-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_13434036-13564185

-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.77218_t
Valid prediction for GlimmerHMM_glimmerT_44394-T1
Valid prediction for snap_scaffold_18-snap.2860-T1
Valid prediction for GeneMark_model.77240_t
Valid prediction for GeneMark_model.77216_t
Valid prediction for GeneMark_model.77215_t
Valid prediction for CodingQuarry_transcript_23878-T1
Couldn't classify 128282, 128341
Couldn't classify 128757, 128822
Sorry, prediction CodingQuarry_transcript_23881-T1 fails validation.
(ATG)	 CC	128282-128341	CT	GCC
(CTC)	 GC	128757-128822	CA	GAC
Valid prediction for GeneMark_model.77229_t
Valid prediction for snap_scaffold_18-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_44407-T1
Valid prediction for GeneMark_model.77213_t
Valid prediction for GeneMark_model.77227_t
Valid prediction for snap_scaffold_18-snap.2866-T1
Valid prediction for snap_scaffold_18-snap.2863-T1
Valid prediction for snap_scaffold_18-snap.2855-T1
Valid prediction for GeneMark_model.77223_t
Valid prediction for Augustus_model.g29695.t1
Valid prediction for GeneMark_model.77235_t
Valid prediction for GeneMark_model.77225_t
Valid prediction for GeneMark_model.77219_t
Valid prediction for GlimmerHMM_glimmerT_44392-T1
Valid prediction for GeneMark_model.77245_t
Valid prediction for GlimmerHMM_glimmerT_44396-T1
Valid prediction for snap_scaffold_18-snap.2869-T1
Valid prediction for GeneMark_model.77233_t
Valid prediction for CodingQuarry_transcript_23877-T1
Valid prediction for snap_scaffold_18-snap.2871-T1
Valid prediction for snap_scaffold_18-snap.2858-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_44406-T1
Valid prediction for HiQ_model.g29688.t1
Valid prediction for GeneMark_model.77242_t
Valid prediction for GeneMark_model.77238_t
Valid prediction for snap_scaffold_18-snap.2857-T1
Valid prediction for GlimmerHMM_glimmerT_44398-T1
Valid prediction for GlimmerHMM_glimmerT_44405-T1
Valid prediction for snap_scaffold_18-snap.2874-T1
Valid prediction for snap_scaffold_18-snap.2865-T1
Valid prediction for snap_scaffold_18-snap.2861-T1
Valid prediction for pasa_asmbl_21036.p1
Valid prediction for GeneMark_model.77247_t
Valid prediction for HiQ_model.g29689.t1
Valid prediction for snap_scaffold_18-snap.2878-T1
Valid prediction for GeneMark_model.77243_t
Valid prediction for pasa_asmbl_21042.p1
Couldn't classify 16107, 16250
Sorry, prediction pasa_asmbl_21038.p1 fails validation.
(GTG)	 GT	16107-16250	GT	AGG
(TGT)	 AG	17728-17901	GT	AGG
(ACC)	 AG	19225-19383	GT	AGG
(GTG)	 AG	20354-20578	GT	AGG
(TAT)	 AG	20725-20808	GT	AGG
(ATG)	 AG	21379-21473	GT	GTG
(ATT)	 AG	21608-21796	GT	GGG
(GCG)	 AG	22553-22644	GT	TAG
(GCG)	 AG	23068-23328	GT	TGG
(ACC)	 AG	23674-23744	GT	ATG
(GAC)	 AG	23990-24105	GT	TGG
(GTA)	 AG	24802-24951	GT	AGG
(AGA)	 AG	25670-25773	GT	CTG
(ATA)	 AG	26130-26218	GT	TGG
(TCC)	 AG	26402-26707	GA	GAG
-recovered pasa_asmbl_21038.p1, initial, 21379, 21473
-recovered pasa_asmbl_21038.p1, terminal, 26402, 26707
-recovered pasa_asmbl_21038.p1, internal, 17728, 17901
-recovered pasa_asmbl_21038.p1, internal, 19225, 19383
-recovered pasa_asmbl_21038.p1, internal, 20354, 20578
-recovered pasa_asmbl_21038.p1, internal, 20725, 20808
-recovered pasa_asmbl_21038.p1, internal, 21379, 21473
-recovered pasa_asmbl_21038.p1, internal, 21608, 21796
-recovered pasa_asmbl_21038.p1, internal, 22553, 22644
-recovered pasa_asmbl_21038.p1, internal, 23068, 23328
-recovered pasa_asmbl_21038.p1, internal, 23674, 23744
-recovered pasa_asmbl_21038.p1, internal, 23990, 24105
-recovered pasa_asmbl_21038.p1, internal, 24802, 24951
-recovered pasa_asmbl_21038.p1, internal, 25670, 25773
-recovered pasa_asmbl_21038.p1, internal, 26130, 26218
Couldn't classify 54530, 54694
Sorry, prediction pasa_asmbl_21066.p1 fails validation.
(GTC)	 AG	54530-54694	GT	AGG
(GGG)	 AG	54942-55097	GT	AGG
(GAG)	 AG	55908-55997	CA	AAC
-recovered pasa_asmbl_21066.p1, terminal, 55908, 55997
-recovered pasa_asmbl_21066.p1, internal, 54530, 54694
-recovered pasa_asmbl_21066.p1, internal, 54942, 55097
Valid prediction for Augustus_model.g29692.t1
Valid prediction for HiQ_model.g29690.t1
Valid prediction for GeneMark_model.77237_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: -)Valid prediction for GlimmerHMM_glimmerT_44399-T1
Valid prediction for GeneMark_model.77228_t
Valid prediction for GeneMark_model.77241_t
Valid prediction for GeneMark_model.77236_t
Valid prediction for snap_scaffold_18-snap.2870-T1
Valid prediction for GeneMark_model.77222_t
Valid prediction for GeneMark_model.77248_t
Valid prediction for snap_scaffold_18-snap.2879-T1
Valid prediction for snap_scaffold_18-snap.2868-T1
Valid prediction for GeneMark_model.77217_t
Valid prediction for GlimmerHMM_glimmerT_44403-T1
Valid prediction for GeneMark_model.77246_t
Valid prediction for pasa_asmbl_20203.p1
Valid prediction for GlimmerHMM_glimmerT_44401-T1
Valid prediction for CodingQuarry_transcript_23880-T1
Valid prediction for GeneMark_model.77244_t
Valid prediction for snap_scaffold_18-snap.2875-T1
Valid prediction for snap_scaffold_18-snap.2873-T1
Valid prediction for GeneMark_model.77230_t
Valid prediction for GeneMark_model.77221_t
Valid prediction for GeneMark_model.77231_t
Valid prediction for snap_scaffold_18-snap.2864-T1
Valid prediction for Augustus_model.g29696.t1
Valid prediction for GlimmerHMM_glimmerT_44402-T1
Valid prediction for GeneMark_model.77234_t
Valid prediction for snap_scaffold_18-snap.2862-T1
Valid prediction for GlimmerHMM_glimmerT_44400-T1
Valid prediction for GeneMark_model.77226_t
Valid prediction for snap_scaffold_18-snap.2872-T1
Valid prediction for GlimmerHMM_glimmerT_44393-T1
Couldn't classify 83643, 84117
Couldn't classify 84562, 84602
Sorry, prediction CodingQuarry_transcript_23879-T1 fails validation.
(ATG)	 CC	83643-84117	AG	GGA
(TGG)	 GG	84562-84602	CA	AGC
Valid prediction for GeneMark_model.77239_t
Valid prediction for GeneMark_model.77232_t
Valid prediction for snap_scaffold_18-snap.2856-T1
Valid prediction for Augustus_model.g29694.t1
Valid prediction for GlimmerHMM_glimmerT_44397-T1
Valid prediction for GlimmerHMM_glimmerT_44395-T1
Valid prediction for GlimmerHMM_glimmerT_44404-T1
Valid prediction for HiQ_model.g29691.t1
Valid prediction for GeneMark_model.77214_t
Valid prediction for Augustus_model.g29693.t1
Valid prediction for snap_scaffold_18-snap.2877-T1
Valid prediction for GeneMark_model.77224_t
Valid prediction for GeneMark_model.77220_t
Valid prediction for snap_scaffold_18-snap.2859-T1
Valid prediction for snap_scaffold_18-snap.2867-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8237, rend_intergenic: 5174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11168, rend_intergenic: 8344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20862, rend_intergenic: 16037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26763, rend_intergenic: 21379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41556, rend_intergenic: 31289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46490, rend_intergenic: 45134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57391, rend_intergenic: 54029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62148, rend_intergenic: 61269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67609, rend_intergenic: 64100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71560, rend_intergenic: 67613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82669, rend_intergenic: 75355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106822, rend_intergenic: 84190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118264, rend_intergenic: 107548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128830, rend_intergenic: 119704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 130150
-exon list size: 595


building trellis

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98.7    
98.8    
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99.2    
99.3    
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99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 8237, rend_intergenic: 5174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11168, rend_intergenic: 8344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20862, rend_intergenic: 16037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26763, rend_intergenic: 21379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41556, rend_intergenic: 31289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46490, rend_intergenic: 45134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57391, rend_intergenic: 54029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62148, rend_intergenic: 61269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67609, rend_intergenic: 64100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71560, rend_intergenic: 67613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82669, rend_intergenic: 75355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106822, rend_intergenic: 84190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118264, rend_intergenic: 107548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128830, rend_intergenic: 119704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support