-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_17730298-17987864

-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_18922-T1
Valid prediction for GlimmerHMM_glimmerT_18941-T1
Valid prediction for pasa_asmbl_50499.p1
Valid prediction for GlimmerHMM_glimmerT_18943-T1
Valid prediction for GlimmerHMM_glimmerT_18939-T1
Valid prediction for snap_scaffold_7-snap.3404-T1
Valid prediction for GlimmerHMM_glimmerT_18913-T1
Valid prediction for GlimmerHMM_glimmerT_18926-T1
Valid prediction for snap_scaffold_7-snap.3424-T1
Valid prediction for snap_scaffold_7-snap.3409-T1
Valid prediction for snap_scaffold_7-snap.3435-T1
Valid prediction for snap_scaffold_7-snap.3431-T1
Valid prediction for GlimmerHMM_glimmerT_18924-T1
Valid prediction for GlimmerHMM_glimmerT_18937-T1
Valid prediction for CodingQuarry_transcript_57748-T1
Valid prediction for GlimmerHMM_glimmerT_18919-T1
Valid prediction for CodingQuarry_transcript_57750-T1
Valid prediction for snap_scaffold_7-snap.3412-T1
Valid prediction for snap_scaffold_7-snap.3436-T1
Valid prediction for snap_scaffold_7-snap.3422-T1
Valid prediction for Augustus_model.g12695.t1
Valid prediction for GlimmerHMM_glimmerT_18925-T1
Valid prediction for GlimmerHMM_glimmerT_18912-T1
Valid prediction for GlimmerHMM_glimmerT_18916-T1
Valid prediction for snap_scaffold_7-snap.3419-T1
Valid prediction for snap_scaffold_7-snap.3426-T1
Valid prediction for snap_scaffold_7-snap.3439-T1
Valid prediction for snap_scaffold_7-snap.3411-T1
Valid prediction for snap_scaffold_7-snap.3421-T1
Valid prediction for snap_scaffold_7-snap.3440-T1
Valid prediction for Augustus_model.g12693.t1
Valid prediction for GlimmerHMM_glimmerT_18928-T1
Valid prediction for snap_scaffold_7-snap.3437-T1
Valid prediction for pasa_asmbl_50496.p1
Valid prediction for pasa_asmbl_50500.p1
Valid prediction for HiQ_model.g12690.t1
Valid prediction for GlimmerHMM_glimmerT_18923-T1
Valid prediction for snap_scaffold_7-snap.3399-T1
Valid prediction for snap_scaffold_7-snap.3442-T1
Valid prediction for snap_scaffold_7-snap.3413-T1
Valid prediction for snap_scaffold_7-snap.3429-T1
Valid prediction for HiQ_model.g12691.t1
Valid prediction for Augustus_model.g12686.t1
Valid prediction for pasa_asmbl_50504.p1
Valid prediction for snap_scaffold_7-snap.3417-T1
Valid prediction for snap_scaffold_7-snap.3397-T1
Valid prediction for snap_scaffold_7-snap.3441-T1
Couldn't classify 1371, 1434
Sorry, prediction pasa_asmbl_50492.p1 fails validation.
(AGA)	 GG	1371-1434	GT	AGG
(TCG)	 AG	1621-1719	GT	AGG
(CTC)	 AG	2229-2291	GT	CAG
(ACA)	 AG	2721-2771	GT	AGG
(TGG)	 AG	3590-3640	GT	AGG
(GGT)	 AG	4555-4620	GT	AAG
(ATT)	 AG	4789-4936	GT	GGG
(AGA)	 AG	5086-5189	GT	GGG
(GAA)	 AG	7288-7514	GT	AGG
(GCT)	 AG	7649-8162	GT	AGG
(GTG)	 AG	8722-8900	GC	GAG
-recovered pasa_asmbl_50492.p1, terminal, 8722, 8900
-recovered pasa_asmbl_50492.p1, internal, 1621, 1719
-recovered pasa_asmbl_50492.p1, internal, 2229, 2291
-recovered pasa_asmbl_50492.p1, internal, 2721, 2771
-recovered pasa_asmbl_50492.p1, internal, 3590, 3640
-recovered pasa_asmbl_50492.p1, internal, 4555, 4620
-recovered pasa_asmbl_50492.p1, internal, 4789, 4936
-recovered pasa_asmbl_50492.p1, internal, 5086, 5189
-recovered pasa_asmbl_50492.p1, internal, 7288, 7514
-recovered pasa_asmbl_50492.p1, internal, 7649, 8162
-recovered pasa_asmbl_50492.p1, internal, 8722, 8900
Valid prediction for GlimmerHMM_glimmerT_18921-T1
Valid prediction for snap_scaffold_7-snap.3403-T1
Valid prediction for snap_scaffold_7-snap.3407-T1
Valid prediction for CodingQuarry_transcript_57749-T1
Valid prediction for snap_scaffold_7-snap.3418-T1
Valid prediction for snap_scaffold_7-snap.3402-T1
Valid prediction for Augustus_model.g12692.t1
Valid prediction for snap_scaffold_7-snap.3410-T1
Valid prediction for snap_scaffold_7-snap.3415-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_18915-T1
Valid prediction for GlimmerHMM_glimmerT_18914-T1
Couldn't classify 201400, 201465
Couldn't classify 203879, 203931
Sorry, prediction pasa_asmbl_51437.p1 fails validation.
(GGA)	 TG	201400-201465	GT	AGG
(GTC)	 AG	202831-203007	GT	AGG
(GTG)	 AG	203247-203493	GT	CGG
(GTG)	 AG	203879-203931	AG	GCA
-recovered pasa_asmbl_51437.p1, internal, 202831, 203007
-recovered pasa_asmbl_51437.p1, internal, 203247, 203493
Valid prediction for Augustus_model.g12699.t1
Valid prediction for snap_scaffold_7-snap.3406-T1
Valid prediction for snap_scaffold_7-snap.3432-T1
Couldn't classify 208144, 208221
Sorry, prediction pasa_asmbl_51435.p1 fails validation.
(GAG)	 CT	208144-208221	GT	GGG
(GTC)	 AG	208455-208668	GT	CCG
(GTG)	 AG	209776-210083	GC	GAG
-recovered pasa_asmbl_51435.p1, terminal, 209776, 210083
-recovered pasa_asmbl_51435.p1, internal, 208455, 208668
-recovered pasa_asmbl_51435.p1, internal, 209776, 210083
Valid prediction for snap_scaffold_7-snap.3427-T1
Valid prediction for GlimmerHMM_glimmerT_18936-T1
Valid prediction for HiQ_model.g12696.t1
Valid prediction for GlimmerHMM_glimmerT_18929-T1
Valid prediction for snap_scaffold_7-snap.3405-T1
Valid prediction for snap_scaffold_7-snap.3428-T1
Valid prediction for Augustus_model.g12694.t1
Couldn't classify 204848, 204889
Couldn't classify 207698, 207855
Sorry, prediction pasa_asmbl_51436.p1 fails validation.
(CTG)	 TG	204848-204889	GT	AGG
(CTA)	 AG	205935-206079	GT	GGG
(GTA)	 AG	206506-206775	GT	AGG
(GCA)	 AG	207698-207855	AC	CCA
-recovered pasa_asmbl_51436.p1, internal, 205935, 206079
-recovered pasa_asmbl_51436.p1, internal, 206506, 206775
Valid prediction for GlimmerHMM_glimmerT_18938-T1
Valid prediction for CodingQuarry_transcript_57751-T1
Valid prediction for GlimmerHMM_glimmerT_18920-T1
Valid prediction for snap_scaffold_7-snap.3434-T1
Valid prediction for snap_scaffold_7-snap.3398-T1
Valid prediction for snap_scaffold_7-snap.3416-T1
Valid prediction for snap_scaffold_7-snap.3438-T1
Valid prediction for GlimmerHMM_glimmerT_18918-T1
Valid prediction for GlimmerHMM_glimmerT_18917-T1
Couldn't classify 192956, 193049
Couldn't classify 194154, 194221
Sorry, prediction pasa_asmbl_51566.p1 fails validation.
(GAG)	 CT	192956-193049	GT	GGG
(GGC)	 AG	193675-193827	GT	TGG
(CCA)	 AG	194154-194221	CC	CCC
-recovered pasa_asmbl_51566.p1, internal, 193675, 193827
Couldn't classify 34134, 34469
Sorry, prediction pasa_asmbl_51444.p1 fails validation.
(CAA)	 TC	34134-34469	TC	CCT
Valid prediction for snap_scaffold_7-snap.3433-T1
Valid prediction for snap_scaffold_7-snap.3408-T1
Valid prediction for Augustus_model.g12689.t1
Valid prediction for snap_scaffold_7-snap.3425-T1
Valid prediction for GlimmerHMM_glimmerT_18933-T1
Valid prediction for GlimmerHMM_glimmerT_18930-T1
Valid prediction for Augustus_model.g12698.t1
Valid prediction for CodingQuarry_transcript_57752-T1
Valid prediction for snap_scaffold_7-snap.3420-T1
Valid prediction for HiQ_model.g12697.t1
Valid prediction for Augustus_model.g12688.t1
Valid prediction for GlimmerHMM_glimmerT_18934-T1
Valid prediction for snap_scaffold_7-snap.3401-T1
Valid prediction for GlimmerHMM_glimmerT_18931-T1
Valid prediction for snap_scaffold_7-snap.3423-T1
Valid prediction for GlimmerHMM_glimmerT_18932-T1
Couldn't classify 11278, 11310
Couldn't classify 18892, 18969
Sorry, prediction pasa_asmbl_51445.p1 fails validation.
(GTC)	 AG	11278-11310	GT	AGG
(GTG)	 AG	12027-12117	GT	TGG
(TGT)	 AG	12824-12903	GC	AGG
(ACC)	 AG	13052-13143	GT	GTG
(TCA)	 AG	15856-15997	GT	TGG
(GTC)	 AG	18892-18969	TT	AGT
-recovered pasa_asmbl_51445.p1, internal, 11278, 11310
-recovered pasa_asmbl_51445.p1, internal, 12027, 12117
-recovered pasa_asmbl_51445.p1, internal, 12824, 12903
-recovered pasa_asmbl_51445.p1, internal, 13052, 13143
-recovered pasa_asmbl_51445.p1, internal, 15856, 15997
Couldn't classify 199564, 199723
Couldn't classify 199890, 200146
Sorry, prediction pasa_asmbl_51438.p2 fails validation.
(GGT)	 CG	199564-199723	GT	GGG
(AGG)	 AG	199890-200146	GG	AAG
Couldn't classify 34995, 35190
Sorry, prediction pasa_asmbl_51443.p1 fails validation.
(GGG)	 CG	34995-35190	GT	AGG
(TGG)	 AG	35567-35677	GT	AGG
(CCC)	 AG	35906-36130	GT	GTG
(CGG)	 AG	36241-36387	GT	AAG
(GTA)	 AG	36647-36792	CA	GAC
-recovered pasa_asmbl_51443.p1, terminal, 36647, 36792
-recovered pasa_asmbl_51443.p1, internal, 35567, 35677
-recovered pasa_asmbl_51443.p1, internal, 35906, 36130
-recovered pasa_asmbl_51443.p1, internal, 36241, 36387
Valid prediction for snap_scaffold_7-snap.3414-T1
Valid prediction for snap_scaffold_7-snap.3400-T1
Valid prediction for pasa_asmbl_51439.p1
Valid prediction for GlimmerHMM_glimmerT_18942-T1
Valid prediction for GlimmerHMM_glimmerT_18927-T1
Valid prediction for pasa_asmbl_51529.p1
Valid prediction for snap_scaffold_7-snap.3430-T1
Valid prediction for GlimmerHMM_glimmerT_18935-T1
Valid prediction for Augustus_model.g12687.t1
Valid prediction for GlimmerHMM_glimmerT_18940-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21350, rend_intergenic: 18893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32849, rend_intergenic: 21458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46253, rend_intergenic: 33314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52810, rend_intergenic: 48343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62059, rend_intergenic: 53454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63443, rend_intergenic: 62369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70899, rend_intergenic: 63448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98805, rend_intergenic: 96643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128444, rend_intergenic: 113594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133038, rend_intergenic: 128455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146039, rend_intergenic: 134508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166113, rend_intergenic: 162126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181708, rend_intergenic: 172066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195836, rend_intergenic: 194353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205334, rend_intergenic: 196822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238643, rend_intergenic: 224691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239923, rend_intergenic: 239015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252454, rend_intergenic: 240941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 257567
-exon list size: 507


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 21350, rend_intergenic: 18893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32849, rend_intergenic: 21458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46253, rend_intergenic: 33314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52810, rend_intergenic: 48343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62059, rend_intergenic: 53454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63443, rend_intergenic: 62369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70899, rend_intergenic: 63448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98805, rend_intergenic: 96643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128444, rend_intergenic: 113594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133038, rend_intergenic: 128455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146039, rend_intergenic: 134508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166113, rend_intergenic: 162126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181708, rend_intergenic: 172066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195836, rend_intergenic: 194353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205334, rend_intergenic: 196822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238643, rend_intergenic: 224691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239923, rend_intergenic: 239015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252454, rend_intergenic: 240941  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