-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_13316599-13521198

-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 GlimmerHMM_glimmerT_16151-T1
Valid prediction for snap_scaffold_6-snap.2793-T1
Valid prediction for Augustus_model.g10889.t1
Couldn't classify 33957, 34061
Sorry, prediction pasa_asmbl_47463.p1 fails validation.
(GTT)	 GG	33957-34061	GT	ATG
(GCA)	 AG	34181-34289	GT	AGG
(CCT)	 AG	34377-34517	GT	TGG
(CTC)	 AG	34808-34977	GC	AGG
-recovered pasa_asmbl_47463.p1, terminal, 34808, 34977
-recovered pasa_asmbl_47463.p1, internal, 34181, 34289
-recovered pasa_asmbl_47463.p1, internal, 34377, 34517
-recovered pasa_asmbl_47463.p1, internal, 34808, 34977
Valid prediction for snap_scaffold_6-snap.2789-T1
Valid prediction for snap_scaffold_6-snap.2780-T1
Valid prediction for snap_scaffold_6-snap.2806-T1
Valid prediction for snap_scaffold_6-snap.2808-T1
Valid prediction for GeneMark_model.26967_t
Valid prediction for snap_scaffold_6-snap.2805-T1
Valid prediction for GeneMark_model.26995_t
Valid prediction for GeneMark_model.27005_t
Valid prediction for GeneMark_model.26990_t
Valid prediction for GlimmerHMM_glimmerT_16154-T1
Valid prediction for Augustus_model.g10891.t1
Valid prediction for GlimmerHMM_glimmerT_16152-T1
Valid prediction for GeneMark_model.26988_t
Valid prediction for GeneMark_model.26981_t
Valid prediction for GeneMark_model.26965_t
Valid prediction for GeneMark_model.26960_t
Valid prediction for snap_scaffold_6-snap.2795-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.27007_t
Valid prediction for GeneMark_model.26973_t
Couldn't classify 1188, 1916
Sorry, prediction pasa_asmbl_47461.p1 fails validation.
(TGT)	 AA	1188-1916	GT	GAG
Valid prediction for GeneMark_model.27008_t
Valid prediction for Augustus_model.g10887.t1
Valid prediction for GlimmerHMM_glimmerT_16143-T1
Valid prediction for GeneMark_model.26992_t
Valid prediction for GeneMark_model.27011_t
Valid prediction for GeneMark_model.26997_t
Valid prediction for snap_scaffold_6-snap.2807-T1
Valid prediction for GeneMark_model.27015_t
Valid prediction for GlimmerHMM_glimmerT_16149-T1
Valid prediction for Augustus_model.g10883.t1
Valid prediction for snap_scaffold_6-snap.2801-T1
Valid prediction for GlimmerHMM_glimmerT_16147-T1
Valid prediction for GlimmerHMM_glimmerT_16148-T1
Valid prediction for GlimmerHMM_glimmerT_16170-T1
Valid prediction for GeneMark_model.26972_t
Valid prediction for GeneMark_model.26966_t
Valid prediction for GlimmerHMM_glimmerT_16159-T1
Valid prediction for GlimmerHMM_glimmerT_16156-T1
Valid prediction for GeneMark_model.26994_t
Valid prediction for GeneMark_model.27000_t
Valid prediction for snap_scaffold_6-snap.2802-T1
Valid prediction for snap_scaffold_6-snap.2788-T1
Valid prediction for GeneMark_model.26955_t
Valid prediction for GlimmerHMM_glimmerT_16161-T1
Valid prediction for snap_scaffold_6-snap.2787-T1
Valid prediction for Augustus_model.g10880.t1
Valid prediction for GlimmerHMM_glimmerT_16141-T1
Valid prediction for GlimmerHMM_glimmerT_16153-T1
Valid prediction for snap_scaffold_6-snap.2796-T1
Valid prediction for GeneMark_model.26961_t
Valid prediction for GeneMark_model.27013_t
Valid prediction for GeneMark_model.26956_t
Valid prediction for snap_scaffold_6-snap.2794-T1
Valid prediction for snap_scaffold_6-snap.2783-T1
Valid prediction for GeneMark_model.26978_t
Valid prediction for snap_scaffold_6-snap.2804-T1
Valid prediction for snap_scaffold_6-snap.2785-T1
Valid prediction for snap_scaffold_6-snap.2798-T1
Couldn't classify 43459, 44157
Sorry, prediction pasa_asmbl_48849.p1 fails validation.
(TAT)	 GG	43459-44157	GA	TTG
Valid prediction for GlimmerHMM_glimmerT_16167-T1
Valid prediction for GeneMark_model.26969_t
Valid prediction for GeneMark_model.26962_t
Valid prediction for GeneMark_model.26999_t
Valid prediction for GeneMark_model.26970_t
Valid prediction for GeneMark_model.27017_t
Valid prediction for snap_scaffold_6-snap.2790-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 Augustus_model.g10886.t1
Valid prediction for GeneMark_model.26998_t
Valid prediction for snap_scaffold_6-snap.2779-T1
Valid prediction for CodingQuarry_transcript_55150-T1
Valid prediction for GeneMark_model.26979_t
Valid prediction for snap_scaffold_6-snap.2803-T1
Valid prediction for GeneMark_model.27014_t
Valid prediction for GeneMark_model.26989_t
Valid prediction for GlimmerHMM_glimmerT_16146-T1
Valid prediction for snap_scaffold_6-snap.2800-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16158-T1
Valid prediction for GlimmerHMM_glimmerT_16168-T1
Valid prediction for snap_scaffold_6-snap.2791-T1
Valid prediction for GlimmerHMM_glimmerT_16157-T1
Valid prediction for GlimmerHMM_glimmerT_16169-T1
Valid prediction for GeneMark_model.27016_t
Valid prediction for GeneMark_model.26985_t
Valid prediction for GeneMark_model.27012_t
Valid prediction for GeneMark_model.26983_t
Valid prediction for GlimmerHMM_glimmerT_16166-T1
Valid prediction for GeneMark_model.27001_t
Valid prediction for GeneMark_model.26986_t
Valid prediction for GeneMark_model.26993_t
Valid prediction for GeneMark_model.27009_t
Valid prediction for GeneMark_model.26959_t
Valid prediction for GlimmerHMM_glimmerT_16165-T1
Valid prediction for GeneMark_model.26957_t
Valid prediction for GlimmerHMM_glimmerT_16142-T1
Valid prediction for GeneMark_model.26971_t
Valid prediction for GeneMark_model.26974_t
Valid prediction for GlimmerHMM_glimmerT_16172-T1
Valid prediction for GeneMark_model.26984_t
Valid prediction for GeneMark_model.26980_t
Valid prediction for snap_scaffold_6-snap.2782-T1
Valid prediction for GeneMark_model.26987_t
Valid prediction for GeneMark_model.26977_t
Valid prediction for snap_scaffold_6-snap.2792-T1
Valid prediction for snap_scaffold_6-snap.2778-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g10890.t1
Valid prediction for GlimmerHMM_glimmerT_16150-T1
Valid prediction for Augustus_model.g10885.t1
Valid prediction for GlimmerHMM_glimmerT_16155-T1
Valid prediction for GeneMark_model.27010_t
Valid prediction for Augustus_model.g10882.t1
Valid prediction for GeneMark_model.27018_t
Valid prediction for GlimmerHMM_glimmerT_16162-T1
Valid prediction for Augustus_model.g10884.t1
Valid prediction for snap_scaffold_6-snap.2786-T1
Valid prediction for GlimmerHMM_glimmerT_16171-T1
Valid prediction for GlimmerHMM_glimmerT_16163-T1
Valid prediction for GeneMark_model.27003_t
Valid prediction for snap_scaffold_6-snap.2797-T1
Valid prediction for pasa_asmbl_48847.p1
Valid prediction for snap_scaffold_6-snap.2799-T1
Valid prediction for GlimmerHMM_glimmerT_16145-T1
Valid prediction for GeneMark_model.27006_t
Valid prediction for GeneMark_model.26975_t
Valid prediction for Augustus_model.g10881.t1
Valid prediction for GlimmerHMM_glimmerT_16160-T1
Valid prediction for Augustus_model.g10894.t1
Valid prediction for snap_scaffold_6-snap.2784-T1
Valid prediction for Augustus_model.g10893.t1
Valid prediction for GeneMark_model.26968_t
Valid prediction for Augustus_model.g10892.t1
Valid prediction for Augustus_model.g10895.t1
Valid prediction for snap_scaffold_6-snap.2781-T1
Valid prediction for GlimmerHMM_glimmerT_16164-T1
Valid prediction for snap_scaffold_6-snap.2809-T1
Valid prediction for GeneMark_model.27002_t
Valid prediction for GlimmerHMM_glimmerT_16144-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.26976_t
Valid prediction for GeneMark_model.26991_t
Valid prediction for GeneMark_model.27004_t
Valid prediction for GeneMark_model.26996_t
Valid prediction for HiQ_model.g10888.t1
Valid prediction for GeneMark_model.26963_t
Valid prediction for snap_scaffold_6-snap.2777-T1
Valid prediction for GeneMark_model.26958_t
Valid prediction for GeneMark_model.26982_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28212, rend_intergenic: 20859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34024, rend_intergenic: 33469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77045, rend_intergenic: 49494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101783, rend_intergenic: 81776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122939, rend_intergenic: 114366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128196, rend_intergenic: 123258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149542, rend_intergenic: 132761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196946, rend_intergenic: 158941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201160, rend_intergenic: 197246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204600
-exon list size: 716


building trellis

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-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 28212, rend_intergenic: 20859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34024, rend_intergenic: 33469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77045, rend_intergenic: 49494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101783, rend_intergenic: 81776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122939, rend_intergenic: 114366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128196, rend_intergenic: 123258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149542, rend_intergenic: 132761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196946, rend_intergenic: 158941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201160, rend_intergenic: 197246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support