-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_16109676-16277079

-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_14-snap.3402-T1
Valid prediction for GlimmerHMM_glimmerT_36143-T1
Valid prediction for snap_scaffold_14-snap.3390-T1
Couldn't classify 2153, 2221
Sorry, prediction pasa_asmbl_12651.p1 fails validation.
(CGT)	 CA	2153-2221	GT	AGG
(ATG)	 AG	2615-2702	GT	TGG
(GTA)	 AG	2934-2975	GT	AGG
(ACA)	 AG	3355-3525	GT	AGG
(TGG)	 AG	3742-3886	GT	AGG
(TGA)	 AG	4308-4470	CC	AAC
-recovered pasa_asmbl_12651.p1, initial, 2615, 2702
-recovered pasa_asmbl_12651.p1, terminal, 4308, 4470
-recovered pasa_asmbl_12651.p1, internal, 2615, 2702
-recovered pasa_asmbl_12651.p1, internal, 2934, 2975
-recovered pasa_asmbl_12651.p1, internal, 3355, 3525
-recovered pasa_asmbl_12651.p1, internal, 3742, 3886
Valid prediction for snap_scaffold_14-snap.3419-T1
Valid prediction for snap_scaffold_14-snap.3388-T1
Valid prediction for GeneMark_model.62063_t
Valid prediction for GeneMark_model.62079_t
Valid prediction for GeneMark_model.62038_t
Valid prediction for GeneMark_model.62057_t
Valid prediction for snap_scaffold_14-snap.3400-T1
Valid prediction for GlimmerHMM_glimmerT_36140-T1
Valid prediction for GeneMark_model.62077_t
Valid prediction for GlimmerHMM_glimmerT_36151-T1
Valid prediction for GeneMark_model.62073_t
Valid prediction for GlimmerHMM_glimmerT_36154-T1
Valid prediction for snap_scaffold_14-snap.3408-T1
Valid prediction for GeneMark_model.62094_t
Valid prediction for GeneMark_model.62048_t
Valid prediction for GeneMark_model.62088_t
Valid prediction for GlimmerHMM_glimmerT_36153-T1
Valid prediction for GeneMark_model.62071_t
Valid prediction for GeneMark_model.62086_t
Valid prediction for snap_scaffold_14-snap.3397-T1
Valid prediction for snap_scaffold_14-snap.3420-T1
Valid prediction for GlimmerHMM_glimmerT_36150-T1
Valid prediction for GeneMark_model.62040_t
Valid prediction for GeneMark_model.62050_t
Valid prediction for GeneMark_model.62082_t
Valid prediction for snap_scaffold_14-snap.3409-T1
Valid prediction for GlimmerHMM_glimmerT_36157-T1
Valid prediction for GeneMark_model.62084_t
Valid prediction for GeneMark_model.62061_t
Valid prediction for GeneMark_model.62059_t
Valid prediction for snap_scaffold_14-snap.3406-T1
Valid prediction for snap_scaffold_14-snap.3414-T1
Valid prediction for GlimmerHMM_glimmerT_36142-T1
Valid prediction for GeneMark_model.62093_t
Valid prediction for GeneMark_model.62068_t
Couldn't classify 12608, 12684
Sorry, prediction pasa_asmbl_12653.p1 fails validation.
(ATG)	 AG	11245-11312	GT	AGG
(AGG)	 AG	12145-12362	GT	TGG
(GAT)	 AG	12608-12684	TA	GGT
-recovered pasa_asmbl_12653.p1, initial, 11245, 11312
-recovered pasa_asmbl_12653.p1, internal, 11245, 11312
-recovered pasa_asmbl_12653.p1, internal, 12145, 12362
Valid prediction for GeneMark_model.62092_t
Valid prediction for snap_scaffold_14-snap.3399-T1
Valid prediction for snap_scaffold_14-snap.3416-T1
Valid prediction for GeneMark_model.62043_t
Valid prediction for GlimmerHMM_glimmerT_36145-T1
Valid prediction for GeneMark_model.62056_t
Valid prediction for GeneMark_model.62047_t
Valid prediction for snap_scaffold_14-snap.3392-T1
Valid prediction for GeneMark_model.62054_t
Valid prediction for snap_scaffold_14-snap.3404-T1
Valid prediction for GeneMark_model.62075_t
Valid prediction for snap_scaffold_14-snap.3393-T1
Valid prediction for GeneMark_model.62097_t
Valid prediction for snap_scaffold_14-snap.3411-T1
Valid prediction for snap_scaffold_14-snap.3413-T1
Valid prediction for snap_scaffold_14-snap.3395-T1
Valid prediction for GeneMark_model.62090_t
Valid prediction for GeneMark_model.62069_t
Valid prediction for GeneMark_model.62045_t
Valid prediction for GeneMark_model.62052_t
Valid prediction for snap_scaffold_14-snap.3417-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_14-snap.3407-T1
Valid prediction for GeneMark_model.62080_t
Valid prediction for GeneMark_model.62066_t
Valid prediction for GeneMark_model.62060_t
Valid prediction for GeneMark_model.62085_t
Valid prediction for snap_scaffold_14-snap.3391-T1
Valid prediction for GlimmerHMM_glimmerT_36152-T1
Valid prediction for GeneMark_model.62046_t
Valid prediction for GeneMark_model.62039_t
Valid prediction for GeneMark_model.62087_t
Valid prediction for snap_scaffold_14-snap.3398-T1
Valid prediction for snap_scaffold_14-snap.3421-T1
Valid prediction for GeneMark_model.62049_t
Valid prediction for GlimmerHMM_glimmerT_36146-T1
Valid prediction for snap_scaffold_14-snap.3401-T1
Valid prediction for snap_scaffold_14-snap.3418-T1
Valid prediction for GeneMark_model.62064_t
Valid prediction for GeneMark_model.62076_t
Valid prediction for GlimmerHMM_glimmerT_36141-T1
Valid prediction for GeneMark_model.62051_t
Valid prediction for GeneMark_model.62091_t
Valid prediction for GlimmerHMM_glimmerT_36144-T1
Valid prediction for GeneMark_model.62041_t
Valid prediction for GeneMark_model.62078_t
Valid prediction for GlimmerHMM_glimmerT_36156-T1
Valid prediction for snap_scaffold_14-snap.3405-T1
Valid prediction for snap_scaffold_14-snap.3415-T1
Valid prediction for snap_scaffold_14-snap.3412-T1
Valid prediction for GlimmerHMM_glimmerT_36148-T1
Valid prediction for GlimmerHMM_glimmerT_36155-T1
Valid prediction for snap_scaffold_14-snap.3396-T1
Valid prediction for snap_scaffold_14-snap.3403-T1
Valid prediction for snap_scaffold_14-snap.3394-T1
Valid prediction for GeneMark_model.62074_t
Valid prediction for GeneMark_model.62070_t
Valid prediction for snap_scaffold_14-snap.3410-T1
Valid prediction for GlimmerHMM_glimmerT_36147-T1
Valid prediction for GeneMark_model.62065_t
Valid prediction for CodingQuarry_transcript_15923-T1
Valid prediction for GeneMark_model.62081_t
Valid prediction for GeneMark_model.62067_t
Valid prediction for GeneMark_model.62096_t
Couldn't classify 144553, 144693
Sorry, prediction pasa_asmbl_13755.p1 fails validation.
(AAC)	 GA	144553-144693	GT	TGG
(CTG)	 AG	145953-145988	GT	GGG
(TGG)	 AG	146758-146816	GT	TGG
(GTA)	 AG	149057-149086	GT	AGG
(AGA)	 AG	151708-151747	TA	AGT
-recovered pasa_asmbl_13755.p1, terminal, 151708, 151747
-recovered pasa_asmbl_13755.p1, internal, 145953, 145988
-recovered pasa_asmbl_13755.p1, internal, 146758, 146816
-recovered pasa_asmbl_13755.p1, internal, 149057, 149086
Valid prediction for GeneMark_model.62055_t
Valid prediction for GeneMark_model.62062_t
Valid prediction for GeneMark_model.62037_t
Couldn't classify 160665, 160771
Sorry, prediction pasa_asmbl_13753.p1 fails validation.
(CCT)	 CA	160665-160771	GT	ATG
(GTA)	 AG	161049-161138	GT	GGG
(GTT)	 AG	161274-161472	CC	AAC
-recovered pasa_asmbl_13753.p1, terminal, 161274, 161472
-recovered pasa_asmbl_13753.p1, internal, 161049, 161138
Valid prediction for GeneMark_model.62089_t
Valid prediction for GeneMark_model.62095_t
Valid prediction for GeneMark_model.62058_t
Valid prediction for GeneMark_model.62044_t
Valid prediction for snap_scaffold_14-snap.3422-T1
Valid prediction for GlimmerHMM_glimmerT_36149-T1
Valid prediction for GeneMark_model.62042_t
Valid prediction for GeneMark_model.62072_t
Valid prediction for snap_scaffold_14-snap.3389-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12858, rend_intergenic: 11939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29090, rend_intergenic: 19181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47318, rend_intergenic: 40933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51057, rend_intergenic: 48112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56553, rend_intergenic: 51058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61130, rend_intergenic: 60773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63230, rend_intergenic: 61388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63691, rend_intergenic: 63575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74923, rend_intergenic: 66686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80992, rend_intergenic: 78632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84496, rend_intergenic: 81339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99804, rend_intergenic: 89679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112703, rend_intergenic: 100643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115634, rend_intergenic: 113024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115954, rend_intergenic: 115823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132523, rend_intergenic: 116110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136927, rend_intergenic: 133685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142095, rend_intergenic: 137283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151972, rend_intergenic: 142924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164836, rend_intergenic: 152129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167404
-exon list size: 695


building trellis

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99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 12858, rend_intergenic: 11939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29090, rend_intergenic: 19181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47318, rend_intergenic: 40933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51057, rend_intergenic: 48112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56553, rend_intergenic: 51058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61130, rend_intergenic: 60773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63230, rend_intergenic: 61388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63691, rend_intergenic: 63575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74923, rend_intergenic: 66686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80992, rend_intergenic: 78632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84496, rend_intergenic: 81339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99804, rend_intergenic: 89679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112703, rend_intergenic: 100643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115634, rend_intergenic: 113024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115954, rend_intergenic: 115823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132523, rend_intergenic: 116110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136927, rend_intergenic: 133685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142095, rend_intergenic: 137283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151972, rend_intergenic: 142924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164836, rend_intergenic: 152129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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