-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_4197067-4475856

-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_9-snap.941-T1
Valid prediction for snap_scaffold_9-snap.923-T1
Couldn't classify 7140, 7277
Sorry, prediction pasa_asmbl_53940.p1 fails validation.
(GCC)	 CC	7140-7277	GT	CGG
(ATA)	 AG	9096-9245	GC	AGG
(GAG)	 AG	9814-10533	TA	AGT
-recovered pasa_asmbl_53940.p1, terminal, 9814, 10533
-recovered pasa_asmbl_53940.p1, internal, 9096, 9245
Valid prediction for snap_scaffold_9-snap.922-T1
Couldn't classify 6484, 6590
Couldn't classify 7009, 7049
Sorry, prediction pasa_asmbl_53943.p1 fails validation.
(ACT)	 AG	6484-6590	GT	GGG
(AAT)	 AG	6708-6868	GT	TGG
(CCT)	 AG	7009-7049	CC	CCC
-recovered pasa_asmbl_53943.p1, internal, 6484, 6590
-recovered pasa_asmbl_53943.p1, internal, 6708, 6868
Valid prediction for GlimmerHMM_glimmerT_21980-T1
Valid prediction for Augustus_model.g14616.t1
Couldn't classify 40890, 41000
Sorry, prediction pasa_asmbl_54760.p1 fails validation.
(ATG)	 AG	38428-38640	GT	AGG
(GCG)	 AG	38893-39009	GT	AGG
(GTG)	 AG	39133-39288	GT	AGG
(AAA)	 AG	39466-39546	GT	CTG
(GTC)	 AG	40093-40194	GT	AGG
(GAG)	 AG	40890-41000	CT	AAC
-recovered pasa_asmbl_54760.p1, initial, 38428, 38640
-recovered pasa_asmbl_54760.p1, internal, 38428, 38640
-recovered pasa_asmbl_54760.p1, internal, 38893, 39009
-recovered pasa_asmbl_54760.p1, internal, 39133, 39288
-recovered pasa_asmbl_54760.p1, internal, 39466, 39546
-recovered pasa_asmbl_54760.p1, internal, 40093, 40194
Valid prediction for GlimmerHMM_glimmerT_22016-T1
Valid prediction for snap_scaffold_9-snap.905-T1
Valid prediction for GlimmerHMM_glimmerT_22017-T1
Valid prediction for GlimmerHMM_glimmerT_21982-T1
Valid prediction for snap_scaffold_9-snap.944-T1
Valid prediction for Augustus_model.g14620.t1
Valid prediction for snap_scaffold_9-snap.913-T1
Valid prediction for snap_scaffold_9-snap.919-T1
Valid prediction for snap_scaffold_9-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_21984-T1
Valid prediction for snap_scaffold_9-snap.934-T1
Valid prediction for snap_scaffold_9-snap.903-T1
Valid prediction for snap_scaffold_9-snap.939-T1
Couldn't classify 21877, 22063
Couldn't classify 22144, 22355
Sorry, prediction pasa_asmbl_54738.p1 fails validation.
(AGA)	 AT	21877-22063	GT	AGG
(GTC)	 AG	22144-22355	GT	CAG
-recovered pasa_asmbl_54738.p1, internal, 22144, 22355
Valid prediction for GlimmerHMM_glimmerT_21993-T1
Valid prediction for snap_scaffold_9-snap.930-T1
Valid prediction for snap_scaffold_9-snap.917-T1
Valid prediction for GlimmerHMM_glimmerT_21991-T1
Valid prediction for GlimmerHMM_glimmerT_21994-T1
Valid prediction for Augustus_model.g14626.t1
Valid prediction for GlimmerHMM_glimmerT_22004-T1
Valid prediction for GlimmerHMM_glimmerT_21986-T1
Valid prediction for GlimmerHMM_glimmerT_21997-T1
Valid prediction for GlimmerHMM_glimmerT_21989-T1
Valid prediction for Augustus_model.g14629.t1
Valid prediction for snap_scaffold_9-snap.948-T1
Valid prediction for snap_scaffold_9-snap.932-T1
Valid prediction for Augustus_model.g14613.t1
Couldn't classify 104753, 105100
Sorry, prediction pasa_asmbl_54687.p1 fails validation.
(ACA)	 TG	104753-105100	AG	GAA
Valid prediction for snap_scaffold_9-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_21999-T1
Valid prediction for Augustus_model.g14621.t1
Valid prediction for GlimmerHMM_glimmerT_22003-T1
Valid prediction for snap_scaffold_9-snap.936-T1
Valid prediction for Augustus_model.g14617.t1
Valid prediction for snap_scaffold_9-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_21979-T1
Valid prediction for Augustus_model.g14614.t1
Valid prediction for Augustus_model.g14623.t1
Valid prediction for GlimmerHMM_glimmerT_22007-T1
Valid prediction for GlimmerHMM_glimmerT_21981-T1
Valid prediction for snap_scaffold_9-snap.937-T1
Couldn't classify 1196, 1342
Couldn't classify 3099, 3163
Sorry, prediction pasa_asmbl_53937.p1 fails validation.
(GGT)	 CT	1196-1342	GT	AGG
(AGT)	 AG	1647-1780	GT	AGG
(GTC)	 AG	1875-1975	GT	AGG
(GGG)	 AG	2227-2358	GT	GGG
(CTC)	 AG	2466-2561	GT	AGG
(GTC)	 AG	2662-2766	GT	AGG
(GGA)	 AG	3099-3163	GC	GAG
-recovered pasa_asmbl_53937.p1, internal, 1647, 1780
-recovered pasa_asmbl_53937.p1, internal, 1875, 1975
-recovered pasa_asmbl_53937.p1, internal, 2227, 2358
-recovered pasa_asmbl_53937.p1, internal, 2466, 2561
-recovered pasa_asmbl_53937.p1, internal, 2662, 2766
-recovered pasa_asmbl_53937.p1, internal, 3099, 3163
Valid prediction for GlimmerHMM_glimmerT_22012-T1
Couldn't classify 13009, 13104
Sorry, prediction pasa_asmbl_53947.p2 fails validation.
(ATG)	 AC	11807-11899	GT	AGG
(GCG)	 AG	12751-12861	GT	AGG
(GAG)	 AG	13009-13104	GG	CGG
-recovered pasa_asmbl_53947.p2, initial, 11807, 11899
-recovered pasa_asmbl_53947.p2, internal, 12751, 12861
Couldn't classify 100093, 100254
Sorry, prediction pasa_asmbl_53948.p1 fails validation.
(ATG)	 AC	97894-98100	GT	TGG
(GCA)	 AG	98761-98992	GT	AGG
(GAA)	 AG	99396-99517	GT	GGG
(GCA)	 AG	100093-100254	GT	AGG
-recovered pasa_asmbl_53948.p1, initial, 97894, 98100
-recovered pasa_asmbl_53948.p1, internal, 98761, 98992
-recovered pasa_asmbl_53948.p1, internal, 99396, 99517
-recovered pasa_asmbl_53948.p1, internal, 100093, 100254
Valid prediction for snap_scaffold_9-snap.909-T1
Valid prediction for snap_scaffold_9-snap.935-T1
Valid prediction for GlimmerHMM_glimmerT_21996-T1
Valid prediction for snap_scaffold_9-snap.929-T1
Valid prediction for GlimmerHMM_glimmerT_22009-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_9-snap.907-T1
Valid prediction for Augustus_model.g14630.t1
Valid prediction for GlimmerHMM_glimmerT_21988-T1
Valid prediction for snap_scaffold_9-snap.912-T1
Valid prediction for snap_scaffold_9-snap.927-T1
Valid prediction for snap_scaffold_9-snap.904-T1
Valid prediction for Augustus_model.g14622.t1
Valid prediction for snap_scaffold_9-snap.925-T1
Valid prediction for snap_scaffold_9-snap.908-T1
Valid prediction for GlimmerHMM_glimmerT_21978-T1
Valid prediction for GlimmerHMM_glimmerT_21983-T1
Valid prediction for HiQ_model.g14618.t1
Valid prediction for GlimmerHMM_glimmerT_22008-T1
Valid prediction for GlimmerHMM_glimmerT_22011-T1
Valid prediction for snap_scaffold_9-snap.920-T1
Couldn't classify 221284, 221370
Couldn't classify 224577, 225011
Sorry, prediction pasa_asmbl_54964.p1 fails validation.
(TCT)	 CA	221284-221370	GT	AAG
(AAC)	 AG	221734-221823	GT	CTG
(AAG)	 AG	222122-222256	GT	CGG
(GTC)	 AG	224577-225011	GG	CAG
-recovered pasa_asmbl_54964.p1, internal, 221734, 221823
-recovered pasa_asmbl_54964.p1, internal, 222122, 222256
Valid prediction for snap_scaffold_9-snap.910-T1
Valid prediction for GlimmerHMM_glimmerT_22013-T1
Valid prediction for GlimmerHMM_glimmerT_22002-T1
Valid prediction for GlimmerHMM_glimmerT_22005-T1
Valid prediction for Augustus_model.g14625.t1
Valid prediction for snap_scaffold_9-snap.942-T1
Valid prediction for GlimmerHMM_glimmerT_22014-T1
Valid prediction for Augustus_model.g14634.t1
Valid prediction for Augustus_model.g14624.t1
Valid prediction for snap_scaffold_9-snap.928-T1
Valid prediction for snap_scaffold_9-snap.940-T1
Valid prediction for GlimmerHMM_glimmerT_22000-T1
Valid prediction for snap_scaffold_9-snap.916-T1
Valid prediction for GlimmerHMM_glimmerT_21995-T1
Valid prediction for Augustus_model.g14633.t1
Valid prediction for Augustus_model.g14627.t1
Valid prediction for Augustus_model.g14628.t1
Valid prediction for snap_scaffold_9-snap.911-T1
Valid prediction for snap_scaffold_9-snap.943-T1
Couldn't classify 182946, 183614
Sorry, prediction pasa_asmbl_54966.p1 fails validation.
(CTG)	 AG	182946-183614	CG	AGC
Valid prediction for snap_scaffold_9-snap.931-T1
Valid prediction for snap_scaffold_9-snap.924-T1
Valid prediction for snap_scaffold_9-snap.915-T1
Valid prediction for GlimmerHMM_glimmerT_22001-T1
Valid prediction for GlimmerHMM_glimmerT_21992-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.947-T1
Valid prediction for snap_scaffold_9-snap.914-T1
Valid prediction for Augustus_model.g14632.t1
Valid prediction for GlimmerHMM_glimmerT_21998-T1
Valid prediction for GlimmerHMM_glimmerT_21985-T1
Valid prediction for GlimmerHMM_glimmerT_22006-T1
Valid prediction for Augustus_model.g14619.t1
Valid prediction for GlimmerHMM_glimmerT_21990-T1
Valid prediction for snap_scaffold_9-snap.906-T1
Valid prediction for Augustus_model.g14631.t1
Valid prediction for GlimmerHMM_glimmerT_22015-T1
Valid prediction for snap_scaffold_9-snap.946-T1
Valid prediction for snap_scaffold_9-snap.921-T1
Valid prediction for snap_scaffold_9-snap.933-T1
Valid prediction for GlimmerHMM_glimmerT_22010-T1
Valid prediction for GlimmerHMM_glimmerT_21987-T1
Valid prediction for Augustus_model.g14615.t1
Valid prediction for snap_scaffold_9-snap.938-T1
Valid prediction for snap_scaffold_9-snap.918-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10533, rend_intergenic: 2253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21562, rend_intergenic: 12257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33124, rend_intergenic: 21701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45126, rend_intergenic: 33127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75149, rend_intergenic: 46523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88744, rend_intergenic: 75336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95005, rend_intergenic: 91545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110841, rend_intergenic: 99364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124257, rend_intergenic: 114873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132017, rend_intergenic: 124919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146466, rend_intergenic: 132185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156968, rend_intergenic: 148032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170037, rend_intergenic: 157343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173425, rend_intergenic: 170577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188571, rend_intergenic: 174664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209465, rend_intergenic: 188953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222401, rend_intergenic: 210184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234163, rend_intergenic: 226772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243986, rend_intergenic: 236242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265380, rend_intergenic: 253359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271351, rend_intergenic: 265567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 277152, rend_intergenic: 271929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 278790
-exon list size: 503


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 10533, rend_intergenic: 2253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21562, rend_intergenic: 12257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33124, rend_intergenic: 21701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45126, rend_intergenic: 33127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75149, rend_intergenic: 46523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88744, rend_intergenic: 75336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95005, rend_intergenic: 91545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110841, rend_intergenic: 99364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124257, rend_intergenic: 114873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132017, rend_intergenic: 124919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146466, rend_intergenic: 132185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156968, rend_intergenic: 148032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170037, rend_intergenic: 157343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173425, rend_intergenic: 170577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188571, rend_intergenic: 174664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209465, rend_intergenic: 188953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222401, rend_intergenic: 210184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234163, rend_intergenic: 226772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243986, rend_intergenic: 236242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265380, rend_intergenic: 253359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271351, rend_intergenic: 265567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 277152, rend_intergenic: 271929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support