-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_2154004-2388371

-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_2-snap.530-T1
Valid prediction for snap_scaffold_2-snap.546-T1
Valid prediction for GlimmerHMM_glimmerT_3328-T1
Valid prediction for snap_scaffold_2-snap.543-T1
Valid prediction for GlimmerHMM_glimmerT_3329-T1
Valid prediction for GlimmerHMM_glimmerT_3327-T1
Valid prediction for snap_scaffold_2-snap.550-T1
Valid prediction for snap_scaffold_2-snap.514-T1
Valid prediction for snap_scaffold_2-snap.519-T1
Valid prediction for snap_scaffold_2-snap.541-T1
Valid prediction for snap_scaffold_2-snap.538-T1
Valid prediction for snap_scaffold_2-snap.558-T1
Valid prediction for snap_scaffold_2-snap.526-T1
Valid prediction for snap_scaffold_2-snap.520-T1
Valid prediction for snap_scaffold_2-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_3356-T1
Valid prediction for Augustus_model.g2239.t1
Valid prediction for GlimmerHMM_glimmerT_3334-T1
Valid prediction for GlimmerHMM_glimmerT_3337-T1
Valid prediction for GlimmerHMM_glimmerT_3354-T1
Couldn't classify 118316, 118481
Couldn't classify 122190, 122259
Sorry, prediction pasa_asmbl_24237.p1 fails validation.
(GCC)	 TT	118316-118481	GT	AGG
(GAT)	 AG	118761-118807	GT	AGG
(GCA)	 AG	118954-119121	GT	AGG
(ATC)	 AG	120425-120485	GT	AGG
(TGT)	 AG	120607-120746	GT	CTG
(GTG)	 AG	121942-122051	GT	AGG
(CTG)	 AG	122190-122259	GT	GGG
-recovered pasa_asmbl_24237.p1, internal, 118761, 118807
-recovered pasa_asmbl_24237.p1, internal, 118954, 119121
-recovered pasa_asmbl_24237.p1, internal, 120425, 120485
-recovered pasa_asmbl_24237.p1, internal, 120607, 120746
-recovered pasa_asmbl_24237.p1, internal, 121942, 122051
-recovered pasa_asmbl_24237.p1, internal, 122190, 122259
Valid prediction for snap_scaffold_2-snap.532-T1
Valid prediction for snap_scaffold_2-snap.512-T1
Valid prediction for snap_scaffold_2-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_3341-T1
Valid prediction for snap_scaffold_2-snap.535-T1
Valid prediction for snap_scaffold_2-snap.523-T1
Couldn't classify 212085, 212171
Couldn't classify 212574, 212693
Sorry, prediction pasa_asmbl_24239.p2 fails validation.
(GAG)	 AA	212085-212171	GT	AGG
(GTT)	 AG	212337-212483	GT	AGG
(ATC)	 AG	212574-212693	AC	AGA
-recovered pasa_asmbl_24239.p2, internal, 212337, 212483
Valid prediction for snap_scaffold_2-snap.539-T1
Valid prediction for snap_scaffold_2-snap.533-T1
Valid prediction for snap_scaffold_2-snap.517-T1
Valid prediction for snap_scaffold_2-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_3332-T1
Valid prediction for snap_scaffold_2-snap.549-T1
Valid prediction for snap_scaffold_2-snap.552-T1
Valid prediction for snap_scaffold_2-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_3348-T1
Valid prediction for snap_scaffold_2-snap.547-T1
Valid prediction for snap_scaffold_2-snap.554-T1
Valid prediction for GlimmerHMM_glimmerT_3352-T1
Valid prediction for GlimmerHMM_glimmerT_3344-T1
Valid prediction for Augustus_model.g2234.t1
Valid prediction for GlimmerHMM_glimmerT_3346-T1
Valid prediction for GlimmerHMM_glimmerT_3347-T1
Valid prediction for Augustus_model.g2246.t1
Valid prediction for snap_scaffold_2-snap.528-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 GlimmerHMM_glimmerT_3357-T1
Valid prediction for snap_scaffold_2-snap.515-T1
Valid prediction for CodingQuarry_transcript_28472-T1
Valid prediction for GlimmerHMM_glimmerT_3343-T1
Valid prediction for Augustus_model.g2236.t1
Couldn't classify 47231, 48066
Couldn't classify 56800, 56865
Sorry, prediction pasa_asmbl_22891.p1 fails validation.
(CCT)	 AC	47231-48066	GT	AGG
(GAA)	 AG	50075-50202	GT	AGG
(ATC)	 AG	51452-51567	GT	AGG
(CTC)	 AG	52104-52301	GT	AGG
(ATG)	 AG	52393-52486	GT	GGG
(TGA)	 AG	53206-53256	GT	AGG
(CCC)	 AG	53779-53966	GT	AGG
(TTG)	 AG	54247-54356	GT	AGG
(CGA)	 AG	55801-55870	GT	TGG
(CCC)	 AG	56184-56261	GT	AGG
(ATC)	 AG	56800-56865	AT	GGA
-recovered pasa_asmbl_22891.p1, initial, 52393, 52486
add_exon() Sorry, pasa_asmbl_22891.p1 50075-50202-terminal-2 is invalid.
-recovered pasa_asmbl_22891.p1, terminal, 50075, 50202
-recovered pasa_asmbl_22891.p1, internal, 50075, 50202
-recovered pasa_asmbl_22891.p1, internal, 51452, 51567
-recovered pasa_asmbl_22891.p1, internal, 52104, 52301
-recovered pasa_asmbl_22891.p1, internal, 52393, 52486
-recovered pasa_asmbl_22891.p1, internal, 53206, 53256
-recovered pasa_asmbl_22891.p1, internal, 53779, 53966
-recovered pasa_asmbl_22891.p1, internal, 54247, 54356
-recovered pasa_asmbl_22891.p1, internal, 55801, 55870
-recovered pasa_asmbl_22891.p1, internal, 56184, 56261
Valid prediction for snap_scaffold_2-snap.553-T1
Valid prediction for GlimmerHMM_glimmerT_3353-T1
Valid prediction for GlimmerHMM_glimmerT_3349-T1
Valid prediction for GlimmerHMM_glimmerT_3335-T1
Couldn't classify 57732, 57796
Sorry, prediction pasa_asmbl_22890.p1 fails validation.
(CTC)	 TG	57732-57796	GT	AGG
(TAC)	 AG	60573-60750	GT	AGG
(GTT)	 AG	61263-61304	GT	AGG
(CTG)	 AG	61444-61549	GT	TGG
(ACT)	 AG	62661-62939	GT	GGG
(GTC)	 AG	63728-63814	GT	GGG
(GAA)	 AG	63960-63991	AG	AGA
-recovered pasa_asmbl_22890.p1, terminal, 63960, 63991
-recovered pasa_asmbl_22890.p1, internal, 60573, 60750
-recovered pasa_asmbl_22890.p1, internal, 61263, 61304
-recovered pasa_asmbl_22890.p1, internal, 61444, 61549
-recovered pasa_asmbl_22890.p1, internal, 62661, 62939
-recovered pasa_asmbl_22890.p1, internal, 63728, 63814
Valid prediction for GlimmerHMM_glimmerT_3331-T1
Valid prediction for Augustus_model.g2243.t1
Valid prediction for Augustus_model.g2242.t1
Valid prediction for snap_scaffold_2-snap.534-T1
Valid prediction for GlimmerHMM_glimmerT_3342-T1
Valid prediction for GlimmerHMM_glimmerT_3345-T1
Valid prediction for GlimmerHMM_glimmerT_3340-T1
Valid prediction for snap_scaffold_2-snap.527-T1
Valid prediction for Augustus_model.g2235.t1
Valid prediction for snap_scaffold_2-snap.537-T1
Valid prediction for Augustus_model.g2241.t1
Valid prediction for snap_scaffold_2-snap.516-T1
Valid prediction for snap_scaffold_2-snap.522-T1
Valid prediction for Augustus_model.g2237.t1
Couldn't classify 72961, 73284
Sorry, prediction pasa_asmbl_22887.p1 fails validation.
(CTC)	 CC	72961-73284	AA	GAA
Valid prediction for snap_scaffold_2-snap.544-T1
Valid prediction for snap_scaffold_2-snap.529-T1
Valid prediction for Augustus_model.g2245.t1
Valid prediction for Augustus_model.g2233.t1
Valid prediction for Augustus_model.g2240.t1
Valid prediction for GlimmerHMM_glimmerT_3339-T1
Valid prediction for GlimmerHMM_glimmerT_3350-T1
Valid prediction for Augustus_model.g2244.t1
Valid prediction for Augustus_model.g2247.t1
Valid prediction for GlimmerHMM_glimmerT_3333-T1
Valid prediction for GlimmerHMM_glimmerT_3336-T1
Valid prediction for snap_scaffold_2-snap.513-T1
Valid prediction for Augustus_model.g2238.t1
Valid prediction for snap_scaffold_2-snap.536-T1
Valid prediction for snap_scaffold_2-snap.531-T1
Valid prediction for snap_scaffold_2-snap.542-T1
Valid prediction for GlimmerHMM_glimmerT_3338-T1
Valid prediction for snap_scaffold_2-snap.551-T1
Valid prediction for snap_scaffold_2-snap.521-T1
Valid prediction for snap_scaffold_2-snap.524-T1
Valid prediction for GlimmerHMM_glimmerT_3351-T1
Valid prediction for GlimmerHMM_glimmerT_3330-T1
Valid prediction for snap_scaffold_2-snap.518-T1
Valid prediction for GlimmerHMM_glimmerT_3355-T1
Valid prediction for snap_scaffold_2-snap.555-T1
Valid prediction for snap_scaffold_2-snap.525-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19326, rend_intergenic: 13279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28594, rend_intergenic: 19477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33031, rend_intergenic: 28596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38072, rend_intergenic: 37578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40702, rend_intergenic: 38356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50132, rend_intergenic: 46227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50442, rend_intergenic: 50248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55604, rend_intergenic: 51182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79151, rend_intergenic: 56818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83202, rend_intergenic: 81273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87639, rend_intergenic: 84502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98512, rend_intergenic: 89366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109145, rend_intergenic: 104877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114135, rend_intergenic: 110048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159514, rend_intergenic: 130490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167092, rend_intergenic: 159630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171641, rend_intergenic: 170538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202760, rend_intergenic: 171641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210419, rend_intergenic: 203585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215075, rend_intergenic: 211631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220621, rend_intergenic: 217314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224235, rend_intergenic: 221841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234368
-exon list size: 441


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 19326, rend_intergenic: 13279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28594, rend_intergenic: 19477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33031, rend_intergenic: 28596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38072, rend_intergenic: 37578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40702, rend_intergenic: 38356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50132, rend_intergenic: 46227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50442, rend_intergenic: 50248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55604, rend_intergenic: 51182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79151, rend_intergenic: 56818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83202, rend_intergenic: 81273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87639, rend_intergenic: 84502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98512, rend_intergenic: 89366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109145, rend_intergenic: 104877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114135, rend_intergenic: 110048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159514, rend_intergenic: 130490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167092, rend_intergenic: 159630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171641, rend_intergenic: 170538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202760, rend_intergenic: 171641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210419, rend_intergenic: 203585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215075, rend_intergenic: 211631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220621, rend_intergenic: 217314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224235, rend_intergenic: 221841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support