-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_17312843-17495625

-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.3379-T1
Valid prediction for snap_scaffold_2-snap.3381-T1
Valid prediction for snap_scaffold_2-snap.3376-T1
Valid prediction for snap_scaffold_2-snap.3386-T1
Valid prediction for GlimmerHMM_glimmerT_5393-T1
Valid prediction for snap_scaffold_2-snap.3387-T1
Valid prediction for Augustus_model.g3622.t1
Valid prediction for CodingQuarry_transcript_28812-T1
Valid prediction for GlimmerHMM_glimmerT_5384-T1
Couldn't classify 151814, 151875
Sorry, prediction pasa_asmbl_25169.p1 fails validation.
(CAA)	 GG	151814-151875	GT	AGG
(ATT)	 AG	152877-153060	GT	GGG
(GAG)	 AG	153358-153453	GT	AAG
(GAG)	 AG	153585-153662	GT	AGG
(ATC)	 AG	153770-153994	GT	AGG
(ATG)	 AG	154687-154815	GT	AGG
(CTG)	 AG	154939-155051	GT	AAG
(TGG)	 AG	155260-155283	GT	ACG
(GAA)	 AG	155732-155831	GT	GGG
(ATC)	 AG	155957-156023	GT	TGG
(CGG)	 AG	156127-156212	GA	AAG
-recovered pasa_asmbl_25169.p1, initial, 154687, 154815
-recovered pasa_asmbl_25169.p1, terminal, 154939, 155051
-recovered pasa_asmbl_25169.p1, terminal, 156127, 156212
-recovered pasa_asmbl_25169.p1, internal, 152877, 153060
-recovered pasa_asmbl_25169.p1, internal, 153358, 153453
-recovered pasa_asmbl_25169.p1, internal, 153585, 153662
-recovered pasa_asmbl_25169.p1, internal, 153770, 153994
-recovered pasa_asmbl_25169.p1, internal, 154687, 154815
-recovered pasa_asmbl_25169.p1, internal, 154939, 155051
-recovered pasa_asmbl_25169.p1, internal, 155260, 155283
-recovered pasa_asmbl_25169.p1, internal, 155732, 155831
-recovered pasa_asmbl_25169.p1, internal, 155957, 156023
Valid prediction for snap_scaffold_2-snap.3396-T1
Valid prediction for snap_scaffold_2-snap.3383-T1
Valid prediction for snap_scaffold_2-snap.3394-T1
Valid prediction for HiQ_model.g3637.t1
Valid prediction for snap_scaffold_2-snap.3362-T1
Valid prediction for Augustus_model.g3635.t1
Valid prediction for Augustus_model.g3623.t1
Valid prediction for CodingQuarry_transcript_28813-T1
Valid prediction for GlimmerHMM_glimmerT_5395-T1
Valid prediction for GlimmerHMM_glimmerT_5397-T1
Couldn't classify 152444, 152493
Couldn't classify 153770, 153889
Sorry, prediction pasa_asmbl_25171.p1 fails validation.
(CAT)	 GT	152444-152493	GT	GGG
(ATT)	 AG	152877-153060	GT	GGG
(GAG)	 AG	153358-153453	GT	AAG
(GAG)	 AG	153585-153662	GT	AGG
(ATC)	 AG	153770-153889	AG	ACA
-recovered pasa_asmbl_25171.p1, internal, 152877, 153060
-recovered pasa_asmbl_25171.p1, internal, 153358, 153453
-recovered pasa_asmbl_25171.p1, internal, 153585, 153662
Valid prediction for pasa_asmbl_25167.p1
Valid prediction for GlimmerHMM_glimmerT_5382-T1
Valid prediction for snap_scaffold_2-snap.3369-T1
Valid prediction for GlimmerHMM_glimmerT_5400-T1
Valid prediction for snap_scaffold_2-snap.3372-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3389-T1
Couldn't classify 138941, 139030
Couldn't classify 140477, 140602
Sorry, prediction pasa_asmbl_25163.p2 fails validation.
(TCT)	 GG	138941-139030	GT	CCG
(GCG)	 AG	139149-139289	GT	CGG
(AAA)	 AG	140095-140204	GT	AAG
(GAA)	 AG	140299-140389	GT	AGG
(GCT)	 AG	140477-140602	GT	CGG
-recovered pasa_asmbl_25163.p2, internal, 139149, 139289
-recovered pasa_asmbl_25163.p2, internal, 140095, 140204
-recovered pasa_asmbl_25163.p2, internal, 140299, 140389
-recovered pasa_asmbl_25163.p2, internal, 140477, 140602
Valid prediction for GlimmerHMM_glimmerT_5390-T1
Valid prediction for snap_scaffold_2-snap.3373-T1
Couldn't classify 140708, 140853
Sorry, prediction pasa_asmbl_25164.p1 fails validation.
(CAG)	 TG	140708-140853	GT	AAG
(AGA)	 AG	140966-141086	GT	GGG
(CAG)	 AG	141373-141468	GT	AGG
(CCT)	 AG	141618-141680	GT	AGG
(GGA)	 AG	141767-141920	GT	AGG
(GTA)	 AG	142215-142399	GG	AAG
-recovered pasa_asmbl_25164.p1, terminal, 142215, 142399
-recovered pasa_asmbl_25164.p1, internal, 140966, 141086
-recovered pasa_asmbl_25164.p1, internal, 141373, 141468
-recovered pasa_asmbl_25164.p1, internal, 141618, 141680
-recovered pasa_asmbl_25164.p1, internal, 141767, 141920
Valid prediction for GlimmerHMM_glimmerT_5378-T1
Valid prediction for snap_scaffold_2-snap.3364-T1
Valid prediction for snap_scaffold_2-snap.3361-T1
Valid prediction for snap_scaffold_2-snap.3378-T1
Valid prediction for snap_scaffold_2-snap.3393-T1
Valid prediction for snap_scaffold_2-snap.3385-T1
Valid prediction for GlimmerHMM_glimmerT_5376-T1
Valid prediction for GlimmerHMM_glimmerT_5402-T1
Valid prediction for snap_scaffold_2-snap.3392-T1
Valid prediction for GlimmerHMM_glimmerT_5388-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_2-snap.3398-T1
Valid prediction for snap_scaffold_2-snap.3390-T1
Valid prediction for snap_scaffold_2-snap.3370-T1
Valid prediction for HiQ_model.g3634.t1
Valid prediction for Augustus_model.g3633.t1
Valid prediction for GlimmerHMM_glimmerT_5394-T1
Valid prediction for GlimmerHMM_glimmerT_5380-T1
Valid prediction for CodingQuarry_transcript_28815-T1
Valid prediction for snap_scaffold_2-snap.3363-T1
Couldn't classify 10462, 10679
Couldn't classify 11046, 11064
Sorry, prediction pasa_asmbl_23731.p1 fails validation.
(GAG)	 GG	10462-10679	GT	AGG
(GGC)	 AG	10778-10849	GT	GGG
(GGA)	 AG	11046-11064	TG	CAT
-recovered pasa_asmbl_23731.p1, internal, 10778, 10849
Valid prediction for Augustus_model.g3638.t1
Valid prediction for snap_scaffold_2-snap.3397-T1
Valid prediction for GlimmerHMM_glimmerT_5405-T1
Valid prediction for snap_scaffold_2-snap.3360-T1
Valid prediction for snap_scaffold_2-snap.3382-T1
Valid prediction for snap_scaffold_2-snap.3366-T1
Valid prediction for snap_scaffold_2-snap.3374-T1
Valid prediction for Augustus_model.g3627.t1
Valid prediction for GlimmerHMM_glimmerT_5389-T1
Valid prediction for Augustus_model.g3628.t1
Valid prediction for GlimmerHMM_glimmerT_5383-T1
Valid prediction for Augustus_model.g3624.t1
Valid prediction for CodingQuarry_transcript_28814-T1
Valid prediction for pasa_asmbl_23732.p1
Valid prediction for snap_scaffold_2-snap.3367-T1
Valid prediction for snap_scaffold_2-snap.3391-T1
Valid prediction for snap_scaffold_2-snap.3371-T1
Couldn't classify 12551, 12708
Couldn't classify 13725, 14001
Sorry, prediction pasa_asmbl_23730.p1 fails validation.
(CTG)	 AT	12551-12708	GT	AGG
(TGT)	 AG	13266-13412	GT	GAG
(GGC)	 AG	13515-13583	GT	ACG
(CTC)	 AG	13725-14001	GA	AGG
-recovered pasa_asmbl_23730.p1, internal, 13266, 13412
-recovered pasa_asmbl_23730.p1, internal, 13515, 13583
Valid prediction for snap_scaffold_2-snap.3395-T1
Valid prediction for GlimmerHMM_glimmerT_5396-T1
Valid prediction for GlimmerHMM_glimmerT_5379-T1
Valid prediction for GlimmerHMM_glimmerT_5387-T1
Valid prediction for snap_scaffold_2-snap.3384-T1
Valid prediction for snap_scaffold_2-snap.3377-T1
Valid prediction for GlimmerHMM_glimmerT_5381-T1
Valid prediction for GlimmerHMM_glimmerT_5399-T1
Valid prediction for GlimmerHMM_glimmerT_5404-T1
Valid prediction for pasa_asmbl_23729.p1
Valid prediction for snap_scaffold_2-snap.3368-T1
Valid prediction for CodingQuarry_transcript_28811-T1
Valid prediction for GlimmerHMM_glimmerT_5398-T1
Valid prediction for snap_scaffold_2-snap.3388-T1
Valid prediction for snap_scaffold_2-snap.3365-T1
Valid prediction for GlimmerHMM_glimmerT_5377-T1
Valid prediction for GlimmerHMM_glimmerT_5385-T1
Valid prediction for Augustus_model.g3636.t1
Valid prediction for Augustus_model.g3631.t1
Valid prediction for GlimmerHMM_glimmerT_5403-T1
Valid prediction for Augustus_model.g3629.t1
Couldn't classify 14173, 14341
Sorry, prediction pasa_asmbl_23726.p1 fails validation.
(CGC)	 CT	14173-14341	GT	AGG
(AAC)	 AG	14461-14581	GT	AGG
(GTT)	 AG	15027-15176	GT	AGG
(GTT)	 AG	15301-15420	GT	AGG
(GTG)	 AG	15524-15637	GT	GGG
(ATA)	 AG	15954-16060	GT	TGG
(GTG)	 AG	16207-16600	GT	AGG
(GGC)	 AG	16815-16875	CT	AGC
-recovered pasa_asmbl_23726.p1, terminal, 16815, 16875
-recovered pasa_asmbl_23726.p1, internal, 14461, 14581
-recovered pasa_asmbl_23726.p1, internal, 15027, 15176
-recovered pasa_asmbl_23726.p1, internal, 15301, 15420
-recovered pasa_asmbl_23726.p1, internal, 15524, 15637
-recovered pasa_asmbl_23726.p1, internal, 15954, 16060
-recovered pasa_asmbl_23726.p1, internal, 16207, 16600
Valid prediction for Augustus_model.g3630.t1
Valid prediction for Augustus_model.g3626.t1
Valid prediction for GlimmerHMM_glimmerT_5392-T1
Valid prediction for pasa_asmbl_23725.p1
Valid prediction for snap_scaffold_2-snap.3380-T1
Valid prediction for GlimmerHMM_glimmerT_5386-T1
Valid prediction for GlimmerHMM_glimmerT_5391-T1
Valid prediction for snap_scaffold_2-snap.3375-T1
Valid prediction for Augustus_model.g3639.t1
Valid prediction for snap_scaffold_2-snap.3399-T1
Valid prediction for Augustus_model.g3632.t1
Valid prediction for GlimmerHMM_glimmerT_5401-T1
Valid prediction for Augustus_model.g3625.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18377, rend_intergenic: 13807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29708, rend_intergenic: 19136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46177, rend_intergenic: 37837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49791, rend_intergenic: 46790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61224, rend_intergenic: 52792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72539, rend_intergenic: 67268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73090, rend_intergenic: 72857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80143, rend_intergenic: 74441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87562, rend_intergenic: 81560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96110, rend_intergenic: 92565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124016, rend_intergenic: 103666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131405, rend_intergenic: 129186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135217, rend_intergenic: 132142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182783
-exon list size: 480


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 18377, rend_intergenic: 13807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29708, rend_intergenic: 19136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46177, rend_intergenic: 37837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49791, rend_intergenic: 46790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61224, rend_intergenic: 52792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72539, rend_intergenic: 67268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73090, rend_intergenic: 72857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80143, rend_intergenic: 74441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87562, rend_intergenic: 81560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96110, rend_intergenic: 92565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124016, rend_intergenic: 103666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131405, rend_intergenic: 129186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135217, rend_intergenic: 132142  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