-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_2564840-2808202

-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 GlimmerHMM_glimmerT_34186-T1
Valid prediction for GeneMark_model.58495_t
Valid prediction for Augustus_model.g23001.t1
Valid prediction for snap_scaffold_14-snap.478-T1
Valid prediction for GeneMark_model.58481_t
Valid prediction for GlimmerHMM_glimmerT_34199-T1
Valid prediction for GeneMark_model.58490_t
Valid prediction for snap_scaffold_14-snap.461-T1
Valid prediction for snap_scaffold_14-snap.475-T1
Valid prediction for Augustus_model.g23002.t1
Valid prediction for GlimmerHMM_glimmerT_34185-T1
Couldn't classify 159822, 159887
Couldn't classify 163179, 163256
Sorry, prediction pasa_asmbl_11854.p1 fails validation.
(AGC)	 TC	159822-159887	GT	AGG
(CTC)	 AG	160695-160832	GT	AGG
(AGG)	 AG	161068-161238	GT	GGG
(GCT)	 AG	162080-162193	GT	AGG
(GCG)	 AG	162819-162854	GT	AGG
(GAG)	 AG	163179-163256	AC	GCA
-recovered pasa_asmbl_11854.p1, internal, 160695, 160832
-recovered pasa_asmbl_11854.p1, internal, 161068, 161238
-recovered pasa_asmbl_11854.p1, internal, 162080, 162193
-recovered pasa_asmbl_11854.p1, internal, 162819, 162854
Couldn't classify 163445, 163455
Sorry, prediction pasa_asmbl_11855.p1 fails validation.
(AAA)	 AC	163445-163455	GT	AGG
(AGC)	 AG	163742-163912	GT	AGG
(TAC)	 AG	164555-164648	GT	AGG
(ATT)	 AG	165062-165154	GT	AGG
(GTG)	 AG	165528-165692	GT	AGG
(GTG)	 AG	166525-166689	GT	AGG
(GTG)	 AG	166774-166905	GT	AGG
(GGG)	 AG	166991-167123	GT	CGG
(GCG)	 AG	167278-167426	AC	AGA
-recovered pasa_asmbl_11855.p1, terminal, 167278, 167426
-recovered pasa_asmbl_11855.p1, internal, 163742, 163912
-recovered pasa_asmbl_11855.p1, internal, 164555, 164648
-recovered pasa_asmbl_11855.p1, internal, 165062, 165154
-recovered pasa_asmbl_11855.p1, internal, 165528, 165692
-recovered pasa_asmbl_11855.p1, internal, 166525, 166689
-recovered pasa_asmbl_11855.p1, internal, 166774, 166905
-recovered pasa_asmbl_11855.p1, internal, 166991, 167123
Valid prediction for GlimmerHMM_glimmerT_34211-T1
Valid prediction for snap_scaffold_14-snap.476-T1
Valid prediction for snap_scaffold_14-snap.470-T1
Valid prediction for snap_scaffold_14-snap.484-T1
Valid prediction for pasa_asmbl_11850.p1
Valid prediction for snap_scaffold_14-snap.469-T1
Valid prediction for GlimmerHMM_glimmerT_34204-T1
Valid prediction for snap_scaffold_14-snap.456-T1
Valid prediction for snap_scaffold_14-snap.479-T1
Valid prediction for snap_scaffold_14-snap.487-T1
Valid prediction for snap_scaffold_14-snap.481-T1
Valid prediction for GlimmerHMM_glimmerT_34198-T1
Valid prediction for GeneMark_model.58496_t
Valid prediction for GeneMark_model.58485_t
Valid prediction for GlimmerHMM_glimmerT_34207-T1
Valid prediction for GlimmerHMM_glimmerT_34192-T1
Valid prediction for GeneMark_model.58493_t
Valid prediction for GeneMark_model.58509_t
Valid prediction for GlimmerHMM_glimmerT_34205-T1
Valid prediction for Augustus_model.g23005.t1
Valid prediction for snap_scaffold_14-snap.485-T1
Valid prediction for GeneMark_model.58482_t
Valid prediction for GlimmerHMM_glimmerT_34187-T1
Valid prediction for GlimmerHMM_glimmerT_34210-T1
Valid prediction for GlimmerHMM_glimmerT_34213-T1
Valid prediction for GeneMark_model.58488_t
Valid prediction for Augustus_model.g22999.t1
Valid prediction for GlimmerHMM_glimmerT_34184-T1
Valid prediction for snap_scaffold_14-snap.480-T1
Valid prediction for GlimmerHMM_glimmerT_34193-T1
Valid prediction for GlimmerHMM_glimmerT_34201-T1
Valid prediction for snap_scaffold_14-snap.486-T1
Valid prediction for GeneMark_model.58505_t
Valid prediction for snap_scaffold_14-snap.462-T1
Valid prediction for GeneMark_model.58504_t
Valid prediction for Augustus_model.g23006.t1
Couldn't classify 158700, 158763
Couldn't classify 159458, 159526
Sorry, prediction pasa_asmbl_11853.p1 fails validation.
(TGG)	 AC	158700-158763	GT	CTG
(CCA)	 AG	159027-159199	GT	AGG
(GCC)	 AG	159458-159526	AA	ACA
-recovered pasa_asmbl_11853.p1, internal, 159027, 159199
Valid prediction for snap_scaffold_14-snap.457-T1
Valid prediction for snap_scaffold_14-snap.455-T1
Valid prediction for GeneMark_model.58506_t
Valid prediction for GeneMark_model.58502_t
Valid prediction for Augustus_model.g23007.t1
Valid prediction for GeneMark_model.58516_t
Valid prediction for HiQ_model.g22995.t1
Couldn't classify 94541, 94843
Sorry, prediction pasa_asmbl_12950.p1 fails validation.
(GCT)	 CA	94541-94843	TC	TCT
Valid prediction for snap_scaffold_14-snap.465-T1
Valid prediction for GlimmerHMM_glimmerT_34202-T1
Valid prediction for CodingQuarry_transcript_15548-T1
Valid prediction for Augustus_model.g23003.t1
Valid prediction for GeneMark_model.58507_t
Valid prediction for GeneMark_model.58491_t
Valid prediction for GeneMark_model.58498_t
Valid prediction for GeneMark_model.58510_t
Valid prediction for GeneMark_model.58480_t
Valid prediction for Augustus_model.g22996.t1
Valid prediction for GlimmerHMM_glimmerT_34208-T1
Valid prediction for snap_scaffold_14-snap.474-T1
Valid prediction for GlimmerHMM_glimmerT_34194-T1
Valid prediction for snap_scaffold_14-snap.466-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 GlimmerHMM_glimmerT_34196-T1
Valid prediction for snap_scaffold_14-snap.483-T1
Valid prediction for snap_scaffold_14-snap.489-T1
Valid prediction for GeneMark_model.58500_t
Valid prediction for Augustus_model.g23004.t1
Valid prediction for GeneMark_model.58511_t
Valid prediction for snap_scaffold_14-snap.477-T1
Valid prediction for snap_scaffold_14-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_34189-T1
Valid prediction for GlimmerHMM_glimmerT_34200-T1
Couldn't classify 202513, 202611
Couldn't classify 203250, 203318
Sorry, prediction pasa_asmbl_13800.p1 fails validation.
(TTT)	 CC	202513-202611	GT	AGG
(CCT)	 AG	202787-202969	GT	AGG
(CAA)	 AG	203250-203318	GG	ACG
-recovered pasa_asmbl_13800.p1, internal, 202787, 202969
Couldn't classify 41890, 41966
Couldn't classify 43509, 43577
Sorry, prediction pasa_asmbl_12957.p1 fails validation.
(CCT)	 AT	41890-41966	GT	GTG
(GTT)	 AG	42568-42711	GT	CAG
(CTC)	 AG	42867-42999	GT	CCG
(TTT)	 AG	43509-43577	AA	CCA
-recovered pasa_asmbl_12957.p1, internal, 42568, 42711
-recovered pasa_asmbl_12957.p1, internal, 42867, 42999
Valid prediction for snap_scaffold_14-snap.492-T1
Valid prediction for CodingQuarry_transcript_15550-T1
Valid prediction for snap_scaffold_14-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_34195-T1
Couldn't classify 204233, 204289
Sorry, prediction pasa_asmbl_12947.p1 fails validation.
(CAT)	 AG	204233-204289	GT	GTG
(TCG)	 AG	204663-204768	GT	AGG
(TCA)	 AG	205098-205258	GC	AGG
(TGT)	 AG	205382-205449	GT	AAG
(TAA)	 AG	205557-205625	GT	AAG
(CTC)	 AG	205786-206021	GT	AGG
(GCA)	 AG	206539-206702	GT	CAG
(ATA)	 AG	206823-207077	GT	ATG
(CTT)	 AG	207207-207314	CA	GAC
-recovered pasa_asmbl_12947.p1, terminal, 207207, 207314
-recovered pasa_asmbl_12947.p1, internal, 204233, 204289
-recovered pasa_asmbl_12947.p1, internal, 204663, 204768
-recovered pasa_asmbl_12947.p1, internal, 205098, 205258
-recovered pasa_asmbl_12947.p1, internal, 205382, 205449
-recovered pasa_asmbl_12947.p1, internal, 205557, 205625
-recovered pasa_asmbl_12947.p1, internal, 205786, 206021
-recovered pasa_asmbl_12947.p1, internal, 206539, 206702
-recovered pasa_asmbl_12947.p1, internal, 206823, 207077
Valid prediction for GlimmerHMM_glimmerT_34212-T1
Valid prediction for GeneMark_model.58513_t
Valid prediction for GeneMark_model.58487_t
Valid prediction for GeneMark_model.58512_t
Valid prediction for snap_scaffold_14-snap.468-T1
Valid prediction for GeneMark_model.58484_t
Valid prediction for GlimmerHMM_glimmerT_34206-T1
Valid prediction for GeneMark_model.58489_t
Valid prediction for GlimmerHMM_glimmerT_34209-T1
Couldn't classify 48027, 48224
Couldn't classify 50489, 50664
Sorry, prediction pasa_asmbl_12954.p1 fails validation.
(GAG)	 TG	48027-48224	GT	AGG
(TGC)	 AG	48612-48741	GT	CGG
(ATG)	 AG	50186-50266	GT	GAG
(ATG)	 AG	50489-50664	GC	ATG
-recovered pasa_asmbl_12954.p1, initial, 50186, 50266
add_exon() Sorry, pasa_asmbl_12954.p1 50489-50664-initial-1 is invalid.
-recovered pasa_asmbl_12954.p1, initial, 50489, 50664
-recovered pasa_asmbl_12954.p1, internal, 48612, 48741
-recovered pasa_asmbl_12954.p1, internal, 50186, 50266
-recovered pasa_asmbl_12954.p1, internal, 50489, 50664
Valid prediction for snap_scaffold_14-snap.463-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.458-T1
Valid prediction for GlimmerHMM_glimmerT_34203-T1
Valid prediction for snap_scaffold_14-snap.460-T1
Valid prediction for GeneMark_model.58492_t
Valid prediction for Augustus_model.g23000.t1
Couldn't classify 44492, 44624
Couldn't classify 47674, 47783
Sorry, prediction pasa_asmbl_12956.p2 fails validation.
(GAC)	 TG	44492-44624	GT	TGG
(AGA)	 AG	44776-44909	GT	TGG
(CAT)	 AG	45328-45451	GT	AGG
(GCA)	 AG	45642-45722	GT	TGG
(CTG)	 AG	46988-47151	GT	TGG
(GTC)	 AG	47310-47475	GT	AGG
(GTA)	 AG	47674-47783	GT	ACG
-recovered pasa_asmbl_12956.p2, internal, 44776, 44909
-recovered pasa_asmbl_12956.p2, internal, 45328, 45451
-recovered pasa_asmbl_12956.p2, internal, 45642, 45722
-recovered pasa_asmbl_12956.p2, internal, 46988, 47151
-recovered pasa_asmbl_12956.p2, internal, 47310, 47475
-recovered pasa_asmbl_12956.p2, internal, 47674, 47783
Valid prediction for GeneMark_model.58499_t
Valid prediction for snap_scaffold_14-snap.473-T1
Valid prediction for Augustus_model.g23009.t1
Valid prediction for snap_scaffold_14-snap.464-T1
Valid prediction for GeneMark_model.58501_t
Valid prediction for Augustus_model.g23010.t1
Valid prediction for GeneMark_model.58515_t
Valid prediction for snap_scaffold_14-snap.472-T1
Valid prediction for snap_scaffold_14-snap.490-T1
Valid prediction for snap_scaffold_14-snap.471-T1
Valid prediction for GeneMark_model.58486_t
Valid prediction for GlimmerHMM_glimmerT_34191-T1
Valid prediction for GlimmerHMM_glimmerT_34188-T1
Valid prediction for GeneMark_model.58497_t
Valid prediction for GlimmerHMM_glimmerT_34197-T1
Valid prediction for GeneMark_model.58508_t
Valid prediction for Augustus_model.g23011.t1
Valid prediction for snap_scaffold_14-snap.491-T1
Valid prediction for Augustus_model.g23008.t1
Valid prediction for Augustus_model.g22997.t1
Couldn't classify 50749, 51099
Sorry, prediction pasa_asmbl_12953.p1 fails validation.
(AGG)	 GC	50749-51099	AC	AGA
Valid prediction for CodingQuarry_transcript_15549-T1
Valid prediction for GeneMark_model.58494_t
Valid prediction for snap_scaffold_14-snap.467-T1
Valid prediction for Augustus_model.g22998.t1
Valid prediction for GeneMark_model.58514_t
Valid prediction for GlimmerHMM_glimmerT_34190-T1
Valid prediction for snap_scaffold_14-snap.459-T1
Valid prediction for GeneMark_model.58483_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 76302, rend_intergenic: 72837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79786, rend_intergenic: 77016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152209, rend_intergenic: 151854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 243363
-exon list size: 479


building trellis

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97.9    
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98.3    
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99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 76302, rend_intergenic: 72837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79786, rend_intergenic: 77016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152209, rend_intergenic: 151854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support