-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_5288233-5425050

-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 snap_scaffold_25-snap.1156-T1
Valid prediction for GeneMark_model.96857_t
Valid prediction for snap_scaffold_25-snap.1171-T1
Valid prediction for GeneMark_model.96868_t
Valid prediction for GeneMark_model.96823_t
Valid prediction for GeneMark_model.96827_t
Valid prediction for snap_scaffold_25-snap.1140-T1
Valid prediction for GeneMark_model.96839_t
Valid prediction for snap_scaffold_25-snap.1168-T1
Valid prediction for GeneMark_model.96842_t
Valid prediction for snap_scaffold_25-snap.1159-T1
Valid prediction for Augustus_model.g37001.t1
Valid prediction for GeneMark_model.96818_t
Valid prediction for GeneMark_model.96863_t
Valid prediction for GeneMark_model.96869_t
Valid prediction for snap_scaffold_25-snap.1146-T1
Valid prediction for snap_scaffold_25-snap.1149-T1
Valid prediction for snap_scaffold_25-snap.1144-T1
Valid prediction for GlimmerHMM_glimmerT_55466-T1
Valid prediction for GeneMark_model.96853_t
Valid prediction for GlimmerHMM_glimmerT_55460-T1
Valid prediction for GlimmerHMM_glimmerT_55465-T1
Valid prediction for snap_scaffold_25-snap.1153-T1
Valid prediction for GeneMark_model.96832_t
Valid prediction for snap_scaffold_25-snap.1157-T1
Valid prediction for GeneMark_model.96837_t
Valid prediction for Augustus_model.g36999.t1
Valid prediction for GeneMark_model.96820_t
Valid prediction for snap_scaffold_25-snap.1142-T1
Valid prediction for GeneMark_model.96845_t
Valid prediction for GeneMark_model.96865_t
Valid prediction for GlimmerHMM_glimmerT_55461-T1
Valid prediction for GeneMark_model.96858_t
Valid prediction for snap_scaffold_25-snap.1141-T1
Valid prediction for GlimmerHMM_glimmerT_55475-T1
Valid prediction for GeneMark_model.96841_t
Valid prediction for snap_scaffold_25-snap.1167-T1
Valid prediction for GeneMark_model.96860_t
Valid prediction for Augustus_model.g36998.t1
Valid prediction for snap_scaffold_25-snap.1162-T1
Valid prediction for snap_scaffold_25-snap.1165-T1
Valid prediction for GlimmerHMM_glimmerT_55472-T1
Valid prediction for GeneMark_model.96831_t
Valid prediction for snap_scaffold_25-snap.1160-T1
Valid prediction for GlimmerHMM_glimmerT_55477-T1
Valid prediction for GeneMark_model.96867_t
Valid prediction for GlimmerHMM_glimmerT_55481-T1
Valid prediction for GeneMark_model.96829_t
Valid prediction for GeneMark_model.96835_t
Valid prediction for Augustus_model.g37012.t1
Valid prediction for GeneMark_model.96848_t
Valid prediction for GeneMark_model.96847_t
Valid prediction for GeneMark_model.96850_t
Valid prediction for GlimmerHMM_glimmerT_55474-T1
Valid prediction for GlimmerHMM_glimmerT_55464-T1
Valid prediction for snap_scaffold_25-snap.1148-T1
Valid prediction for Augustus_model.g37002.t1
Valid prediction for GeneMark_model.96825_t
Valid prediction for snap_scaffold_25-snap.1139-T1
Valid prediction for Augustus_model.g37010.t1
Valid prediction for GeneMark_model.96833_t
Valid prediction for GlimmerHMM_glimmerT_55482-T1
Valid prediction for GeneMark_model.96852_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 snap_scaffold_25-snap.1166-T1
Valid prediction for GeneMark_model.96844_t
Couldn't classify 38463, 38692
Couldn't classify 39196, 39376
Sorry, prediction pasa_asmbl_34518.p2 fails validation.
(AAG)	 CA	38463-38692	GT	AGG
(GCC)	 AG	39196-39376	GG	CAG
Valid prediction for Augustus_model.g36997.t1
Valid prediction for GeneMark_model.96870_t
Valid prediction for GlimmerHMM_glimmerT_55471-T1
Valid prediction for snap_scaffold_25-snap.1147-T1
Couldn't classify 30540, 30591
Couldn't classify 34799, 34930
Sorry, prediction pasa_asmbl_34237.p1 fails validation.
(GCC)	 CG	30540-30591	GT	TGG
(TGA)	 AG	31861-31957	GT	AGG
(CCG)	 AG	32119-32277	GT	AGG
(GTT)	 AG	32376-32445	GT	AGG
(ATG)	 AG	34799-34930	GT	AGG
-recovered pasa_asmbl_34237.p1, initial, 34799, 34930
-recovered pasa_asmbl_34237.p1, internal, 31861, 31957
-recovered pasa_asmbl_34237.p1, internal, 32119, 32277
-recovered pasa_asmbl_34237.p1, internal, 32376, 32445
-recovered pasa_asmbl_34237.p1, internal, 34799, 34930
Valid prediction for GeneMark_model.96849_t
Valid prediction for snap_scaffold_25-snap.1150-T1
Valid prediction for Augustus_model.g37003.t1
Valid prediction for GlimmerHMM_glimmerT_55473-T1
Valid prediction for GeneMark_model.96822_t
Valid prediction for GeneMark_model.96838_t
Valid prediction for GlimmerHMM_glimmerT_55467-T1
Valid prediction for Augustus_model.g37011.t1
Valid prediction for GeneMark_model.96866_t
Valid prediction for GeneMark_model.96851_t
Valid prediction for GeneMark_model.96830_t
Valid prediction for HiQ_model.g37006.t1
Valid prediction for snap_scaffold_25-snap.1152-T1
Valid prediction for GlimmerHMM_glimmerT_55480-T1
Valid prediction for GeneMark_model.96821_t
Valid prediction for GlimmerHMM_glimmerT_55478-T1
Valid prediction for snap_scaffold_25-snap.1164-T1
Valid prediction for snap_scaffold_25-snap.1143-T1
Valid prediction for GeneMark_model.96836_t
Valid prediction for GeneMark_model.96843_t
Valid prediction for Augustus_model.g37007.t1
Valid prediction for GeneMark_model.96854_t
Valid prediction for GlimmerHMM_glimmerT_55479-T1
Valid prediction for GlimmerHMM_glimmerT_55459-T1
Valid prediction for GeneMark_model.96828_t
Valid prediction for GlimmerHMM_glimmerT_55483-T1
Valid prediction for snap_scaffold_25-snap.1138-T1
Valid prediction for snap_scaffold_25-snap.1137-T1
Valid prediction for GeneMark_model.96856_t
Valid prediction for snap_scaffold_25-snap.1161-T1
Valid prediction for snap_scaffold_25-snap.1163-T1
Valid prediction for GeneMark_model.96864_t
Valid prediction for snap_scaffold_25-snap.1145-T1
Valid prediction for GeneMark_model.96861_t
Valid prediction for GeneMark_model.96834_t
Valid prediction for snap_scaffold_25-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_55468-T1
Valid prediction for snap_scaffold_25-snap.1151-T1
Valid prediction for GeneMark_model.96840_t
Valid prediction for GlimmerHMM_glimmerT_55463-T1
Valid prediction for HiQ_model.g37013.t1
Valid prediction for Augustus_model.g37005.t1
Valid prediction for GeneMark_model.96819_t
Valid prediction for snap_scaffold_25-snap.1158-T1
Valid prediction for GeneMark_model.96862_t
Valid prediction for GlimmerHMM_glimmerT_55470-T1
Valid prediction for Augustus_model.g37000.t1
Valid prediction for GlimmerHMM_glimmerT_55469-T1
Valid prediction for GeneMark_model.96826_t
Valid prediction for snap_scaffold_25-snap.1170-T1
Valid prediction for Augustus_model.g37008.t1
Valid prediction for Augustus_model.g37004.t1
Valid prediction for GeneMark_model.96824_t
Valid prediction for GlimmerHMM_glimmerT_55462-T1
Valid prediction for snap_scaffold_25-snap.1154-T1
Valid prediction for snap_scaffold_25-snap.1169-T1
Couldn't classify 38, 92
Couldn't classify 1826, 2033
Sorry, prediction pasa_asmbl_34238.p1 fails validation.
(GAC)	 TA	38-92	GT	AAG
(ATC)	 AG	433-1594	GT	AGG
(TGG)	 AG	1826-2033	AG	GTA
-recovered pasa_asmbl_34238.p1, internal, 433, 1594
Valid prediction for Augustus_model.g37009.t1
Valid prediction for GlimmerHMM_glimmerT_55476-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17221, rend_intergenic: 7363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20645, rend_intergenic: 17938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31103, rend_intergenic: 22177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33725, rend_intergenic: 33326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62167, rend_intergenic: 58750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63867, rend_intergenic: 62594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73419, rend_intergenic: 66604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77129, rend_intergenic: 74645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77962, rend_intergenic: 77188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100254, rend_intergenic: 90978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111256, rend_intergenic: 101494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123721, rend_intergenic: 114229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128186, rend_intergenic: 124832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136772, rend_intergenic: 130957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136818
-exon list size: 694


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 17221, rend_intergenic: 7363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20645, rend_intergenic: 17938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31103, rend_intergenic: 22177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33725, rend_intergenic: 33326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62167, rend_intergenic: 58750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63867, rend_intergenic: 62594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73419, rend_intergenic: 66604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77129, rend_intergenic: 74645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77962, rend_intergenic: 77188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100254, rend_intergenic: 90978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111256, rend_intergenic: 101494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123721, rend_intergenic: 114229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128186, rend_intergenic: 124832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136772, rend_intergenic: 130957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support