-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_1554799-1681327

-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_46592-T1
Valid prediction for GlimmerHMM_glimmerT_46602-T1
Valid prediction for GlimmerHMM_glimmerT_46591-T1
Valid prediction for pasa_asmbl_25579.p1
Valid prediction for GeneMark_model.81081_t
Valid prediction for GeneMark_model.81092_t
Valid prediction for CodingQuarry_transcript_30369-T1
Valid prediction for CodingQuarry_transcript_30374-T1
Valid prediction for snap_scaffold_20-snap.384-T1
Valid prediction for GlimmerHMM_glimmerT_46593-T1
Valid prediction for Augustus_model.g31117.t1
Valid prediction for Augustus_model.g31112.t1
Valid prediction for GeneMark_model.81078_t
Valid prediction for snap_scaffold_20-snap.383-T1
Valid prediction for Augustus_model.g31107.t1
Valid prediction for CodingQuarry_transcript_30366-T1
Valid prediction for GeneMark_model.81093_t
Valid prediction for snap_scaffold_20-snap.376-T1
Valid prediction for snap_scaffold_20-snap.358-T1
Valid prediction for GeneMark_model.81094_t
Couldn't classify 18412, 18412
Sorry, prediction pasa_asmbl_25582.p1 fails validation.
(AGT)	 GA	18412-18412	GT	AAG
(TGT)	 AG	19004-19176	GT	AGG
(GTG)	 AG	19307-19502	GT	GGG
(GAT)	 AG	19940-20119	GT	CTG
(CCC)	 AG	20385-20651	GT	AGG
(CCT)	 AG	20778-20782	GC	GAG
-recovered pasa_asmbl_25582.p1, terminal, 20778, 20782
-recovered pasa_asmbl_25582.p1, internal, 19004, 19176
-recovered pasa_asmbl_25582.p1, internal, 19307, 19502
-recovered pasa_asmbl_25582.p1, internal, 19940, 20119
-recovered pasa_asmbl_25582.p1, internal, 20385, 20651
-recovered pasa_asmbl_25582.p1, internal, 20778, 20782
Valid prediction for CodingQuarry_transcript_30375-T1
Couldn't classify 114170, 114303
Sorry, prediction pasa_asmbl_25596.p1 fails validation.
(ATG)	 CT	113521-113529	GT	AGG
(CAT)	 AG	113922-114081	GT	AGG
(GAG)	 AG	114170-114303	GA	GAG
-recovered pasa_asmbl_25596.p1, initial, 113521, 113529
-recovered pasa_asmbl_25596.p1, internal, 113922, 114081
Valid prediction for pasa_asmbl_25581.p1
Valid prediction for Augustus_model.g31118.t1
Valid prediction for GeneMark_model.81070_t
Couldn't classify 114400, 114574
Sorry, prediction pasa_asmbl_25597.p1 fails validation.
(GAG)	 AA	114400-114574	GT	TGG
(GAG)	 AG	114777-114860	GT	AGG
(TGA)	 AG	115135-115374	GT	AGG
(GAG)	 AG	115546-116246	GC	GAG
-recovered pasa_asmbl_25597.p1, terminal, 115546, 116246
-recovered pasa_asmbl_25597.p1, internal, 114777, 114860
-recovered pasa_asmbl_25597.p1, internal, 115135, 115374
-recovered pasa_asmbl_25597.p1, internal, 115546, 116246
Valid prediction for snap_scaffold_20-snap.352-T1
Valid prediction for GeneMark_model.81088_t
Valid prediction for pasa_asmbl_25590.p1
Valid prediction for GeneMark_model.81074_t
Valid prediction for GeneMark_model.81090_t
Valid prediction for snap_scaffold_20-snap.381-T1
Valid prediction for snap_scaffold_20-snap.362-T1
Valid prediction for snap_scaffold_20-snap.375-T1
Couldn't classify 122294, 123145
Sorry, prediction pasa_asmbl_25599.p1 fails validation.
(AAG)	 AG	122294-123145	GA	GTG
Valid prediction for snap_scaffold_20-snap.370-T1
Valid prediction for snap_scaffold_20-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_46598-T1
Valid prediction for Augustus_model.g31123.t1
Valid prediction for GlimmerHMM_glimmerT_46588-T1
Valid prediction for GlimmerHMM_glimmerT_46603-T1
Valid prediction for Augustus_model.g31110.t1
Valid prediction for HiQ_model.g31111.t1
Valid prediction for GeneMark_model.81096_t
Valid prediction for snap_scaffold_20-snap.374-T1
Valid prediction for GeneMark_model.81072_t
Valid prediction for Augustus_model.g31113.t1
Valid prediction for Augustus_model.g31105.t1
Valid prediction for GeneMark_model.81085_t
Couldn't classify 77972, 78880
Sorry, prediction pasa_asmbl_25593.p1 fails validation.
(CCA)	 CC	77972-78880	GG	AAG
Valid prediction for Augustus_model.g31125.t1
Valid prediction for GeneMark_model.81071_t
Valid prediction for pasa_asmbl_25594.p1
Valid prediction for snap_scaffold_20-snap.353-T1
Valid prediction for GeneMark_model.81089_t
Valid prediction for Augustus_model.g31119.t1
Valid prediction for HiQ_model.g31124.t1
Valid prediction for Augustus_model.g31106.t1
Couldn't classify 6000, 7490
Sorry, prediction pasa_asmbl_25580.p1 fails validation.
(ACC)	 AA	6000-7490	AT	AGA
Valid prediction for snap_scaffold_20-snap.364-T1
Valid prediction for GlimmerHMM_glimmerT_46589-T1
Valid prediction for HiQ_model.g31109.t1
Valid prediction for snap_scaffold_20-snap.369-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.81076_t
Valid prediction for GlimmerHMM_glimmerT_46604-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.372-T1
Valid prediction for GlimmerHMM_glimmerT_46599-T1
Valid prediction for snap_scaffold_20-snap.356-T1
Couldn't classify 22609, 22609
Couldn't classify 29528, 29571
Sorry, prediction pasa_asmbl_25587.p2 fails validation.
(AGT)	 AA	22609-22609	GT	AAG
(TGT)	 AG	25251-25313	GT	GGG
(TCT)	 AG	27026-27124	GT	GGG
(ATT)	 AG	27500-27640	GT	GGG
(ATA)	 AG	28753-28887	GT	AGG
(ATA)	 AG	29201-29338	GT	AGG
(AGT)	 AG	29528-29571	GT	AGG
-recovered pasa_asmbl_25587.p2, internal, 25251, 25313
-recovered pasa_asmbl_25587.p2, internal, 27026, 27124
-recovered pasa_asmbl_25587.p2, internal, 27500, 27640
-recovered pasa_asmbl_25587.p2, internal, 28753, 28887
-recovered pasa_asmbl_25587.p2, internal, 29201, 29338
-recovered pasa_asmbl_25587.p2, internal, 29528, 29571
Valid prediction for GlimmerHMM_glimmerT_46586-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 CodingQuarry_transcript_30371-T1
Valid prediction for Augustus_model.g31115.t1
Valid prediction for GeneMark_model.81080_t
Couldn't classify 36662, 36776
Couldn't classify 37066, 37307
Sorry, prediction pasa_asmbl_27241.p1 fails validation.
(GAA)	 TT	36662-36776	GT	AGG
(AAG)	 AG	37066-37307	CC	AGC
Valid prediction for GeneMark_model.81075_t
Valid prediction for snap_scaffold_20-snap.354-T1
Valid prediction for CodingQuarry_transcript_30370-T1
Valid prediction for Augustus_model.g31120.t1
Valid prediction for Augustus_model.g31121.t1
Valid prediction for GlimmerHMM_glimmerT_46601-T1
Couldn't classify 61999, 62049
Sorry, prediction pasa_asmbl_26521.p2 fails validation.
(GCT)	 CA	61999-62049	GT	TGG
(ATC)	 AG	62195-62278	GT	AGG
(TTC)	 AG	64950-65071	GT	GTG
(TGT)	 AG	65395-65482	GA	GAG
-recovered pasa_asmbl_26521.p2, terminal, 65395, 65482
-recovered pasa_asmbl_26521.p2, internal, 62195, 62278
-recovered pasa_asmbl_26521.p2, internal, 64950, 65071
Valid prediction for pasa_asmbl_26530.p1
Valid prediction for Augustus_model.g31122.t1
Valid prediction for GeneMark_model.81084_t
Valid prediction for Augustus_model.g31114.t1
Valid prediction for pasa_asmbl_26515.p1
Valid prediction for snap_scaffold_20-snap.363-T1
Valid prediction for snap_scaffold_20-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_46587-T1
Valid prediction for snap_scaffold_20-snap.378-T1
Valid prediction for CodingQuarry_transcript_30372-T1
Valid prediction for snap_scaffold_20-snap.371-T1
Valid prediction for CodingQuarry_transcript_30373-T1
Valid prediction for GeneMark_model.81095_t
Valid prediction for GlimmerHMM_glimmerT_46590-T1
Valid prediction for GeneMark_model.81086_t
Valid prediction for GlimmerHMM_glimmerT_46600-T1
Valid prediction for snap_scaffold_20-snap.361-T1
Valid prediction for snap_scaffold_20-snap.377-T1
Valid prediction for snap_scaffold_20-snap.360-T1
Valid prediction for snap_scaffold_20-snap.355-T1
Valid prediction for GeneMark_model.81077_t
Valid prediction for GlimmerHMM_glimmerT_46596-T1
Valid prediction for GeneMark_model.81091_t
Couldn't classify 61402, 61533
Sorry, prediction pasa_asmbl_26525.p1 fails validation.
(ATG)	 AT	54776-54877	GT	AGG
(AAC)	 AG	55440-55562	GT	CGG
(GTG)	 AG	55646-55696	GT	CTG
(GCA)	 AG	56064-56155	GT	AGG
(GGT)	 AG	56251-56339	GT	AGG
(GCT)	 AG	56901-57031	GT	AAG
(GAG)	 AG	57202-57291	GT	AGG
(TTG)	 AG	57577-57639	GT	GTG
(TTC)	 AG	58717-58818	GT	AGG
(GTG)	 AG	59070-59203	GT	AGG
(GTA)	 AG	59316-59391	GT	GTG
(ATC)	 AG	59978-60051	GT	CTG
(ACT)	 AG	60595-60712	GT	AGG
(GTG)	 AG	61402-61533	TC	GGT
-recovered pasa_asmbl_26525.p1, initial, 54776, 54877
-recovered pasa_asmbl_26525.p1, internal, 55440, 55562
-recovered pasa_asmbl_26525.p1, internal, 55646, 55696
-recovered pasa_asmbl_26525.p1, internal, 56064, 56155
-recovered pasa_asmbl_26525.p1, internal, 56251, 56339
-recovered pasa_asmbl_26525.p1, internal, 56901, 57031
-recovered pasa_asmbl_26525.p1, internal, 57202, 57291
-recovered pasa_asmbl_26525.p1, internal, 57577, 57639
-recovered pasa_asmbl_26525.p1, internal, 58717, 58818
-recovered pasa_asmbl_26525.p1, internal, 59070, 59203
-recovered pasa_asmbl_26525.p1, internal, 59316, 59391
-recovered pasa_asmbl_26525.p1, internal, 59978, 60051
-recovered pasa_asmbl_26525.p1, internal, 60595, 60712
Valid prediction for snap_scaffold_20-snap.379-T1
Valid prediction for Augustus_model.g31108.t1
Couldn't classify 52954, 53280
Sorry, prediction pasa_asmbl_26526.p1 fails validation.
(CTC)	 CT	52954-53280	AA	ACA
Valid prediction for snap_scaffold_20-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_46594-T1
Valid prediction for snap_scaffold_20-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_46595-T1
Couldn't classify 31007, 31157
Sorry, prediction pasa_asmbl_26529.p1 fails validation.
(CTG)	 TA	31007-31157	GT	AGG
(AAG)	 AG	32253-33211	TG	AGT
-recovered pasa_asmbl_26529.p1, terminal, 32253, 33211
Valid prediction for GeneMark_model.81073_t
Valid prediction for snap_scaffold_20-snap.366-T1
Valid prediction for GeneMark_model.81082_t
Valid prediction for GlimmerHMM_glimmerT_46597-T1
Valid prediction for snap_scaffold_20-snap.368-T1
Valid prediction for snap_scaffold_20-snap.380-T1
Valid prediction for snap_scaffold_20-snap.357-T1
Valid prediction for GeneMark_model.81083_t
Valid prediction for snap_scaffold_20-snap.373-T1
Valid prediction for Augustus_model.g31116.t1
Valid prediction for GeneMark_model.81087_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18489, rend_intergenic: 17448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19520, rend_intergenic: 18729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36024, rend_intergenic: 19920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39535, rend_intergenic: 36579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40368, rend_intergenic: 39536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45190, rend_intergenic: 40822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57954, rend_intergenic: 46018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64525, rend_intergenic: 60400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71197, rend_intergenic: 65016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106015, rend_intergenic: 101130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 126529
-exon list size: 506


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 18489, rend_intergenic: 17448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19520, rend_intergenic: 18729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36024, rend_intergenic: 19920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39535, rend_intergenic: 36579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40368, rend_intergenic: 39536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45190, rend_intergenic: 40822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57954, rend_intergenic: 46018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64525, rend_intergenic: 60400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71197, rend_intergenic: 65016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106015, rend_intergenic: 101130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support