-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_14112854-14292185

-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.2953-T1
Valid prediction for GlimmerHMM_glimmerT_35855-T1
Valid prediction for snap_scaffold_14-snap.2922-T1
Valid prediction for GlimmerHMM_glimmerT_35854-T1
Valid prediction for snap_scaffold_14-snap.2936-T1
Valid prediction for GeneMark_model.61475_t
Valid prediction for snap_scaffold_14-snap.2949-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2937-T1
Valid prediction for GlimmerHMM_glimmerT_35849-T1
Valid prediction for GeneMark_model.61473_t
Valid prediction for HiQ_model.g24133.t1
Valid prediction for GeneMark_model.61457_t
Valid prediction for snap_scaffold_14-snap.2934-T1
Valid prediction for Augustus_model.g24143.t1
Valid prediction for GlimmerHMM_glimmerT_35864-T1
Valid prediction for Augustus_model.g24142.t1
Valid prediction for snap_scaffold_14-snap.2932-T1
Valid prediction for snap_scaffold_14-snap.2927-T1
Valid prediction for GeneMark_model.61441_t
Couldn't classify 17909, 18310
Sorry, prediction pasa_asmbl_12507.p1 fails validation.
(ACC)	 TC	17909-18310	TT	AAT
Valid prediction for Augustus_model.g24148.t1
Couldn't classify 27730, 27829
Sorry, prediction pasa_asmbl_12514.p1 fails validation.
(GGA)	 TG	27730-27829	GT	AGG
(GAA)	 AG	29877-30022	GT	AGG
(GAG)	 AG	30136-30288	GT	AGG
(GGC)	 AG	30624-30722	GT	AGG
(AAT)	 AG	31875-31937	GT	ACG
(GCC)	 AG	32330-32396	GT	AGG
(AGA)	 AG	34095-34160	GT	ATG
(GCA)	 AG	34281-34401	GT	AAG
(ATC)	 AG	34650-34745	GT	AGG
(CTG)	 AG	34895-34958	GT	AGG
(CTG)	 AG	35060-35101	GT	AGG
(GGC)	 AG	36470-36603	GT	AGG
(ATA)	 AG	36732-36834	GA	AAG
-recovered pasa_asmbl_12514.p1, terminal, 36732, 36834
-recovered pasa_asmbl_12514.p1, internal, 29877, 30022
-recovered pasa_asmbl_12514.p1, internal, 30136, 30288
-recovered pasa_asmbl_12514.p1, internal, 30624, 30722
-recovered pasa_asmbl_12514.p1, internal, 31875, 31937
-recovered pasa_asmbl_12514.p1, internal, 32330, 32396
-recovered pasa_asmbl_12514.p1, internal, 34095, 34160
-recovered pasa_asmbl_12514.p1, internal, 34281, 34401
-recovered pasa_asmbl_12514.p1, internal, 34650, 34745
-recovered pasa_asmbl_12514.p1, internal, 34895, 34958
-recovered pasa_asmbl_12514.p1, internal, 35060, 35101
-recovered pasa_asmbl_12514.p1, internal, 36470, 36603
Valid prediction for GeneMark_model.61444_t
Valid prediction for GeneMark_model.61447_t
Valid prediction for GlimmerHMM_glimmerT_35868-T1
Valid prediction for GeneMark_model.61469_t
Valid prediction for GeneMark_model.61480_t
Valid prediction for pasa_asmbl_12505.p1
Valid prediction for GlimmerHMM_glimmerT_35851-T1
Valid prediction for snap_scaffold_14-snap.2920-T1
Valid prediction for GlimmerHMM_glimmerT_35860-T1
Valid prediction for GeneMark_model.61482_t
Valid prediction for GlimmerHMM_glimmerT_35866-T1
Valid prediction for GlimmerHMM_glimmerT_35857-T1
Valid prediction for GeneMark_model.61458_t
Valid prediction for Augustus_model.g24139.t1
Valid prediction for snap_scaffold_14-snap.2921-T1
Valid prediction for GeneMark_model.61438_t
Valid prediction for GlimmerHMM_glimmerT_35870-T1
Valid prediction for snap_scaffold_14-snap.2948-T1
Valid prediction for GlimmerHMM_glimmerT_35847-T1
Valid prediction for GlimmerHMM_glimmerT_35859-T1
Valid prediction for pasa_asmbl_12508.p1
Valid prediction for GeneMark_model.61464_t
Valid prediction for snap_scaffold_14-snap.2951-T1
Valid prediction for GeneMark_model.61442_t
Valid prediction for snap_scaffold_14-snap.2917-T1
Valid prediction for GeneMark_model.61453_t
Valid prediction for GeneMark_model.61471_t
Valid prediction for GeneMark_model.61449_t
Valid prediction for snap_scaffold_14-snap.2939-T1
Valid prediction for Augustus_model.g24141.t1
Valid prediction for GeneMark_model.61466_t
Valid prediction for Augustus_model.g24136.t1
Valid prediction for snap_scaffold_14-snap.2931-T1
Valid prediction for snap_scaffold_14-snap.2935-T1
Valid prediction for Augustus_model.g24134.t1
Valid prediction for CodingQuarry_transcript_15877-T1
Valid prediction for snap_scaffold_14-snap.2944-T1
Valid prediction for HiQ_model.g24135.t1
Valid prediction for snap_scaffold_14-snap.2947-T1
Valid prediction for GeneMark_model.61462_t
Valid prediction for snap_scaffold_14-snap.2924-T1
Valid prediction for snap_scaffold_14-snap.2923-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.61477_t
Valid prediction for GeneMark_model.61455_t
Valid prediction for GlimmerHMM_glimmerT_35848-T1
Valid prediction for snap_scaffold_14-snap.2930-T1
Valid prediction for GeneMark_model.61440_t

-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.2926-T1
Valid prediction for snap_scaffold_14-snap.2955-T1
Valid prediction for snap_scaffold_14-snap.2925-T1
Valid prediction for snap_scaffold_14-snap.2918-T1
Valid prediction for snap_scaffold_14-snap.2952-T1
Valid prediction for GlimmerHMM_glimmerT_35867-T1
Valid prediction for GlimmerHMM_glimmerT_35858-T1
Valid prediction for GeneMark_model.61478_t
Valid prediction for GeneMark_model.61465_t
Valid prediction for snap_scaffold_14-snap.2954-T1
Valid prediction for GeneMark_model.61454_t
Valid prediction for snap_scaffold_14-snap.2929-T1
Valid prediction for GeneMark_model.61443_t
Valid prediction for Augustus_model.g24147.t1
Valid prediction for snap_scaffold_14-snap.2933-T1
Valid prediction for GeneMark_model.61481_t
Couldn't classify 34943, 35053
Sorry, prediction pasa_asmbl_13667.p1 fails validation.
(GTG)	 AC	34943-35053	GT	CTG
(ATA)	 AG	35188-35239	GT	AGG
(ATG)	 AG	37278-37405	GT	CAG
(CCC)	 AG	38072-38149	GT	TGG
(ATC)	 AG	39384-39523	GT	TGG
(CTT)	 AG	40518-40563	GT	TGG
(CTA)	 AG	40910-40987	AG	GAA
add_exon() Sorry, pasa_asmbl_13667.p1 37278-37405-initial-1 is invalid.
-recovered pasa_asmbl_13667.p1, initial, 37278, 37405
-recovered pasa_asmbl_13667.p1, terminal, 40910, 40987
-recovered pasa_asmbl_13667.p1, internal, 35188, 35239
-recovered pasa_asmbl_13667.p1, internal, 37278, 37405
-recovered pasa_asmbl_13667.p1, internal, 38072, 38149
-recovered pasa_asmbl_13667.p1, internal, 39384, 39523
-recovered pasa_asmbl_13667.p1, internal, 40518, 40563
Valid prediction for GlimmerHMM_glimmerT_35852-T1
Valid prediction for GeneMark_model.61476_t
Valid prediction for GlimmerHMM_glimmerT_35863-T1
Valid prediction for GlimmerHMM_glimmerT_35850-T1
Valid prediction for GeneMark_model.61474_t
Valid prediction for GeneMark_model.61445_t
Valid prediction for Augustus_model.g24145.t1
Valid prediction for Augustus_model.g24146.t1
Valid prediction for snap_scaffold_14-snap.2938-T1
Valid prediction for snap_scaffold_14-snap.2942-T1
Valid prediction for snap_scaffold_14-snap.2940-T1
Valid prediction for GlimmerHMM_glimmerT_35862-T1
Valid prediction for GeneMark_model.61459_t
Valid prediction for GlimmerHMM_glimmerT_35869-T1
Valid prediction for GlimmerHMM_glimmerT_35853-T1
Valid prediction for GeneMark_model.61484_t
Valid prediction for snap_scaffold_14-snap.2928-T1
Valid prediction for Augustus_model.g24140.t1
Valid prediction for GeneMark_model.61463_t
Valid prediction for GlimmerHMM_glimmerT_35861-T1
Valid prediction for GlimmerHMM_glimmerT_35856-T1
Valid prediction for snap_scaffold_14-snap.2950-T1
Valid prediction for GeneMark_model.61450_t
Valid prediction for GeneMark_model.61468_t
Valid prediction for Augustus_model.g24137.t1
Valid prediction for snap_scaffold_14-snap.2919-T1
Valid prediction for Augustus_model.g24138.t1
Valid prediction for GeneMark_model.61479_t
Valid prediction for GeneMark_model.61483_t
Valid prediction for GeneMark_model.61439_t
Valid prediction for snap_scaffold_14-snap.2943-T1
Valid prediction for GlimmerHMM_glimmerT_35865-T1
Valid prediction for GeneMark_model.61470_t
Valid prediction for snap_scaffold_14-snap.2941-T1
Valid prediction for GeneMark_model.61448_t
Valid prediction for GeneMark_model.61472_t
Valid prediction for snap_scaffold_14-snap.2946-T1
Valid prediction for GeneMark_model.61437_t
Valid prediction for GeneMark_model.61456_t
Valid prediction for snap_scaffold_14-snap.2945-T1
Valid prediction for GeneMark_model.61451_t
Valid prediction for snap_scaffold_14-snap.2916-T1
Valid prediction for GeneMark_model.61446_t
Valid prediction for Augustus_model.g24144.t1
Valid prediction for GeneMark_model.61467_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7993, rend_intergenic: 5483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11717, rend_intergenic: 8255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36834, rend_intergenic: 27655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47734, rend_intergenic: 47705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81397, rend_intergenic: 74525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132324, rend_intergenic: 126884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155331, rend_intergenic: 142935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162915, rend_intergenic: 162218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169031, rend_intergenic: 166942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170769, rend_intergenic: 169468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179332
-exon list size: 612


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 7993, rend_intergenic: 5483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11717, rend_intergenic: 8255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36834, rend_intergenic: 27655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47734, rend_intergenic: 47705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81397, rend_intergenic: 74525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132324, rend_intergenic: 126884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155331, rend_intergenic: 142935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162915, rend_intergenic: 162218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169031, rend_intergenic: 166942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170769, rend_intergenic: 169468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support