-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_11446127-11605826

-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 GeneMark_model.76652_t
Valid prediction for GlimmerHMM_glimmerT_44187-T1
Valid prediction for GlimmerHMM_glimmerT_44183-T1
Valid prediction for snap_scaffold_18-snap.2454-T1
Valid prediction for GeneMark_model.76648_t
Valid prediction for GeneMark_model.76656_t
Valid prediction for snap_scaffold_18-snap.2481-T1
Valid prediction for GeneMark_model.76654_t
Valid prediction for HiQ_model.g29568.t1
Valid prediction for snap_scaffold_18-snap.2465-T1
Valid prediction for snap_scaffold_18-snap.2478-T1
Valid prediction for CodingQuarry_transcript_23857-T1
Valid prediction for GeneMark_model.76631_t
Valid prediction for GlimmerHMM_glimmerT_44188-T1
Valid prediction for GeneMark_model.76644_t
Valid prediction for GlimmerHMM_glimmerT_44176-T1
Valid prediction for snap_scaffold_18-snap.2476-T1
Valid prediction for GeneMark_model.76647_t
Valid prediction for GeneMark_model.76626_t
Valid prediction for HiQ_model.g29577.t1
Valid prediction for pasa_asmbl_20969.p1
Valid prediction for GeneMark_model.76640_t
Valid prediction for GeneMark_model.76649_t
Valid prediction for snap_scaffold_18-snap.2447-T1
Valid prediction for HiQ_model.g29580.t1
Valid prediction for CodingQuarry_transcript_23859-T1
Valid prediction for GeneMark_model.76630_t
Valid prediction for Augustus_model.g29578.t1
Valid prediction for snap_scaffold_18-snap.2463-T1
Valid prediction for snap_scaffold_18-snap.2453-T1
Couldn't classify 24585, 24710
Sorry, prediction pasa_asmbl_20968.p1 fails validation.
(ACT)	 AG	24585-24710	GT	AGG
(ATT)	 AG	25278-25398	GT	AGG
(TTA)	 AG	25499-25574	GT	AGG
(GTT)	 AG	25842-25914	GT	AGG
(CTC)	 AG	26254-26381	GT	AGG
(GAA)	 AG	26592-26743	GT	AGG
(GAA)	 AG	26822-27138	CG	GAC
-recovered pasa_asmbl_20968.p1, terminal, 26822, 27138
-recovered pasa_asmbl_20968.p1, internal, 24585, 24710
-recovered pasa_asmbl_20968.p1, internal, 25278, 25398
-recovered pasa_asmbl_20968.p1, internal, 25499, 25574
-recovered pasa_asmbl_20968.p1, internal, 25842, 25914
-recovered pasa_asmbl_20968.p1, internal, 26254, 26381
-recovered pasa_asmbl_20968.p1, internal, 26592, 26743
Valid prediction for GeneMark_model.76642_t
Valid prediction for GeneMark_model.76624_t
Valid prediction for GlimmerHMM_glimmerT_44192-T1
Valid prediction for snap_scaffold_18-snap.2468-T1
Valid prediction for snap_scaffold_18-snap.2473-T1
Valid prediction for snap_scaffold_18-snap.2475-T1
Valid prediction for snap_scaffold_18-snap.2457-T1
Valid prediction for snap_scaffold_18-snap.2487-T1
Valid prediction for pasa_asmbl_21102.p1
Valid prediction for snap_scaffold_18-snap.2449-T1
Valid prediction for GeneMark_model.76633_t
Valid prediction for snap_scaffold_18-snap.2470-T1
Valid prediction for CodingQuarry_transcript_23854-T1
Valid prediction for snap_scaffold_18-snap.2485-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.2459-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.76636_t
Valid prediction for Augustus_model.g29574.t1
Valid prediction for snap_scaffold_18-snap.2451-T1
Valid prediction for GeneMark_model.76650_t
Valid prediction for GeneMark_model.76643_t
Valid prediction for CodingQuarry_transcript_23855-T1
Valid prediction for CodingQuarry_transcript_23858-T1
Valid prediction for GeneMark_model.76628_t
Valid prediction for GeneMark_model.76638_t

-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: -)Couldn't classify 146994, 147094
Sorry, prediction pasa_asmbl_20162.p1 fails validation.
(ATG)	 TT	144945-144990	GT	AGG
(GTC)	 AG	145579-145691	GT	AGG
(TTT)	 AG	145891-146028	GT	AGG
(GGA)	 AG	146292-146394	GT	TGG
(GCG)	 AG	146994-147094	GT	CGG
-recovered pasa_asmbl_20162.p1, initial, 144945, 144990
-recovered pasa_asmbl_20162.p1, internal, 145579, 145691
-recovered pasa_asmbl_20162.p1, internal, 145891, 146028
-recovered pasa_asmbl_20162.p1, internal, 146292, 146394
-recovered pasa_asmbl_20162.p1, internal, 146994, 147094
Valid prediction for snap_scaffold_18-snap.2477-T1
Valid prediction for Augustus_model.g29575.t1
Valid prediction for Augustus_model.g29571.t1
Valid prediction for snap_scaffold_18-snap.2483-T1
Valid prediction for GlimmerHMM_glimmerT_44190-T1
Valid prediction for GeneMark_model.76657_t
Valid prediction for snap_scaffold_18-snap.2456-T1
Valid prediction for Augustus_model.g29579.t1
Valid prediction for snap_scaffold_18-snap.2461-T1
Valid prediction for snap_scaffold_18-snap.2452-T1
Valid prediction for CodingQuarry_transcript_23856-T1
Valid prediction for Augustus_model.g29567.t1
Valid prediction for snap_scaffold_18-snap.2482-T1
Valid prediction for snap_scaffold_18-snap.2448-T1
Valid prediction for GeneMark_model.76639_t
Valid prediction for snap_scaffold_18-snap.2466-T1
Valid prediction for GlimmerHMM_glimmerT_44178-T1
Valid prediction for GeneMark_model.76623_t
Valid prediction for GeneMark_model.76637_t
Valid prediction for GeneMark_model.76646_t
Valid prediction for snap_scaffold_18-snap.2455-T1
Valid prediction for GlimmerHMM_glimmerT_44174-T1
Valid prediction for GlimmerHMM_glimmerT_44175-T1
Couldn't classify 137918, 138096
Sorry, prediction pasa_asmbl_20165.p1 fails validation.
(ATG)	 CC	136627-136825	GT	AGG
(GTG)	 AG	137918-138096	CG	ACC
-recovered pasa_asmbl_20165.p1, initial, 136627, 136825
Valid prediction for GeneMark_model.76651_t
Valid prediction for GlimmerHMM_glimmerT_44186-T1
Valid prediction for snap_scaffold_18-snap.2464-T1
Valid prediction for snap_scaffold_18-snap.2474-T1
Valid prediction for snap_scaffold_18-snap.2462-T1
Valid prediction for GeneMark_model.76653_t
Valid prediction for GlimmerHMM_glimmerT_44191-T1
Valid prediction for snap_scaffold_18-snap.2469-T1
Valid prediction for GlimmerHMM_glimmerT_44185-T1
Valid prediction for GlimmerHMM_glimmerT_44179-T1
Couldn't classify 49479, 49683
Couldn't classify 50875, 51258
Sorry, prediction pasa_asmbl_20167.p1 fails validation.
(TTC)	 AT	49479-49683	GT	AGG
(ATA)	 AG	49914-50084	GT	AGG
(GAC)	 AG	50413-50519	GT	AGG
(GTG)	 AG	50875-51258	CT	CCC
-recovered pasa_asmbl_20167.p1, internal, 49914, 50084
-recovered pasa_asmbl_20167.p1, internal, 50413, 50519
Valid prediction for GeneMark_model.76659_t
Valid prediction for GeneMark_model.76641_t
Valid prediction for Augustus_model.g29570.t1
Valid prediction for snap_scaffold_18-snap.2480-T1
Valid prediction for GeneMark_model.76629_t
Valid prediction for GeneMark_model.76658_t
Valid prediction for snap_scaffold_18-snap.2471-T1
Valid prediction for Augustus_model.g29576.t1
Valid prediction for snap_scaffold_18-snap.2479-T1
Valid prediction for Augustus_model.g29573.t1
Valid prediction for GlimmerHMM_glimmerT_44172-T1
Valid prediction for GeneMark_model.76660_t
Valid prediction for GeneMark_model.76632_t
Valid prediction for snap_scaffold_18-snap.2460-T1
Valid prediction for GlimmerHMM_glimmerT_44182-T1
Valid prediction for snap_scaffold_18-snap.2484-T1
Valid prediction for snap_scaffold_18-snap.2486-T1
Valid prediction for GeneMark_model.76645_t
Valid prediction for Augustus_model.g29569.t1
Valid prediction for GeneMark_model.76634_t
Valid prediction for GlimmerHMM_glimmerT_44171-T1
Valid prediction for GeneMark_model.76661_t
Valid prediction for Augustus_model.g29566.t1
Valid prediction for GeneMark_model.76655_t
Valid prediction for GeneMark_model.76625_t
Valid prediction for GeneMark_model.76635_t
Valid prediction for GlimmerHMM_glimmerT_44180-T1
Valid prediction for GlimmerHMM_glimmerT_44189-T1
Valid prediction for snap_scaffold_18-snap.2450-T1
Valid prediction for GlimmerHMM_glimmerT_44184-T1
Valid prediction for Augustus_model.g29572.t1
Valid prediction for GlimmerHMM_glimmerT_44173-T1
Valid prediction for snap_scaffold_18-snap.2472-T1
Valid prediction for GlimmerHMM_glimmerT_44177-T1
Valid prediction for snap_scaffold_18-snap.2467-T1
Couldn't classify 55479, 55538
Sorry, prediction pasa_asmbl_20166.p1 fails validation.
(CAG)	 GC	55479-55538	GT	TGG
(GCT)	 AG	55661-55690	GT	GGG
(ATT)	 AG	56334-56407	GT	AGG
(CGA)	 AG	57715-57808	GT	AGG
(CTT)	 AG	58636-58710	GT	TGG
(CTT)	 AG	59128-59199	GT	AGG
(GAG)	 AG	60721-60822	AG	AGA
-recovered pasa_asmbl_20166.p1, terminal, 60721, 60822
-recovered pasa_asmbl_20166.p1, internal, 55661, 55690
-recovered pasa_asmbl_20166.p1, internal, 56334, 56407
-recovered pasa_asmbl_20166.p1, internal, 57715, 57808
-recovered pasa_asmbl_20166.p1, internal, 58636, 58710
-recovered pasa_asmbl_20166.p1, internal, 59128, 59199
Valid prediction for GlimmerHMM_glimmerT_44181-T1
Valid prediction for snap_scaffold_18-snap.2458-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10743, rend_intergenic: 6971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15472, rend_intergenic: 12280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23155, rend_intergenic: 16387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35658, rend_intergenic: 33984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40917, rend_intergenic: 39480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45519, rend_intergenic: 43584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48565, rend_intergenic: 47674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64253, rend_intergenic: 60592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72514, rend_intergenic: 64308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96004, rend_intergenic: 94860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105219, rend_intergenic: 99960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109740, rend_intergenic: 106673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120695, rend_intergenic: 113880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125114, rend_intergenic: 121228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129423, rend_intergenic: 128656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136125, rend_intergenic: 129687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151240, rend_intergenic: 148823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 98882, rend_intergenic: 98879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159700
-exon list size: 567


building trellis

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98.6    
98.8    
98.9    
99.1    
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99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 10743, rend_intergenic: 6971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15472, rend_intergenic: 12280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23155, rend_intergenic: 16387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35658, rend_intergenic: 33984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40917, rend_intergenic: 39480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45519, rend_intergenic: 43584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48565, rend_intergenic: 47674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64253, rend_intergenic: 60592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72514, rend_intergenic: 64308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96004, rend_intergenic: 94860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105219, rend_intergenic: 99960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109740, rend_intergenic: 106673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120695, rend_intergenic: 113880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125114, rend_intergenic: 121228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129423, rend_intergenic: 128656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136125, rend_intergenic: 129687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151240, rend_intergenic: 148823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 98882, rend_intergenic: 98879  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