-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_2863225-2999528

-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_10-snap.640-T1
Couldn't classify 51001, 51213
Sorry, prediction pasa_asmbl_4294.p1 fails validation.
(GTG)	 CA	51001-51213	GT	TGG
(GTC)	 AG	51413-51519	GT	AGG
(ACA)	 AG	51932-51995	AA	AGA
-recovered pasa_asmbl_4294.p1, terminal, 51932, 51995
-recovered pasa_asmbl_4294.p1, internal, 51413, 51519
Valid prediction for GlimmerHMM_glimmerT_24857-T1
Valid prediction for snap_scaffold_10-snap.628-T1
Valid prediction for snap_scaffold_10-snap.618-T1
Valid prediction for Augustus_model.g16659.t1
Valid prediction for GlimmerHMM_glimmerT_24871-T1
Valid prediction for snap_scaffold_10-snap.622-T1
Valid prediction for GeneMark_model.42483_t
Valid prediction for GeneMark_model.42471_t
Valid prediction for snap_scaffold_10-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_24856-T1
Valid prediction for Augustus_model.g16672.t1
Valid prediction for snap_scaffold_10-snap.625-T1
Valid prediction for GeneMark_model.42479_t
Valid prediction for GeneMark_model.42465_t
Valid prediction for GeneMark_model.42487_t
Valid prediction for GlimmerHMM_glimmerT_24860-T1
Valid prediction for GeneMark_model.42478_t
Valid prediction for GlimmerHMM_glimmerT_24872-T1
Valid prediction for snap_scaffold_10-snap.609-T1
Valid prediction for GeneMark_model.42474_t
Valid prediction for GeneMark_model.42470_t
Valid prediction for Augustus_model.g16665.t1
Valid prediction for GlimmerHMM_glimmerT_24874-T1
Valid prediction for GlimmerHMM_glimmerT_24870-T1
Valid prediction for HiQ_model.g16662.t1
Valid prediction for GlimmerHMM_glimmerT_24869-T1
Valid prediction for snap_scaffold_10-snap.630-T1
Valid prediction for GlimmerHMM_glimmerT_24873-T1
Valid prediction for GlimmerHMM_glimmerT_24878-T1
Valid prediction for snap_scaffold_10-snap.621-T1
Valid prediction for GeneMark_model.42481_t
Valid prediction for GeneMark_model.42460_t
Valid prediction for Augustus_model.g16669.t1
Valid prediction for GeneMark_model.42485_t
Valid prediction for GlimmerHMM_glimmerT_24864-T1
Valid prediction for GeneMark_model.42469_t
Couldn't classify 34641, 34819
Sorry, prediction pasa_asmbl_4293.p1 fails validation.
(AAC)	 AG	34641-34819	GT	AGG
(CGT)	 AG	35376-35520	GT	AGG
(ATA)	 AG	35638-35751	GT	AGG
(GCA)	 AG	35840-35968	GT	AGG
(CTG)	 AG	36241-36350	GT	AGG
(GGC)	 AG	36447-36589	GT	AGG
(GTT)	 AG	36719-36910	GT	GGG
(GTG)	 AG	37035-37144	GT	AGG
(ACG)	 AG	37236-37376	GT	CTG
(GCC)	 AG	37801-38058	GG	GAG
add_exon() Sorry, pasa_asmbl_4293.p1 34641-34819-terminal-2 is invalid.
-recovered pasa_asmbl_4293.p1, terminal, 34641, 34819
-recovered pasa_asmbl_4293.p1, terminal, 37801, 38058
-recovered pasa_asmbl_4293.p1, internal, 34641, 34819
-recovered pasa_asmbl_4293.p1, internal, 35376, 35520
-recovered pasa_asmbl_4293.p1, internal, 35638, 35751
-recovered pasa_asmbl_4293.p1, internal, 35840, 35968
-recovered pasa_asmbl_4293.p1, internal, 36241, 36350
-recovered pasa_asmbl_4293.p1, internal, 36447, 36589
-recovered pasa_asmbl_4293.p1, internal, 36719, 36910
-recovered pasa_asmbl_4293.p1, internal, 37035, 37144
-recovered pasa_asmbl_4293.p1, internal, 37236, 37376
Valid prediction for snap_scaffold_10-snap.637-T1
Valid prediction for GeneMark_model.42497_t
Valid prediction for GeneMark_model.42467_t
Valid prediction for GlimmerHMM_glimmerT_24877-T1
Valid prediction for GeneMark_model.42495_t
Valid prediction for GlimmerHMM_glimmerT_24866-T1
Valid prediction for Augustus_model.g16666.t1
Valid prediction for Augustus_model.g16664.t1
Valid prediction for Augustus_model.g16667.t1
Valid prediction for snap_scaffold_10-snap.638-T1
Valid prediction for GeneMark_model.42463_t
Valid prediction for snap_scaffold_10-snap.611-T1
Valid prediction for snap_scaffold_10-snap.613-T1
Valid prediction for GeneMark_model.42489_t
Valid prediction for snap_scaffold_10-snap.616-T1
Valid prediction for GlimmerHMM_glimmerT_24859-T1
Valid prediction for snap_scaffold_10-snap.633-T1
Valid prediction for GeneMark_model.42499_t
Valid prediction for GlimmerHMM_glimmerT_24861-T1
Valid prediction for GeneMark_model.42490_t
Valid prediction for GlimmerHMM_glimmerT_24863-T1
Valid prediction for GlimmerHMM_glimmerT_24867-T1
Valid prediction for snap_scaffold_10-snap.626-T1
Valid prediction for Augustus_model.g16668.t1
Valid prediction for GeneMark_model.42476_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: -)Couldn't classify 24614, 24690
Couldn't classify 25452, 25482
Sorry, prediction pasa_asmbl_3059.p1 fails validation.
(AAG)	 GG	24614-24690	GT	AAG
(TCC)	 AG	24876-25313	GT	GGG
(GTC)	 AG	25452-25482	CA	GCC
-recovered pasa_asmbl_3059.p1, internal, 24876, 25313
Valid prediction for GeneMark_model.42466_t
Valid prediction for snap_scaffold_10-snap.634-T1
Valid prediction for GeneMark_model.42488_t
Valid prediction for Augustus_model.g16671.t1
Valid prediction for snap_scaffold_10-snap.629-T1
Valid prediction for Augustus_model.g16661.t1
Valid prediction for GeneMark_model.42491_t
Valid prediction for snap_scaffold_10-snap.619-T1
Valid prediction for GeneMark_model.42492_t
Valid prediction for GlimmerHMM_glimmerT_24862-T1
Valid prediction for GeneMark_model.42462_t
Valid prediction for GlimmerHMM_glimmerT_24876-T1
Valid prediction for GeneMark_model.42464_t
Valid prediction for snap_scaffold_10-snap.612-T1
Valid prediction for GeneMark_model.42473_t
Couldn't classify 25594, 25597
Sorry, prediction pasa_asmbl_3058.p1 fails validation.
(ACC)	 TC	25594-25597	GT	CAG
(GTG)	 AG	25719-25932	GT	AAG
(GCC)	 AG	26054-26138	GT	GGG
(TTT)	 AG	26238-26400	GT	TGG
(ACG)	 AG	26541-26839	GT	AGG
(ATT)	 AG	26987-27134	GT	CGG
(GCA)	 AG	27281-27378	GT	AGG
(GAG)	 AG	27681-28976	AC	AGA
-recovered pasa_asmbl_3058.p1, terminal, 27681, 28976
-recovered pasa_asmbl_3058.p1, internal, 25719, 25932
-recovered pasa_asmbl_3058.p1, internal, 26054, 26138
-recovered pasa_asmbl_3058.p1, internal, 26238, 26400
-recovered pasa_asmbl_3058.p1, internal, 26541, 26839
-recovered pasa_asmbl_3058.p1, internal, 26987, 27134
-recovered pasa_asmbl_3058.p1, internal, 27281, 27378
Valid prediction for Augustus_model.g16673.t1
Couldn't classify 22090, 22177
Couldn't classify 22402, 22658
Sorry, prediction pasa_asmbl_4121.p1 fails validation.
(GAG)	 AC	22090-22177	GT	AGG
(GCG)	 AG	22402-22658	GG	CAG
Valid prediction for GlimmerHMM_glimmerT_24865-T1
Valid prediction for snap_scaffold_10-snap.636-T1
Valid prediction for GlimmerHMM_glimmerT_24875-T1
Couldn't classify 53891, 53959
Sorry, prediction pasa_asmbl_3055.p2 fails validation.
(ACC)	 TC	53891-53959	GT	AGG
(GAG)	 AG	54152-54442	GG	GAG
-recovered pasa_asmbl_3055.p2, terminal, 54152, 54442
Valid prediction for snap_scaffold_10-snap.615-T1
Valid prediction for GeneMark_model.42468_t
Valid prediction for GeneMark_model.42494_t
Valid prediction for snap_scaffold_10-snap.623-T1
Valid prediction for Augustus_model.g16675.t1
Valid prediction for GeneMark_model.42493_t
Valid prediction for GeneMark_model.42484_t
Valid prediction for GeneMark_model.42480_t
Valid prediction for GeneMark_model.42496_t
Valid prediction for snap_scaffold_10-snap.635-T1
Valid prediction for snap_scaffold_10-snap.641-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.617-T1
Couldn't classify 47539, 47916
Sorry, prediction pasa_asmbl_3057.p1 fails validation.
(GAG)	 GG	47539-47916	AA	AGA
Valid prediction for snap_scaffold_10-snap.627-T1
Valid prediction for GlimmerHMM_glimmerT_24868-T1
Valid prediction for snap_scaffold_10-snap.632-T1
Valid prediction for GeneMark_model.42477_t
Valid prediction for snap_scaffold_10-snap.624-T1
Valid prediction for snap_scaffold_10-snap.610-T1
Valid prediction for GeneMark_model.42461_t
Valid prediction for GeneMark_model.42472_t
Valid prediction for Augustus_model.g16670.t1
Valid prediction for GlimmerHMM_glimmerT_24858-T1
Valid prediction for snap_scaffold_10-snap.639-T1
Valid prediction for snap_scaffold_10-snap.620-T1
Valid prediction for Augustus_model.g16674.t1
Valid prediction for snap_scaffold_10-snap.631-T1
Valid prediction for Augustus_model.g16660.t1
Valid prediction for GeneMark_model.42486_t
Valid prediction for GeneMark_model.42475_t
Valid prediction for Augustus_model.g16663.t1
Valid prediction for GeneMark_model.42482_t
Couldn't classify 48688, 49053
Couldn't classify 49602, 49773
Sorry, prediction pasa_asmbl_3056.p1 fails validation.
(CCT)	 CC	48688-49053	GT	AGG
(GAT)	 AG	49161-49297	GT	AGG
(ACG)	 AG	49602-49773	GG	GGG
-recovered pasa_asmbl_3056.p1, internal, 49161, 49297

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17732, rend_intergenic: 14672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24816, rend_intergenic: 22322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28586, rend_intergenic: 25371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41661, rend_intergenic: 40970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51995, rend_intergenic: 42249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66847, rend_intergenic: 62007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71095, rend_intergenic: 66924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78773, rend_intergenic: 72767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89837, rend_intergenic: 85265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97260, rend_intergenic: 93049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101200, rend_intergenic: 97573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121316, rend_intergenic: 109888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125260, rend_intergenic: 121629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127140, rend_intergenic: 125398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131832, rend_intergenic: 127168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136304
-exon list size: 604


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 17732, rend_intergenic: 14672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24816, rend_intergenic: 22322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28586, rend_intergenic: 25371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41661, rend_intergenic: 40970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51995, rend_intergenic: 42249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66847, rend_intergenic: 62007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71095, rend_intergenic: 66924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78773, rend_intergenic: 72767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89837, rend_intergenic: 85265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97260, rend_intergenic: 93049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101200, rend_intergenic: 97573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121316, rend_intergenic: 109888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125260, rend_intergenic: 121629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127140, rend_intergenic: 125398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131832, rend_intergenic: 127168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support