-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_14793601-14984245

-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_42522-T1
Valid prediction for GlimmerHMM_glimmerT_42530-T1
Valid prediction for GeneMark_model.73545_t
Valid prediction for GeneMark_model.73515_t
Couldn't classify 150282, 150770
Sorry, prediction pasa_asmbl_18553.p2 fails validation.
(CAC)	 CT	150282-150770	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_42528-T1
Valid prediction for GeneMark_model.73542_t
Valid prediction for GlimmerHMM_glimmerT_42521-T1
Valid prediction for GeneMark_model.73509_t
Valid prediction for GeneMark_model.73522_t
Couldn't classify 78094, 78264
Sorry, prediction pasa_asmbl_18548.p1 fails validation.
(GGG)	 CA	78094-78264	GT	AGG
(GAT)	 AG	78716-78916	GT	AGG
(GAC)	 AG	79874-80064	GT	TGG
(GTA)	 AG	80286-80385	GT	AGG
(GTG)	 AG	80786-80923	GT	GAG
-recovered pasa_asmbl_18548.p1, terminal, 80786, 80923
-recovered pasa_asmbl_18548.p1, internal, 78716, 78916
-recovered pasa_asmbl_18548.p1, internal, 79874, 80064
-recovered pasa_asmbl_18548.p1, internal, 80286, 80385
-recovered pasa_asmbl_18548.p1, internal, 80786, 80923
Valid prediction for GeneMark_model.73506_t
Valid prediction for snap_scaffold_17-snap.3101-T1
Valid prediction for GeneMark_model.73500_t
Valid prediction for GlimmerHMM_glimmerT_42527-T1
Valid prediction for snap_scaffold_17-snap.3114-T1
Valid prediction for GlimmerHMM_glimmerT_42515-T1
Valid prediction for snap_scaffold_17-snap.3128-T1
Valid prediction for snap_scaffold_17-snap.3123-T1
Valid prediction for GeneMark_model.73535_t
Valid prediction for GeneMark_model.73525_t
Valid prediction for GeneMark_model.73539_t
Valid prediction for snap_scaffold_17-snap.3136-T1
Valid prediction for snap_scaffold_17-snap.3124-T1
Valid prediction for snap_scaffold_17-snap.3118-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.3132-T1
Valid prediction for GeneMark_model.73518_t
Valid prediction for GlimmerHMM_glimmerT_42533-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.73513_t
Valid prediction for GeneMark_model.73548_t
Valid prediction for GlimmerHMM_glimmerT_42531-T1
Valid prediction for GlimmerHMM_glimmerT_42514-T1
Valid prediction for GeneMark_model.73546_t
Valid prediction for GeneMark_model.73503_t
Valid prediction for snap_scaffold_17-snap.3130-T1
Valid prediction for snap_scaffold_17-snap.3116-T1
Valid prediction for GeneMark_model.73523_t
Valid prediction for pasa_asmbl_18549.p1
Valid prediction for snap_scaffold_17-snap.3138-T1
Valid prediction for GlimmerHMM_glimmerT_42534-T1
Valid prediction for GeneMark_model.73538_t
Valid prediction for GlimmerHMM_glimmerT_42511-T1
Couldn't classify 73732, 73957
Sorry, prediction pasa_asmbl_18659.p1 fails validation.
(ACC)	 TC	73732-73957	GT	GGG
(GTG)	 AG	74165-74343	GT	GTG
(GTG)	 AG	75049-75339	AA	AAA
-recovered pasa_asmbl_18659.p1, terminal, 75049, 75339
-recovered pasa_asmbl_18659.p1, internal, 74165, 74343
Valid prediction for GlimmerHMM_glimmerT_42517-T1
Valid prediction for snap_scaffold_17-snap.3126-T1
Valid prediction for GeneMark_model.73532_t
Valid prediction for GeneMark_model.73527_t
Valid prediction for GeneMark_model.73528_t
Valid prediction for GlimmerHMM_glimmerT_42523-T1
Valid prediction for snap_scaffold_17-snap.3120-T1
Valid prediction for snap_scaffold_17-snap.3109-T1
Valid prediction for GeneMark_model.73540_t
Valid prediction for snap_scaffold_17-snap.3119-T1
Valid prediction for GlimmerHMM_glimmerT_42524-T1
Valid prediction for GeneMark_model.73510_t
Valid prediction for snap_scaffold_17-snap.3099-T1
Valid prediction for GeneMark_model.73533_t
Valid prediction for CodingQuarry_transcript_22229-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 GeneMark_model.73524_t
Valid prediction for pasa_asmbl_19501.p1
Valid prediction for GeneMark_model.73529_t
Valid prediction for GeneMark_model.73502_t
Valid prediction for snap_scaffold_17-snap.3111-T1
Valid prediction for snap_scaffold_17-snap.3100-T1
Valid prediction for GeneMark_model.73536_t
Valid prediction for snap_scaffold_17-snap.3139-T1
Valid prediction for GeneMark_model.73505_t
Valid prediction for GeneMark_model.73511_t
Valid prediction for GlimmerHMM_glimmerT_42532-T1
Valid prediction for snap_scaffold_17-snap.3137-T1
Valid prediction for GlimmerHMM_glimmerT_42518-T1
Valid prediction for snap_scaffold_17-snap.3134-T1
Valid prediction for GlimmerHMM_glimmerT_42516-T1
Valid prediction for snap_scaffold_17-snap.3103-T1
Valid prediction for snap_scaffold_17-snap.3131-T1
Valid prediction for snap_scaffold_17-snap.3129-T1
Valid prediction for snap_scaffold_17-snap.3104-T1
Valid prediction for snap_scaffold_17-snap.3113-T1
Valid prediction for snap_scaffold_17-snap.3135-T1
Valid prediction for snap_scaffold_17-snap.3121-T1
Valid prediction for GlimmerHMM_glimmerT_42519-T1
Valid prediction for GeneMark_model.73543_t
Valid prediction for GeneMark_model.73537_t
Valid prediction for GeneMark_model.73504_t
Valid prediction for GlimmerHMM_glimmerT_42512-T1
Valid prediction for snap_scaffold_17-snap.3112-T1
Valid prediction for GeneMark_model.73508_t
Valid prediction for snap_scaffold_17-snap.3127-T1
Valid prediction for GeneMark_model.73531_t
Valid prediction for snap_scaffold_17-snap.3117-T1
Valid prediction for snap_scaffold_17-snap.3122-T1
Couldn't classify 19273, 19404
Sorry, prediction CodingQuarry_transcript_22230-T1 fails validation.
(ATG)	 AC	18757-18900	GT	AGG
(GTG)	 AG	19108-19161	GT	AGG
(GTA)	 AT	19273-19404	GT	TGG
(GAC)	 AG	19537-19605	GG	AAG
-recovered CodingQuarry_transcript_22230-T1, initial, 18757, 18900
-recovered CodingQuarry_transcript_22230-T1, terminal, 19537, 19605
-recovered CodingQuarry_transcript_22230-T1, internal, 19108, 19161
Valid prediction for GeneMark_model.73521_t
Valid prediction for snap_scaffold_17-snap.3115-T1
Valid prediction for snap_scaffold_17-snap.3098-T1
Valid prediction for snap_scaffold_17-snap.3133-T1
Valid prediction for GeneMark_model.73534_t
Valid prediction for GeneMark_model.73501_t
Valid prediction for snap_scaffold_17-snap.3107-T1
Valid prediction for GeneMark_model.73520_t
Valid prediction for snap_scaffold_17-snap.3110-T1
Valid prediction for GeneMark_model.73514_t
Valid prediction for GlimmerHMM_glimmerT_42520-T1
Valid prediction for GeneMark_model.73516_t
Valid prediction for GeneMark_model.73547_t
Valid prediction for GeneMark_model.73519_t
Valid prediction for GlimmerHMM_glimmerT_42509-T1
Valid prediction for snap_scaffold_17-snap.3102-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.73512_t
Valid prediction for GlimmerHMM_glimmerT_42513-T1
Valid prediction for GeneMark_model.73544_t
Valid prediction for snap_scaffold_17-snap.3106-T1
Valid prediction for GlimmerHMM_glimmerT_42525-T1
Valid prediction for snap_scaffold_17-snap.3105-T1
Couldn't classify 2068, 2100
Sorry, prediction GeneMark_model.73549_t fails validation.
(GCA)	 AG	2068-2100	GT	GAG
(GCA)	 AG	2124-2156	GT	GAG
(AGT)	 AG	2184-2198	GT	GGG
(GCA)	 AG	2222-2254	GT	GGG
(GCA)	 AG	2278-2310	GT	GGG
(GCA)	 AG	2334-2407	GT	GGG
(TCC)	 AG	3564-3670	GA	GAG
-recovered GeneMark_model.73549_t, terminal, 3564, 3670
-recovered GeneMark_model.73549_t, internal, 2068, 2100
-recovered GeneMark_model.73549_t, internal, 2124, 2156
-recovered GeneMark_model.73549_t, internal, 2184, 2198
-recovered GeneMark_model.73549_t, internal, 2222, 2254
-recovered GeneMark_model.73549_t, internal, 2278, 2310
-recovered GeneMark_model.73549_t, internal, 2334, 2407
Valid prediction for snap_scaffold_17-snap.3125-T1
Valid prediction for GeneMark_model.73517_t
Valid prediction for snap_scaffold_17-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_42529-T1
Valid prediction for GlimmerHMM_glimmerT_42526-T1
Couldn't classify 151262, 151595
Couldn't classify 151686, 152110
Sorry, prediction pasa_asmbl_19553.p1 fails validation.
(ACT)	 NN	151262-151595	GT	ATG
(CGG)	 AG	151686-152110	AA	CCA
Valid prediction for GeneMark_model.73530_t
Valid prediction for GlimmerHMM_glimmerT_42510-T1
Valid prediction for GeneMark_model.73541_t
Valid prediction for GeneMark_model.73507_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10848, rend_intergenic: 4646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14766, rend_intergenic: 12020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26410, rend_intergenic: 15683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36319, rend_intergenic: 26927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63148, rend_intergenic: 62400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70488, rend_intergenic: 63511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76142, rend_intergenic: 71208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81778, rend_intergenic: 79895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103901, rend_intergenic: 93966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124983, rend_intergenic: 111190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129897, rend_intergenic: 127283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132272, rend_intergenic: 130005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137354, rend_intergenic: 133215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159088, rend_intergenic: 149657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170070, rend_intergenic: 167872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177047, rend_intergenic: 174716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182551, rend_intergenic: 177756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186478, rend_intergenic: 184271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190645
-exon list size: 639


building trellis

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99.2    
99.4    
99.5    
99.7    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 10848, rend_intergenic: 4646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14766, rend_intergenic: 12020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26410, rend_intergenic: 15683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36319, rend_intergenic: 26927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63148, rend_intergenic: 62400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70488, rend_intergenic: 63511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76142, rend_intergenic: 71208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81778, rend_intergenic: 79895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103901, rend_intergenic: 93966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124983, rend_intergenic: 111190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129897, rend_intergenic: 127283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132272, rend_intergenic: 130005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137354, rend_intergenic: 133215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159088, rend_intergenic: 149657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170070, rend_intergenic: 167872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177047, rend_intergenic: 174716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182551, rend_intergenic: 177756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186478, rend_intergenic: 184271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support