlimmerHMM_glimmerT_25556-T1
Valid prediction for GlimmerHMM_glimmerT_25559-T1
Valid prediction for Augustus_model.g16988.t1
Valid prediction for snap_scaffold_10-snap.2385-T1
Valid prediction for snap_scaffold_10-snap.2348-T1
Couldn't classify 132493, 132624
Sorry, prediction pasa_asmbl_4810.p1 fails validation.
(AGG)	 GG	132493-132624	GT	AGG
(GAC)	 AG	132879-133052	GA	AGG
-recovered pasa_asmbl_4810.p1, terminal, 132879, 133052
Valid prediction for snap_scaffold_10-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_25539-T1
Valid prediction for GlimmerHMM_glimmerT_25549-T1
Valid prediction for snap_scaffold_10-snap.2362-T1
Valid prediction for snap_scaffold_10-snap.2389-T1
Valid prediction for GlimmerHMM_glimmerT_25545-T1
Valid prediction for snap_scaffold_10-snap.2392-T1
Valid prediction for CodingQuarry_transcript_5596-T1
Valid prediction for snap_scaffold_10-snap.2372-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15127, rend_intergenic: 3519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19098, rend_intergenic: 15251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42414, rend_intergenic: 28716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50515, rend_intergenic: 42548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60695, rend_intergenic: 50843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77791, rend_intergenic: 75911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81951, rend_intergenic: 80330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105679, rend_intergenic: 92388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108138, rend_intergenic: 105751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141037, rend_intergenic: 134136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152473, rend_intergenic: 146068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196378, rend_intergenic: 156575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198320, rend_intergenic: 196958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209182, rend_intergenic: 199117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215922, rend_intergenic: 210777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235620, rend_intergenic: 220014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239224, rend_intergenic: 237654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247525, rend_intergenic: 241396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262120, rend_intergenic: 248609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266781, rend_intergenic: 262175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 270188, rend_intergenic: 267523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288675, rend_intergenic: 270580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 289604
-exon list size: 491


building trellis

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96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 15127, rend_intergenic: 3519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19098, rend_intergenic: 15251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42414, rend_intergenic: 28716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50515, rend_intergenic: 42548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60695, rend_intergenic: 50843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77791, rend_intergenic: 75911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81951, rend_intergenic: 80330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105679, rend_intergenic: 92388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108138, rend_intergenic: 105751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141037, rend_intergenic: 134136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152473, rend_intergenic: 146068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196378, rend_intergenic: 156575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198320, rend_intergenic: 196958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209182, rend_intergenic: 199117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215922, rend_intergenic: 210777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235620, rend_intergenic: 220014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239224, rend_intergenic: 237654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247525, rend_intergenic: 241396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262120, rend_intergenic: 248609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266781, rend_intergenic: 262175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 270188, rend_intergenic: 267523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288675, rend_intergenic: 270580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support