-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_15595254-15878104

-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 CodingQuarry_transcript_62425-T1
Valid prediction for GlimmerHMM_glimmerT_23514-T1
Valid prediction for Augustus_model.g15668.t1
Valid prediction for GlimmerHMM_glimmerT_23534-T1
Valid prediction for GlimmerHMM_glimmerT_23516-T1
Valid prediction for GlimmerHMM_glimmerT_23531-T1
Valid prediction for pasa_asmbl_54584.p1
Valid prediction for snap_scaffold_9-snap.3165-T1
Valid prediction for snap_scaffold_9-snap.3179-T1
Valid prediction for GlimmerHMM_glimmerT_23520-T1
Valid prediction for Augustus_model.g15666.t1
Valid prediction for snap_scaffold_9-snap.3194-T1
Valid prediction for HiQ_model.g15670.t1
Valid prediction for Augustus_model.g15676.t1
Valid prediction for GlimmerHMM_glimmerT_23532-T1
Valid prediction for GlimmerHMM_glimmerT_23528-T1
Valid prediction for GlimmerHMM_glimmerT_23519-T1
Valid prediction for GlimmerHMM_glimmerT_23522-T1
Valid prediction for GlimmerHMM_glimmerT_23506-T1
Valid prediction for GlimmerHMM_glimmerT_23523-T1
Valid prediction for snap_scaffold_9-snap.3160-T1
Valid prediction for GlimmerHMM_glimmerT_23525-T1
Valid prediction for Augustus_model.g15675.t1
Valid prediction for GlimmerHMM_glimmerT_23511-T1
Valid prediction for snap_scaffold_9-snap.3158-T1
Valid prediction for HiQ_model.g15661.t1
Valid prediction for GlimmerHMM_glimmerT_23510-T1
Valid prediction for snap_scaffold_9-snap.3180-T1
Valid prediction for GlimmerHMM_glimmerT_23517-T1
Valid prediction for snap_scaffold_9-snap.3176-T1
Valid prediction for snap_scaffold_9-snap.3169-T1
Valid prediction for snap_scaffold_9-snap.3170-T1
Valid prediction for snap_scaffold_9-snap.3192-T1
Valid prediction for snap_scaffold_9-snap.3201-T1
Valid prediction for GlimmerHMM_glimmerT_23535-T1
Valid prediction for GlimmerHMM_glimmerT_23505-T1
Valid prediction for snap_scaffold_9-snap.3174-T1
Valid prediction for snap_scaffold_9-snap.3198-T1
Valid prediction for snap_scaffold_9-snap.3190-T1
Valid prediction for snap_scaffold_9-snap.3162-T1
Valid prediction for snap_scaffold_9-snap.3177-T1
Valid prediction for Augustus_model.g15672.t1
Valid prediction for GlimmerHMM_glimmerT_23536-T1
Valid prediction for GlimmerHMM_glimmerT_23504-T1
Couldn't classify 148394, 148532
Sorry, prediction pasa_asmbl_54585.p1 fails validation.
(GTA)	 AC	148394-148532	GT	CAG
(ACA)	 AG	148943-149103	GT	AGG
(GCC)	 AG	149234-149398	GT	GGG
(GAG)	 AG	149485-149628	GT	AGG
(ATT)	 AG	149992-150075	GT	AGG
(GTC)	 AG	150415-150560	GT	CTG
(GGT)	 AG	150766-150874	GT	AGG
(GTG)	 AG	151450-151539	CC	GAC
-recovered pasa_asmbl_54585.p1, terminal, 151450, 151539
-recovered pasa_asmbl_54585.p1, internal, 148943, 149103
-recovered pasa_asmbl_54585.p1, internal, 149234, 149398
-recovered pasa_asmbl_54585.p1, internal, 149485, 149628
-recovered pasa_asmbl_54585.p1, internal, 149992, 150075
-recovered pasa_asmbl_54585.p1, internal, 150415, 150560
-recovered pasa_asmbl_54585.p1, internal, 150766, 150874
Valid prediction for snap_scaffold_9-snap.3205-T1
Valid prediction for Augustus_model.g15674.t1
Valid prediction for snap_scaffold_9-snap.3166-T1
Valid prediction for snap_scaffold_9-snap.3172-T1
Valid prediction for snap_scaffold_9-snap.3186-T1
Valid prediction for Augustus_model.g15669.t1
Valid prediction for snap_scaffold_9-snap.3183-T1
Valid prediction for snap_scaffold_9-snap.3163-T1
Valid prediction for GlimmerHMM_glimmerT_23518-T1
Valid prediction for snap_scaffold_9-snap.3199-T1
Valid prediction for snap_scaffold_9-snap.3188-T1
Valid prediction for snap_scaffold_9-snap.3157-T1
Valid prediction for Augustus_model.g15660.t1
Valid prediction for Augustus_model.g15665.t1
Valid prediction for GlimmerHMM_glimmerT_23530-T1
Valid prediction for GlimmerHMM_glimmerT_23526-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_9-snap.3171-T1
Couldn't classify 246278, 246340
Sorry, prediction pasa_asmbl_55551.p1 fails validation.
(ATG)	 TC	238469-238549	GT	TGG
(CAC)	 AG	238653-238749	GT	TGG
(ATG)	 AG	238909-239039	GT	AGG
(ATA)	 AG	239309-239359	GT	TGG
(GGT)	 AG	240090-240278	GT	AGG
(CTG)	 AG	240461-240582	GT	AGG
(TGA)	 AG	240944-241087	GT	AGG
(GTC)	 AG	241163-241262	GT	AGG
(GTG)	 AG	242337-242533	GT	AAG
(TGT)	 AG	243084-243193	GT	CGG
(ATC)	 AG	243847-243925	GT	AGG
(AAT)	 AG	245254-245421	GT	GGG
(GGA)	 AG	245734-245857	GT	AGG
(CTC)	 AG	246278-246340	GA	GGG
-recovered pasa_asmbl_55551.p1, initial, 238469, 238549
add_exon() Sorry, pasa_asmbl_55551.p1 238909-239039-initial-1 is invalid.
-recovered pasa_asmbl_55551.p1, initial, 238909, 239039
-recovered pasa_asmbl_55551.p1, terminal, 243847, 243925
-recovered pasa_asmbl_55551.p1, internal, 238653, 238749
-recovered pasa_asmbl_55551.p1, internal, 238909, 239039
-recovered pasa_asmbl_55551.p1, internal, 239309, 239359
-recovered pasa_asmbl_55551.p1, internal, 240090, 240278
-recovered pasa_asmbl_55551.p1, internal, 240461, 240582
-recovered pasa_asmbl_55551.p1, internal, 240944, 241087
-recovered pasa_asmbl_55551.p1, internal, 241163, 241262
-recovered pasa_asmbl_55551.p1, internal, 242337, 242533
-recovered pasa_asmbl_55551.p1, internal, 243084, 243193
-recovered pasa_asmbl_55551.p1, internal, 243847, 243925
-recovered pasa_asmbl_55551.p1, internal, 245254, 245421
-recovered pasa_asmbl_55551.p1, internal, 245734, 245857
Valid prediction for snap_scaffold_9-snap.3178-T1
Valid prediction for GlimmerHMM_glimmerT_23515-T1
Valid prediction for snap_scaffold_9-snap.3187-T1
Valid prediction for Augustus_model.g15662.t1
Valid prediction for snap_scaffold_9-snap.3175-T1
Valid prediction for GlimmerHMM_glimmerT_23509-T1
Valid prediction for snap_scaffold_9-snap.3204-T1
Couldn't classify 124938, 124968
Couldn't classify 125862, 125960
Sorry, prediction pasa_asmbl_55554.p1 fails validation.
(AAA)	 AG	124938-124968	GT	AGG
(GGA)	 AG	125074-125180	GT	ATG
(ATC)	 AG	125309-125452	GT	AGG
(GTG)	 AG	125862-125960	GG	GGG
-recovered pasa_asmbl_55554.p1, internal, 124938, 124968
-recovered pasa_asmbl_55554.p1, internal, 125074, 125180
-recovered pasa_asmbl_55554.p1, internal, 125309, 125452
Valid prediction for Augustus_model.g15671.t1
Valid prediction for Augustus_model.g15667.t1
Valid prediction for snap_scaffold_9-snap.3196-T1
Valid prediction for snap_scaffold_9-snap.3202-T1
Valid prediction for pasa_asmbl_55553.p1
Valid prediction for snap_scaffold_9-snap.3161-T1
Valid prediction for GlimmerHMM_glimmerT_23524-T1
Couldn't classify 259596, 259665
Sorry, prediction pasa_asmbl_55547.p1 fails validation.
(ATG)	 CG	256533-256966	GT	AGG
(TTC)	 AG	259596-259665	AA	ACA
-recovered pasa_asmbl_55547.p1, initial, 256533, 256966
Valid prediction for GlimmerHMM_glimmerT_23529-T1
Valid prediction for snap_scaffold_9-snap.3200-T1
Valid prediction for GlimmerHMM_glimmerT_23527-T1
Valid prediction for GlimmerHMM_glimmerT_23508-T1
Valid prediction for Augustus_model.g15664.t1
Valid prediction for Augustus_model.g15663.t1
Valid prediction for snap_scaffold_9-snap.3193-T1
Valid prediction for pasa_asmbl_55543.p1
Valid prediction for GlimmerHMM_glimmerT_23533-T1
Valid prediction for GlimmerHMM_glimmerT_23513-T1
Valid prediction for snap_scaffold_9-snap.3167-T1
Valid prediction for snap_scaffold_9-snap.3164-T1
Valid prediction for snap_scaffold_9-snap.3185-T1
Couldn't classify 263452, 263522
Couldn't classify 265167, 265213
Sorry, prediction pasa_asmbl_55545.p1 fails validation.
(AGC)	 CC	263452-263522	GT	ATG
(GGG)	 AG	263661-263769	GT	AGG
(CCG)	 AG	263983-264126	GT	CGG
(AGA)	 AG	264252-264369	GT	AAG
(CAG)	 AG	264468-264606	GT	AGG
(GTA)	 AG	264799-264923	GT	AGG
(AAT)	 AG	265167-265213	CC	CCC
-recovered pasa_asmbl_55545.p1, internal, 263661, 263769
-recovered pasa_asmbl_55545.p1, internal, 263983, 264126
-recovered pasa_asmbl_55545.p1, internal, 264252, 264369
-recovered pasa_asmbl_55545.p1, internal, 264468, 264606
-recovered pasa_asmbl_55545.p1, internal, 264799, 264923
Valid prediction for snap_scaffold_9-snap.3189-T1
Valid prediction for snap_scaffold_9-snap.3184-T1
Valid prediction for GlimmerHMM_glimmerT_23507-T1
Couldn't classify 248230, 248302
Couldn't classify 248323, 248351
Sorry, prediction CodingQuarry_transcript_62426-T1 fails validation.
(ATG)	 AG	248230-248302	AA	GAA
(GAG)	 GA	248323-248351	AC	AGA
Couldn't classify 129717, 129962
Sorry, prediction pasa_asmbl_55552.p1 fails validation.
(GCC)	 TA	129717-129962	GT	AGG
(GGT)	 AG	130182-130274	TG	GAT
-recovered pasa_asmbl_55552.p1, terminal, 130182, 130274
Couldn't classify 259894, 259978
Couldn't classify 262070, 262113
Sorry, prediction pasa_asmbl_55546.p1 fails validation.
(CTC)	 AC	259894-259978	GT	AGG
(CTA)	 AG	260526-260647	GT	CTG
(GAT)	 AG	261134-261335	GT	AGG
(AAT)	 AG	262070-262113	CG	GTC
-recovered pasa_asmbl_55546.p1, internal, 260526, 260647
-recovered pasa_asmbl_55546.p1, internal, 261134, 261335
Valid prediction for snap_scaffold_9-snap.3173-T1
Valid prediction for snap_scaffold_9-snap.3197-T1
Valid prediction for snap_scaffold_9-snap.3195-T1
Valid prediction for Augustus_model.g15673.t1
Valid prediction for snap_scaffold_9-snap.3159-T1
Couldn't classify 265280, 265373
Couldn't classify 265934, 266742
Sorry, prediction pasa_asmbl_55544.p1 fails validation.
(AGC)	 CC	265280-265373	GT	TGG
(AGA)	 AG	265560-265805	GT	GGG
(GAC)	 AG	265934-266742	AG	CCA
-recovered pasa_asmbl_55544.p1, internal, 265560, 265805
Valid prediction for snap_scaffold_9-snap.3203-T1
Valid prediction for snap_scaffold_9-snap.3181-T1
Valid prediction for GlimmerHMM_glimmerT_23521-T1
Valid prediction for snap_scaffold_9-snap.3191-T1
Valid prediction for snap_scaffold_9-snap.3182-T1
Valid prediction for GlimmerHMM_glimmerT_23512-T1
Valid prediction for snap_scaffold_9-snap.3168-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37537, rend_intergenic: 35536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51990, rend_intergenic: 37852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64649, rend_intergenic: 54396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74845, rend_intergenic: 65132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98740, rend_intergenic: 97817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115231, rend_intergenic: 101882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133969, rend_intergenic: 120679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139107, rend_intergenic: 137922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147362, rend_intergenic: 143238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166042, rend_intergenic: 163798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177815, rend_intergenic: 168081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197267, rend_intergenic: 188591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200748, rend_intergenic: 198011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212027, rend_intergenic: 209049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223342, rend_intergenic: 220582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247348, rend_intergenic: 228628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 14316, rend_intergenic: 14313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 79942, rend_intergenic: 79939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 282851
-exon list size: 435


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 37537, rend_intergenic: 35536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51990, rend_intergenic: 37852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64649, rend_intergenic: 54396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74845, rend_intergenic: 65132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98740, rend_intergenic: 97817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115231, rend_intergenic: 101882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133969, rend_intergenic: 120679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139107, rend_intergenic: 137922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147362, rend_intergenic: 143238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166042, rend_intergenic: 163798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177815, rend_intergenic: 168081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197267, rend_intergenic: 188591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200748, rend_intergenic: 198011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212027, rend_intergenic: 209049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223342, rend_intergenic: 220582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247348, rend_intergenic: 228628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 14316, rend_intergenic: 14313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 79942, rend_intergenic: 79939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support