-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_808492-1006089

-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: +)Couldn't classify 128829, 128836
Sorry, prediction pasa_asmbl_5317.p1 fails validation.
(CCG)	 AT	128829-128836	GT	AGG
(GTA)	 AG	129046-129211	GT	TGG
(AAA)	 AG	129467-129563	GT	TGG
(GTA)	 AG	129772-129977	TA	GAT
-recovered pasa_asmbl_5317.p1, terminal, 129772, 129977
-recovered pasa_asmbl_5317.p1, internal, 129046, 129211
-recovered pasa_asmbl_5317.p1, internal, 129467, 129563
Valid prediction for snap_scaffold_11-snap.214-T1
Couldn't classify 43060, 43263
Sorry, prediction pasa_asmbl_5307.p1 fails validation.
(CGG)	 GA	43060-43263	GT	AGG
(GGT)	 AG	45150-45252	GT	CGG
(GGA)	 AG	45334-45396	GT	AGG
(GTC)	 AG	45481-45531	GT	GGG
(TGT)	 AG	45663-45729	GT	AAG
(TAT)	 AG	46035-46142	GT	AGG
(ATT)	 AG	46283-46364	GT	AGG
(GAG)	 AG	46595-46721	GT	TGG
(GCA)	 AG	46807-46961	GT	ATG
(GCT)	 AG	48397-48521	GT	GCG
(CAT)	 AG	48668-48765	GT	AGG
(CGA)	 AG	48897-49046	GT	CAG
(TCA)	 AG	49250-49302	AG	AAA
-recovered pasa_asmbl_5307.p1, terminal, 49250, 49302
-recovered pasa_asmbl_5307.p1, internal, 45150, 45252
-recovered pasa_asmbl_5307.p1, internal, 45334, 45396
-recovered pasa_asmbl_5307.p1, internal, 45481, 45531
-recovered pasa_asmbl_5307.p1, internal, 45663, 45729
-recovered pasa_asmbl_5307.p1, internal, 46035, 46142
-recovered pasa_asmbl_5307.p1, internal, 46283, 46364
-recovered pasa_asmbl_5307.p1, internal, 46595, 46721
-recovered pasa_asmbl_5307.p1, internal, 46807, 46961
-recovered pasa_asmbl_5307.p1, internal, 48397, 48521
-recovered pasa_asmbl_5307.p1, internal, 48668, 48765
-recovered pasa_asmbl_5307.p1, internal, 48897, 49046
Valid prediction for GlimmerHMM_glimmerT_26419-T1
Valid prediction for snap_scaffold_11-snap.200-T1
Valid prediction for Augustus_model.g17512.t1
Valid prediction for CodingQuarry_transcript_7954-T1
Couldn't classify 49842, 50052
Sorry, prediction pasa_asmbl_5312.p1 fails validation.
(CGT)	 AA	49842-50052	GT	TGG
(AAA)	 AG	50799-50987	GT	AGG
(GTG)	 AG	51107-51260	GT	GAG
(TTA)	 AG	51860-51908	GG	GAG
-recovered pasa_asmbl_5312.p1, terminal, 51860, 51908
-recovered pasa_asmbl_5312.p1, internal, 50799, 50987
-recovered pasa_asmbl_5312.p1, internal, 51107, 51260
Valid prediction for CodingQuarry_transcript_7955-T1
Valid prediction for HiQ_model.g17514.t1
Valid prediction for GlimmerHMM_glimmerT_26436-T1
Valid prediction for Augustus_model.g17518.t1
Valid prediction for snap_scaffold_11-snap.210-T1
Valid prediction for snap_scaffold_11-snap.185-T1
Valid prediction for GlimmerHMM_glimmerT_26422-T1
Valid prediction for snap_scaffold_11-snap.215-T1
Valid prediction for Augustus_model.g17516.t1
Valid prediction for Augustus_model.g17519.t1
Valid prediction for snap_scaffold_11-snap.205-T1
Valid prediction for Augustus_model.g17523.t1
Valid prediction for CodingQuarry_transcript_7952-T1
Valid prediction for pasa_asmbl_5318.p1
Valid prediction for snap_scaffold_11-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_26424-T1
Couldn't classify 118659, 118994
Sorry, prediction pasa_asmbl_5314.p2 fails validation.
(CCA)	 GC	118659-118994	AA	GTA
Valid prediction for snap_scaffold_11-snap.180-T1
Couldn't classify 38820, 38984
Couldn't classify 40082, 40686
Sorry, prediction pasa_asmbl_5301.p1 fails validation.
(GAA)	 AG	38820-38984	GT	AGG
(GAG)	 AG	39133-39235	GT	CAG
(TCA)	 AG	39649-39801	GT	TGG
(GAT)	 AG	40082-40686	CA	GCC
-recovered pasa_asmbl_5301.p1, internal, 38820, 38984
-recovered pasa_asmbl_5301.p1, internal, 39133, 39235
-recovered pasa_asmbl_5301.p1, internal, 39649, 39801
Valid prediction for HiQ_model.g17513.t1
Couldn't classify 121254, 121342
Sorry, prediction pasa_asmbl_5315.p1 fails validation.
(CTG)	 CC	121254-121342	GT	AAG
(ACT)	 AG	121609-121789	GT	AGG
(TCG)	 AG	121995-122171	GT	AGG
(GTG)	 AG	122707-122792	GT	AAG
(AGT)	 AG	123514-123607	GT	AGG
(GAG)	 AG	123709-123760	GT	AGG
(TGA)	 AG	123876-124096	GG	GAG
-recovered pasa_asmbl_5315.p1, terminal, 123876, 124096
-recovered pasa_asmbl_5315.p1, internal, 121609, 121789
-recovered pasa_asmbl_5315.p1, internal, 121995, 122171
-recovered pasa_asmbl_5315.p1, internal, 122707, 122792
-recovered pasa_asmbl_5315.p1, internal, 123514, 123607
-recovered pasa_asmbl_5315.p1, internal, 123709, 123760
Valid prediction for snap_scaffold_11-snap.208-T1
Valid prediction for snap_scaffold_11-snap.182-T1
Valid prediction for snap_scaffold_11-snap.196-T1
Valid prediction for snap_scaffold_11-snap.189-T1
Valid prediction for HiQ_model.g17520.t1
Valid prediction for snap_scaffold_11-snap.204-T1
Valid prediction for snap_scaffold_11-snap.198-T1
Valid prediction for GlimmerHMM_glimmerT_26418-T1
Couldn't classify 117857, 117956
Couldn't classify 118150, 118547
Sorry, prediction pasa_asmbl_5313.p1 fails validation.
(TGG)	 GA	117857-117956	GT	AGG
(GTA)	 AG	118150-118547	GC	CGG
-recovered pasa_asmbl_5313.p1, internal, 118150, 118547
Valid prediction for snap_scaffold_11-snap.211-T1
Valid prediction for GlimmerHMM_glimmerT_26435-T1
Valid prediction for snap_scaffold_11-snap.190-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_26429-T1
Valid prediction for GlimmerHMM_glimmerT_26439-T1
Valid prediction for GlimmerHMM_glimmerT_26434-T1
Valid prediction for snap_scaffold_11-snap.217-T1
Valid prediction for GlimmerHMM_glimmerT_26423-T1
Valid prediction for snap_scaffold_11-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_26441-T1
Valid prediction for GlimmerHMM_glimmerT_26431-T1
Valid prediction for Augustus_model.g17517.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_11-snap.187-T1
Valid prediction for snap_scaffold_11-snap.218-T1
Valid prediction for GlimmerHMM_glimmerT_26432-T1
Valid prediction for snap_scaffold_11-snap.216-T1
Valid prediction for snap_scaffold_11-snap.193-T1
Valid prediction for snap_scaffold_11-snap.209-T1
Valid prediction for snap_scaffold_11-snap.201-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_26414-T1
Valid prediction for snap_scaffold_11-snap.179-T1
Valid prediction for snap_scaffold_11-snap.202-T1
Couldn't classify 49686, 50270
Sorry, prediction pasa_asmbl_6400.p1 fails validation.
(AGT)	 AG	49686-50270	CA	CCC
Valid prediction for snap_scaffold_11-snap.207-T1
Valid prediction for snap_scaffold_11-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_26438-T1
Valid prediction for GlimmerHMM_glimmerT_26425-T1
Valid prediction for snap_scaffold_11-snap.219-T1
Valid prediction for snap_scaffold_11-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_26427-T1
Couldn't classify 39610, 39657
Couldn't classify 44257, 44288
Sorry, prediction pasa_asmbl_6401.p1 fails validation.
(CTC)	 AC	39610-39657	GT	AGG
(GAG)	 AG	40402-40533	GT	AGG
(GAG)	 AG	41591-41773	GT	CGG
(TGC)	 AG	42368-42460	GT	AGG
(GCC)	 AG	43022-43108	GT	CGG
(GCG)	 AG	43217-43250	GT	TTG
(CTC)	 AG	43671-43772	GT	AGG
(AAC)	 AG	44257-44288	GG	AAG
-recovered pasa_asmbl_6401.p1, internal, 40402, 40533
-recovered pasa_asmbl_6401.p1, internal, 41591, 41773
-recovered pasa_asmbl_6401.p1, internal, 42368, 42460
-recovered pasa_asmbl_6401.p1, internal, 43022, 43108
-recovered pasa_asmbl_6401.p1, internal, 43217, 43250
-recovered pasa_asmbl_6401.p1, internal, 43671, 43772
Valid prediction for GlimmerHMM_glimmerT_26437-T1
Valid prediction for GlimmerHMM_glimmerT_26415-T1
Valid prediction for snap_scaffold_11-snap.221-T1
Valid prediction for snap_scaffold_11-snap.197-T1
Valid prediction for snap_scaffold_11-snap.199-T1
Valid prediction for snap_scaffold_11-snap.212-T1
Valid prediction for pasa_asmbl_6399.p1
Valid prediction for pasa_asmbl_7296.p1
Valid prediction for GlimmerHMM_glimmerT_26428-T1
Valid prediction for GlimmerHMM_glimmerT_26442-T1
Valid prediction for snap_scaffold_11-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_26420-T1
Valid prediction for CodingQuarry_transcript_7956-T1
Valid prediction for GlimmerHMM_glimmerT_26440-T1
Valid prediction for Augustus_model.g17524.t1
Valid prediction for GlimmerHMM_glimmerT_26433-T1
Valid prediction for Augustus_model.g17521.t1
Valid prediction for snap_scaffold_11-snap.195-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_26430-T1
Valid prediction for Augustus_model.g17515.t1
Valid prediction for snap_scaffold_11-snap.194-T1
Valid prediction for GlimmerHMM_glimmerT_26421-T1
Valid prediction for Augustus_model.g17522.t1
Valid prediction for snap_scaffold_11-snap.188-T1
Valid prediction for snap_scaffold_11-snap.206-T1
Valid prediction for snap_scaffold_11-snap.186-T1
Valid prediction for GlimmerHMM_glimmerT_26417-T1
Valid prediction for GlimmerHMM_glimmerT_26416-T1
Valid prediction for snap_scaffold_11-snap.184-T1
Valid prediction for Augustus_model.g17511.t1
Valid prediction for snap_scaffold_11-snap.181-T1
Valid prediction for GlimmerHMM_glimmerT_26426-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14345, rend_intergenic: 3085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42115, rend_intergenic: 33551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76383, rend_intergenic: 67015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80109, rend_intergenic: 76549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92510, rend_intergenic: 80337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97162, rend_intergenic: 92593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109148, rend_intergenic: 103607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114247, rend_intergenic: 109346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115569, rend_intergenic: 115235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124096, rend_intergenic: 117091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141652, rend_intergenic: 133034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158876, rend_intergenic: 148449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164190, rend_intergenic: 159116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171162, rend_intergenic: 164775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172164, rend_intergenic: 172000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176837, rend_intergenic: 175321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197598
-exon list size: 423


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 14345, rend_intergenic: 3085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42115, rend_intergenic: 33551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76383, rend_intergenic: 67015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80109, rend_intergenic: 76549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92510, rend_intergenic: 80337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97162, rend_intergenic: 92593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109148, rend_intergenic: 103607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114247, rend_intergenic: 109346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115569, rend_intergenic: 115235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124096, rend_intergenic: 117091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141652, rend_intergenic: 133034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158876, rend_intergenic: 148449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164190, rend_intergenic: 159116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171162, rend_intergenic: 164775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172164, rend_intergenic: 172000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176837, rend_intergenic: 175321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support