-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_13096557-13403611

-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 Augustus_model.g15457.t1
Valid prediction for Augustus_model.g15437.t1
Valid prediction for Augustus_model.g15444.t1
Valid prediction for snap_scaffold_9-snap.2631-T1
Valid prediction for Augustus_model.g15458.t1
Valid prediction for GlimmerHMM_glimmerT_23146-T1
Valid prediction for HiQ_model.g15436.t1
Valid prediction for snap_scaffold_9-snap.2596-T1
Valid prediction for snap_scaffold_9-snap.2605-T1
Valid prediction for snap_scaffold_9-snap.2622-T1
Valid prediction for snap_scaffold_9-snap.2590-T1
Valid prediction for snap_scaffold_9-snap.2647-T1
Valid prediction for snap_scaffold_9-snap.2636-T1
Valid prediction for GlimmerHMM_glimmerT_23154-T1
Valid prediction for GlimmerHMM_glimmerT_23173-T1
Valid prediction for Augustus_model.g15439.t1
Valid prediction for snap_scaffold_9-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_23168-T1
Valid prediction for GlimmerHMM_glimmerT_23163-T1
Valid prediction for GlimmerHMM_glimmerT_23148-T1
Valid prediction for GlimmerHMM_glimmerT_23176-T1
Valid prediction for snap_scaffold_9-snap.2621-T1
Valid prediction for snap_scaffold_9-snap.2615-T1
Valid prediction for HiQ_model.g15441.t1
Valid prediction for GlimmerHMM_glimmerT_23177-T1
Valid prediction for CodingQuarry_transcript_62389-T1
Valid prediction for snap_scaffold_9-snap.2618-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_23171-T1
Valid prediction for Augustus_model.g15451.t1
Valid prediction for snap_scaffold_9-snap.2599-T1
Valid prediction for GlimmerHMM_glimmerT_23156-T1
Valid prediction for snap_scaffold_9-snap.2638-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2652-T1
Valid prediction for pasa_asmbl_54494.p1
Valid prediction for snap_scaffold_9-snap.2650-T1
Valid prediction for snap_scaffold_9-snap.2645-T1
Valid prediction for Augustus_model.g15455.t1
Valid prediction for snap_scaffold_9-snap.2607-T1
Valid prediction for GlimmerHMM_glimmerT_23144-T1
Valid prediction for GlimmerHMM_glimmerT_23150-T1
Valid prediction for Augustus_model.g15453.t1
Valid prediction for HiQ_model.g15443.t1
Valid prediction for GlimmerHMM_glimmerT_23162-T1
Valid prediction for GlimmerHMM_glimmerT_23167-T1
Valid prediction for snap_scaffold_9-snap.2626-T1
Valid prediction for snap_scaffold_9-snap.2617-T1
Valid prediction for GlimmerHMM_glimmerT_23160-T1
Valid prediction for snap_scaffold_9-snap.2600-T1
Valid prediction for Augustus_model.g15438.t1
Valid prediction for snap_scaffold_9-snap.2628-T1
Valid prediction for GlimmerHMM_glimmerT_23165-T1
Valid prediction for Augustus_model.g15459.t1
Valid prediction for snap_scaffold_9-snap.2624-T1
Valid prediction for GlimmerHMM_glimmerT_23164-T1
Valid prediction for pasa_asmbl_54492.p1
Valid prediction for GlimmerHMM_glimmerT_23159-T1
Valid prediction for snap_scaffold_9-snap.2593-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2643-T1
Couldn't classify 172754, 172861
Sorry, prediction pasa_asmbl_54487.p1 fails validation.
(GAG)	 CA	172754-172861	GT	AGG
(GCT)	 AG	173538-173648	GT	CCG
(TTG)	 AG	175749-175841	GA	AAG
-recovered pasa_asmbl_54487.p1, terminal, 175749, 175841
-recovered pasa_asmbl_54487.p1, internal, 173538, 173648
Valid prediction for snap_scaffold_9-snap.2608-T1
Valid prediction for snap_scaffold_9-snap.2595-T1
Valid prediction for GlimmerHMM_glimmerT_23149-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_23152-T1
Couldn't classify 95621, 95746
Couldn't classify 101124, 101362
Sorry, prediction pasa_asmbl_55430.p1 fails validation.
(GAT)	 CA	95621-95746	GT	GGG
(AGC)	 AG	96463-96586	GT	AGG
(ACT)	 AG	98175-98401	GT	AGG
(TCT)	 AG	98634-98786	GT	AGG
(TCT)	 AG	99589-99751	GT	AAG
(TGA)	 AG	101124-101362	AC	ACA
-recovered pasa_asmbl_55430.p1, terminal, 99589, 99751
-recovered pasa_asmbl_55430.p1, internal, 96463, 96586
-recovered pasa_asmbl_55430.p1, internal, 98175, 98401
-recovered pasa_asmbl_55430.p1, internal, 98634, 98786
-recovered pasa_asmbl_55430.p1, internal, 99589, 99751
Valid prediction for snap_scaffold_9-snap.2642-T1
Valid prediction for snap_scaffold_9-snap.2644-T1
Valid prediction for pasa_asmbl_55418.p1
Valid prediction for snap_scaffold_9-snap.2625-T1
Valid prediction for GlimmerHMM_glimmerT_23147-T1
Valid prediction for Augustus_model.g15432.t1
Valid prediction for CodingQuarry_transcript_62393-T1
Valid prediction for snap_scaffold_9-snap.2634-T1
Valid prediction for snap_scaffold_9-snap.2614-T1
Valid prediction for GlimmerHMM_glimmerT_23151-T1
Valid prediction for GlimmerHMM_glimmerT_23158-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g15440.t1
Valid prediction for snap_scaffold_9-snap.2632-T1
Valid prediction for snap_scaffold_9-snap.2613-T1
Valid prediction for snap_scaffold_9-snap.2641-T1
Valid prediction for CodingQuarry_transcript_62392-T1
Valid prediction for HiQ_model.g15450.t1
Valid prediction for snap_scaffold_9-snap.2594-T1
Valid prediction for snap_scaffold_9-snap.2598-T1
Valid prediction for HiQ_model.g15442.t1
Valid prediction for CodingQuarry_transcript_62395-T1
Valid prediction for GlimmerHMM_glimmerT_23175-T1
Valid prediction for snap_scaffold_9-snap.2623-T1
Valid prediction for Augustus_model.g15447.t1
Valid prediction for Augustus_model.g15445.t1
Couldn't classify 93330, 93752
Sorry, prediction pasa_asmbl_55434.p1 fails validation.
(TCC)	 TG	93330-93752	AA	AGA
Valid prediction for Augustus_model.g15449.t1
Valid prediction for snap_scaffold_9-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_23178-T1
Valid prediction for snap_scaffold_9-snap.2651-T1
Valid prediction for GlimmerHMM_glimmerT_23155-T1
Valid prediction for Augustus_model.g15433.t1
Valid prediction for snap_scaffold_9-snap.2606-T1
Valid prediction for snap_scaffold_9-snap.2637-T1
Valid prediction for Augustus_model.g15448.t1
Valid prediction for snap_scaffold_9-snap.2610-T1
Valid prediction for pasa_asmbl_55442.p1
Valid prediction for snap_scaffold_9-snap.2616-T1
Valid prediction for GlimmerHMM_glimmerT_23170-T1
Valid prediction for snap_scaffold_9-snap.2629-T1
Valid prediction for snap_scaffold_9-snap.2627-T1
Valid prediction for snap_scaffold_9-snap.2591-T1
Valid prediction for Augustus_model.g15452.t1
Valid prediction for GlimmerHMM_glimmerT_23153-T1
Valid prediction for snap_scaffold_9-snap.2592-T1
Valid prediction for GlimmerHMM_glimmerT_23172-T1
Valid prediction for Augustus_model.g15454.t1
Valid prediction for snap_scaffold_9-snap.2633-T1
Valid prediction for snap_scaffold_9-snap.2619-T1
Valid prediction for snap_scaffold_9-snap.2611-T1
Valid prediction for GlimmerHMM_glimmerT_23145-T1
Valid prediction for Augustus_model.g15446.t1
Couldn't classify 89975, 90289
Sorry, prediction pasa_asmbl_55437.p1 fails validation.
(CAT)	 AC	89975-90289	CC	ACC
Valid prediction for snap_scaffold_9-snap.2640-T1
Couldn't classify 34478, 34648
Sorry, prediction pasa_asmbl_55443.p1 fails validation.
(TTA)	 TC	34478-34648	GT	GGG
(GCA)	 AG	34861-35004	AA	GAA
-recovered pasa_asmbl_55443.p1, terminal, 34861, 35004
Valid prediction for GlimmerHMM_glimmerT_23169-T1
Valid prediction for snap_scaffold_9-snap.2635-T1
Valid prediction for snap_scaffold_9-snap.2630-T1
Valid prediction for snap_scaffold_9-snap.2603-T1
Valid prediction for GlimmerHMM_glimmerT_23166-T1
Valid prediction for GlimmerHMM_glimmerT_23174-T1
Valid prediction for snap_scaffold_9-snap.2602-T1
Valid prediction for snap_scaffold_9-snap.2649-T1
Valid prediction for snap_scaffold_9-snap.2653-T1
Valid prediction for snap_scaffold_9-snap.2604-T1
Valid prediction for snap_scaffold_9-snap.2639-T1
Valid prediction for GlimmerHMM_glimmerT_23143-T1
Couldn't classify 126460, 126789
Sorry, prediction pasa_asmbl_54488.p2 fails validation.
(CTC)	 CT	126460-126789	TG	AGT
Couldn't classify 102049, 102207
Sorry, prediction pasa_asmbl_55420.p1 fails validation.
(GGT)	 CA	102049-102207	GT	AGG
(AGT)	 AG	103154-103267	GT	AGG
(AAG)	 AG	103492-103583	GT	AGG
(GCT)	 AG	103722-104280	GG	GAG
-recovered pasa_asmbl_55420.p1, terminal, 103722, 104280
-recovered pasa_asmbl_55420.p1, internal, 103154, 103267
-recovered pasa_asmbl_55420.p1, internal, 103492, 103583
Valid prediction for snap_scaffold_9-snap.2609-T1
Valid prediction for Augustus_model.g15435.t1
Valid prediction for Augustus_model.g15434.t1
Valid prediction for GlimmerHMM_glimmerT_23161-T1
Valid prediction for HiQ_model.g15456.t1
Valid prediction for GlimmerHMM_glimmerT_23157-T1
Valid prediction for snap_scaffold_9-snap.2646-T1
Valid prediction for snap_scaffold_9-snap.2648-T1
Valid prediction for snap_scaffold_9-snap.2620-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8953, rend_intergenic: 3023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19668, rend_intergenic: 16377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31925, rend_intergenic: 20746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59104, rend_intergenic: 32881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66302, rend_intergenic: 60346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75470, rend_intergenic: 71016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90134, rend_intergenic: 87772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95680, rend_intergenic: 90232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114944, rend_intergenic: 96386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123993, rend_intergenic: 116510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137407, rend_intergenic: 126028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140872, rend_intergenic: 137607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151656, rend_intergenic: 141665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160381, rend_intergenic: 152384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176616, rend_intergenic: 162129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183097, rend_intergenic: 179660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183957, rend_intergenic: 183400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197970, rend_intergenic: 192371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213708, rend_intergenic: 202390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218553, rend_intergenic: 214542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249528, rend_intergenic: 247859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265677, rend_intergenic: 249790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279553, rend_intergenic: 277098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 280611, rend_intergenic: 279689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289074, rend_intergenic: 282818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294038, rend_intergenic: 289662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 301405, rend_intergenic: 294068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306405, rend_intergenic: 302536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 307055
-exon list size: 570


building trellis

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85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 8953, rend_intergenic: 3023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19668, rend_intergenic: 16377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31925, rend_intergenic: 20746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59104, rend_intergenic: 32881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66302, rend_intergenic: 60346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75470, rend_intergenic: 71016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90134, rend_intergenic: 87772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95680, rend_intergenic: 90232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114944, rend_intergenic: 96386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123993, rend_intergenic: 116510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137407, rend_intergenic: 126028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140872, rend_intergenic: 137607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151656, rend_intergenic: 141665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160381, rend_intergenic: 152384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176616, rend_intergenic: 162129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183097, rend_intergenic: 179660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183957, rend_intergenic: 183400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197970, rend_intergenic: 192371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213708, rend_intergenic: 202390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218553, rend_intergenic: 214542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249528, rend_intergenic: 247859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265677, rend_intergenic: 249790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279553, rend_intergenic: 277098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 280611, rend_intergenic: 279689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289074, rend_intergenic: 282818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294038, rend_intergenic: 289662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 301405, rend_intergenic: 294068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306405, rend_intergenic: 302536  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