-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_2644267-2832291

-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.74151_t
Valid prediction for GeneMark_model.74131_t
Valid prediction for GeneMark_model.74125_t
Valid prediction for snap_scaffold_18-snap.562-T1
Valid prediction for Augustus_model.g28717.t1
Valid prediction for GeneMark_model.74152_t
Valid prediction for GeneMark_model.74165_t
Valid prediction for GeneMark_model.74129_t
Valid prediction for GlimmerHMM_glimmerT_42929-T1
Valid prediction for snap_scaffold_18-snap.542-T1
Valid prediction for GlimmerHMM_glimmerT_42926-T1
Valid prediction for GeneMark_model.74138_t
Valid prediction for GlimmerHMM_glimmerT_42915-T1
Valid prediction for Augustus_model.g28713.t1
Valid prediction for snap_scaffold_18-snap.553-T1
Valid prediction for GlimmerHMM_glimmerT_42922-T1
Valid prediction for GeneMark_model.74141_t
Valid prediction for snap_scaffold_18-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_42931-T1
Valid prediction for GeneMark_model.74153_t
Valid prediction for GlimmerHMM_glimmerT_42919-T1
Valid prediction for GeneMark_model.74135_t
Valid prediction for GeneMark_model.74161_t
Couldn't classify 151289, 151588
Sorry, prediction pasa_asmbl_20446.p1 fails validation.
(GAT)	 GG	151289-151588	GT	AGG
Valid prediction for GeneMark_model.74147_t
Valid prediction for snap_scaffold_18-snap.560-T1
Valid prediction for GeneMark_model.74128_t
Valid prediction for snap_scaffold_18-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_42924-T1
Valid prediction for Augustus_model.g28718.t1
Valid prediction for GlimmerHMM_glimmerT_42933-T1
Valid prediction for GeneMark_model.74149_t
Valid prediction for snap_scaffold_18-snap.539-T1
Valid prediction for GlimmerHMM_glimmerT_42918-T1
Valid prediction for GlimmerHMM_glimmerT_42921-T1
Valid prediction for GeneMark_model.74168_t
Valid prediction for snap_scaffold_18-snap.537-T1
Valid prediction for snap_scaffold_18-snap.569-T1
Valid prediction for GeneMark_model.74157_t
Valid prediction for GeneMark_model.74159_t
Valid prediction for snap_scaffold_18-snap.552-T1
Valid prediction for snap_scaffold_18-snap.540-T1
Valid prediction for GeneMark_model.74139_t
Valid prediction for snap_scaffold_18-snap.551-T1
Valid prediction for Augustus_model.g28708.t1
Valid prediction for snap_scaffold_18-snap.555-T1
Valid prediction for GlimmerHMM_glimmerT_42917-T1
Valid prediction for GeneMark_model.74133_t
Valid prediction for snap_scaffold_18-snap.566-T1
Valid prediction for GeneMark_model.74166_t
Valid prediction for GlimmerHMM_glimmerT_42930-T1
Valid prediction for GeneMark_model.74163_t
Valid prediction for snap_scaffold_18-snap.568-T1
Valid prediction for GeneMark_model.74156_t
Valid prediction for Augustus_model.g28709.t1
Valid prediction for Augustus_model.g28710.t1
Valid prediction for GeneMark_model.74145_t
Valid prediction for snap_scaffold_18-snap.567-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_18-snap.538-T1
Valid prediction for GeneMark_model.74160_t
Valid prediction for GeneMark_model.74162_t
Valid prediction for pasa_asmbl_19774.p1
Couldn't classify 125685, 125781
Sorry, prediction pasa_asmbl_19769.p1 fails validation.
(GAG)	 CA	125685-125781	GT	TGG
(TCA)	 AG	126152-126215	GT	AGG
(ACT)	 AG	127676-127757	GT	CCG
(GGT)	 AG	128096-128218	GT	AGG
(TCT)	 AG	128330-128429	GT	GGG
(ATC)	 AG	128573-128748	GT	AGG
(ATC)	 AG	129418-129501	GG	GAG
-recovered pasa_asmbl_19769.p1, terminal, 129418, 129501
-recovered pasa_asmbl_19769.p1, internal, 126152, 126215
-recovered pasa_asmbl_19769.p1, internal, 127676, 127757
-recovered pasa_asmbl_19769.p1, internal, 128096, 128218
-recovered pasa_asmbl_19769.p1, internal, 128330, 128429
-recovered pasa_asmbl_19769.p1, internal, 128573, 128748
Valid prediction for snap_scaffold_18-snap.549-T1
Valid prediction for snap_scaffold_18-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_42927-T1
Valid prediction for GeneMark_model.74124_t
Valid prediction for pasa_asmbl_19777.p1
Valid prediction for Augustus_model.g28719.t1
Valid prediction for GeneMark_model.74134_t
Valid prediction for snap_scaffold_18-snap.544-T1
Valid prediction for snap_scaffold_18-snap.550-T1
Valid prediction for snap_scaffold_18-snap.543-T1
Valid prediction for GlimmerHMM_glimmerT_42914-T1
Valid prediction for snap_scaffold_18-snap.541-T1
Valid prediction for GlimmerHMM_glimmerT_42923-T1
Valid prediction for GeneMark_model.74144_t
Valid prediction for GeneMark_model.74126_t
Valid prediction for GeneMark_model.74142_t
Valid prediction for GeneMark_model.74140_t
Valid prediction for GeneMark_model.74148_t
Valid prediction for GeneMark_model.74146_t
Valid prediction for GeneMark_model.74136_t
Valid prediction for snap_scaffold_18-snap.573-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_42932-T1
Valid prediction for snap_scaffold_18-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_42920-T1
Valid prediction for GeneMark_model.74158_t
Valid prediction for snap_scaffold_18-snap.557-T1
Valid prediction for snap_scaffold_18-snap.559-T1
Valid prediction for snap_scaffold_18-snap.546-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.74137_t
Valid prediction for GeneMark_model.74143_t
Valid prediction for snap_scaffold_18-snap.558-T1
Valid prediction for GeneMark_model.74167_t
Valid prediction for GeneMark_model.74155_t
Valid prediction for pasa_asmbl_19771.p2
Valid prediction for HiQ_model.g28714.t1
Valid prediction for snap_scaffold_18-snap.561-T1
Valid prediction for GlimmerHMM_glimmerT_42925-T1
Valid prediction for snap_scaffold_18-snap.554-T1
Couldn't classify 111220, 111303
Sorry, prediction pasa_asmbl_19770.p1 fails validation.
(ATG)	 AA	106284-106585	GT	TGG
(GTA)	 AG	107349-107493	GT	AGG
(GTG)	 AG	107655-107843	GT	AGG
(CCC)	 AG	108563-108697	GT	TGG
(GAG)	 AG	110106-110246	GT	AGG
(GGC)	 AG	111010-111090	GT	AGG
(GTG)	 AG	111220-111303	AT	CGA
-recovered pasa_asmbl_19770.p1, initial, 106284, 106585
-recovered pasa_asmbl_19770.p1, internal, 107349, 107493
-recovered pasa_asmbl_19770.p1, internal, 107655, 107843
-recovered pasa_asmbl_19770.p1, internal, 108563, 108697
-recovered pasa_asmbl_19770.p1, internal, 110106, 110246
-recovered pasa_asmbl_19770.p1, internal, 111010, 111090
Valid prediction for HiQ_model.g28715.t1
Valid prediction for GeneMark_model.74154_t
Valid prediction for CodingQuarry_transcript_23651-T1
Valid prediction for snap_scaffold_18-snap.565-T1
Valid prediction for GeneMark_model.74123_t
Valid prediction for snap_scaffold_18-snap.547-T1
Valid prediction for GlimmerHMM_glimmerT_42913-T1
Valid prediction for GeneMark_model.74130_t
Valid prediction for GeneMark_model.74127_t
Valid prediction for GeneMark_model.74164_t
Valid prediction for GlimmerHMM_glimmerT_42912-T1
Valid prediction for HiQ_model.g28716.t1
Valid prediction for snap_scaffold_18-snap.545-T1
Valid prediction for Augustus_model.g28712.t1
Valid prediction for GlimmerHMM_glimmerT_42928-T1
Valid prediction for Augustus_model.g28711.t1
Valid prediction for GeneMark_model.74150_t
Valid prediction for CodingQuarry_transcript_23652-T1
Valid prediction for snap_scaffold_18-snap.563-T1
Valid prediction for GeneMark_model.74132_t
Valid prediction for snap_scaffold_18-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_42916-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17338, rend_intergenic: 13764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27137, rend_intergenic: 22780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57239, rend_intergenic: 28509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66631, rend_intergenic: 61345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71376, rend_intergenic: 68139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80998, rend_intergenic: 74118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101758, rend_intergenic: 97770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126955, rend_intergenic: 123084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143769, rend_intergenic: 138735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176793, rend_intergenic: 170316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188025
-exon list size: 526


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 17338, rend_intergenic: 13764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27137, rend_intergenic: 22780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57239, rend_intergenic: 28509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66631, rend_intergenic: 61345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71376, rend_intergenic: 68139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80998, rend_intergenic: 74118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101758, rend_intergenic: 97770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126955, rend_intergenic: 123084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143769, rend_intergenic: 138735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176793, rend_intergenic: 170316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support