-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_4129371-4312561

-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 CodingQuarry_transcript_5361-T1
Valid prediction for snap_scaffold_10-snap.925-T1
Valid prediction for snap_scaffold_10-snap.912-T1
Valid prediction for snap_scaffold_10-snap.910-T1
Valid prediction for snap_scaffold_10-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_24543-T1
Valid prediction for snap_scaffold_10-snap.895-T1
Valid prediction for snap_scaffold_10-snap.904-T1
Valid prediction for Augustus_model.g16344.t1
Valid prediction for GlimmerHMM_glimmerT_24558-T1
Valid prediction for GlimmerHMM_glimmerT_24563-T1
Valid prediction for snap_scaffold_10-snap.923-T1
Valid prediction for snap_scaffold_10-snap.887-T1
Valid prediction for Augustus_model.g16357.t1
Couldn't classify 91563, 91594
Sorry, prediction pasa_asmbl_3107.p1 fails validation.
(ATG)	 AT	88331-88377	GT	AGG
(GAT)	 AG	88568-88715	GT	AGG
(GGC)	 AG	89191-89302	GT	AGG
(GTG)	 AG	89560-89691	GT	AGG
(TTT)	 AG	91563-91594	CC	TGC
-recovered pasa_asmbl_3107.p1, initial, 88331, 88377
-recovered pasa_asmbl_3107.p1, internal, 88568, 88715
-recovered pasa_asmbl_3107.p1, internal, 89191, 89302
-recovered pasa_asmbl_3107.p1, internal, 89560, 89691
Valid prediction for snap_scaffold_10-snap.931-T1
Valid prediction for snap_scaffold_10-snap.917-T1
Valid prediction for snap_scaffold_10-snap.928-T1
Valid prediction for snap_scaffold_10-snap.908-T1
Valid prediction for snap_scaffold_10-snap.918-T1
Valid prediction for snap_scaffold_10-snap.930-T1
Valid prediction for snap_scaffold_10-snap.900-T1
Valid prediction for snap_scaffold_10-snap.898-T1
Couldn't classify 117357, 117408
Sorry, prediction pasa_asmbl_3108.p1 fails validation.
(CGT)	 AG	117357-117408	GT	AAG
(ATA)	 AG	118866-119039	GT	AGG
(CGA)	 AG	119176-119328	GT	AGG
(GAG)	 AG	120702-120820	GT	AGG
(GCT)	 AG	122858-122949	GT	AAG
(AGT)	 AG	123626-123785	GT	AGG
(CTT)	 AG	123891-123968	AA	GAA
-recovered pasa_asmbl_3108.p1, terminal, 123891, 123968
-recovered pasa_asmbl_3108.p1, internal, 117357, 117408
-recovered pasa_asmbl_3108.p1, internal, 118866, 119039
-recovered pasa_asmbl_3108.p1, internal, 119176, 119328
-recovered pasa_asmbl_3108.p1, internal, 120702, 120820
-recovered pasa_asmbl_3108.p1, internal, 122858, 122949
-recovered pasa_asmbl_3108.p1, internal, 123626, 123785
Valid prediction for snap_scaffold_10-snap.924-T1
Valid prediction for GlimmerHMM_glimmerT_24565-T1
Valid prediction for snap_scaffold_10-snap.891-T1
Valid prediction for Augustus_model.g16350.t1
Valid prediction for GlimmerHMM_glimmerT_24570-T1
Valid prediction for snap_scaffold_10-snap.913-T1
Valid prediction for GlimmerHMM_glimmerT_24552-T1
Valid prediction for CodingQuarry_transcript_5354-T1
Valid prediction for Augustus_model.g16359.t1
Valid prediction for snap_scaffold_10-snap.888-T1
Valid prediction for Augustus_model.g16349.t1
Valid prediction for Augustus_model.g16354.t1
Valid prediction for GlimmerHMM_glimmerT_24549-T1
Valid prediction for GlimmerHMM_glimmerT_24562-T1
Valid prediction for snap_scaffold_10-snap.899-T1
Valid prediction for snap_scaffold_10-snap.907-T1
Valid prediction for snap_scaffold_10-snap.922-T1
Valid prediction for snap_scaffold_10-snap.897-T1
Valid prediction for pasa_asmbl_3115.p1
Valid prediction for GlimmerHMM_glimmerT_24555-T1
Valid prediction for GlimmerHMM_glimmerT_24547-T1
Valid prediction for Augustus_model.g16363.t1
Valid prediction for HiQ_model.g16364.t1
Valid prediction for snap_scaffold_10-snap.890-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 154003, 154049
Sorry, prediction pasa_asmbl_3116.p1 fails validation.
(TTA)	 TT	154003-154049	GT	GTG
(CCG)	 AG	154931-155075	GT	AGG
(TAT)	 AG	155592-155694	GT	TGG
(GGG)	 AG	155868-155969	GT	AGG
(TGA)	 AG	156099-156211	GT	AGG
(GTG)	 AG	156347-156525	GT	AGG
(AGG)	 AG	156630-156716	GT	AGG
(ATG)	 AG	156836-157022	GT	AGG
(GGC)	 AG	158072-158242	CC	AGC
add_exon() Sorry, pasa_asmbl_3116.p1 156836-157022-initial-1 is invalid.
-recovered pasa_asmbl_3116.p1, initial, 156836, 157022
-recovered pasa_asmbl_3116.p1, terminal, 158072, 158242
-recovered pasa_asmbl_3116.p1, internal, 154931, 155075
-recovered pasa_asmbl_3116.p1, internal, 155592, 155694
-recovered pasa_asmbl_3116.p1, internal, 155868, 155969
-recovered pasa_asmbl_3116.p1, internal, 156099, 156211
-recovered pasa_asmbl_3116.p1, internal, 156347, 156525
-recovered pasa_asmbl_3116.p1, internal, 156630, 156716
-recovered pasa_asmbl_3116.p1, internal, 156836, 157022
Valid prediction for GlimmerHMM_glimmerT_24569-T1
Valid prediction for GlimmerHMM_glimmerT_24564-T1
Valid prediction for HiQ_model.g16360.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 GlimmerHMM_glimmerT_24560-T1
Valid prediction for GlimmerHMM_glimmerT_24571-T1
Valid prediction for snap_scaffold_10-snap.902-T1
Valid prediction for GlimmerHMM_glimmerT_24561-T1
Valid prediction for snap_scaffold_10-snap.906-T1
Valid prediction for GlimmerHMM_glimmerT_24568-T1
Couldn't classify 11797, 11883
Couldn't classify 12782, 12895
Sorry, prediction pasa_asmbl_5173.p1 fails validation.
(GGC)	 AC	11797-11883	GT	AGG
(ATC)	 AG	12310-12420	GT	TGG
(ACT)	 AG	12782-12895	CT	GAC
-recovered pasa_asmbl_5173.p1, internal, 12310, 12420
Valid prediction for GlimmerHMM_glimmerT_24572-T1
Valid prediction for snap_scaffold_10-snap.921-T1
Valid prediction for snap_scaffold_10-snap.929-T1
Valid prediction for GlimmerHMM_glimmerT_24553-T1
Valid prediction for snap_scaffold_10-snap.911-T1
Valid prediction for CodingQuarry_transcript_5357-T1
Valid prediction for GlimmerHMM_glimmerT_24550-T1
Valid prediction for pasa_asmbl_4272.p1
Couldn't classify 160807, 161004
Sorry, prediction pasa_asmbl_4265.p1 fails validation.
(CCT)	 CT	160807-161004	GT	CGG
(GAG)	 AG	161119-161371	GT	AGG
(ACT)	 AG	161474-161558	GT	AGG
(TGA)	 AG	162128-162317	GT	AGG
(GAG)	 AG	162416-162559	GC	AAG
-recovered pasa_asmbl_4265.p1, terminal, 162416, 162559
-recovered pasa_asmbl_4265.p1, internal, 161119, 161371
-recovered pasa_asmbl_4265.p1, internal, 161474, 161558
-recovered pasa_asmbl_4265.p1, internal, 162128, 162317
-recovered pasa_asmbl_4265.p1, internal, 162416, 162559
Valid prediction for HiQ_model.g16345.t1
Valid prediction for snap_scaffold_10-snap.901-T1
Valid prediction for snap_scaffold_10-snap.927-T1
Valid prediction for Augustus_model.g16365.t1
Valid prediction for snap_scaffold_10-snap.916-T1
Valid prediction for Augustus_model.g16353.t1
Valid prediction for GlimmerHMM_glimmerT_24544-T1
Valid prediction for Augustus_model.g16351.t1
Valid prediction for GlimmerHMM_glimmerT_24566-T1
Valid prediction for GlimmerHMM_glimmerT_24567-T1
Valid prediction for snap_scaffold_10-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_24546-T1
Valid prediction for GlimmerHMM_glimmerT_24556-T1
Valid prediction for CodingQuarry_transcript_5363-T1
Valid prediction for GlimmerHMM_glimmerT_24545-T1
Valid prediction for Augustus_model.g16352.t1
Valid prediction for GlimmerHMM_glimmerT_24548-T1
Valid prediction for CodingQuarry_transcript_5359-T1
Valid prediction for snap_scaffold_10-snap.892-T1
Valid prediction for snap_scaffold_10-snap.920-T1
Valid prediction for snap_scaffold_10-snap.905-T1
Valid prediction for snap_scaffold_10-snap.903-T1
Valid prediction for GlimmerHMM_glimmerT_24551-T1
Valid prediction for Augustus_model.g16355.t1
Valid prediction for CodingQuarry_transcript_5362-T1
Valid prediction for Augustus_model.g16358.t1
Valid prediction for Augustus_model.g16346.t1
Couldn't classify 70770, 70895
Sorry, prediction pasa_asmbl_4276.p1 fails validation.
(TAC)	 GG	70770-70895	GT	AGG
(GAG)	 AG	71369-71449	GT	AGG
(AGG)	 AG	72523-72617	GT	AGG
(CAC)	 AG	72965-73139	CC	GAC
-recovered pasa_asmbl_4276.p1, terminal, 72965, 73139
-recovered pasa_asmbl_4276.p1, internal, 71369, 71449
-recovered pasa_asmbl_4276.p1, internal, 72523, 72617
Valid prediction for snap_scaffold_10-snap.919-T1
Valid prediction for GlimmerHMM_glimmerT_24554-T1
Valid prediction for snap_scaffold_10-snap.896-T1
Valid prediction for snap_scaffold_10-snap.909-T1
Valid prediction for GlimmerHMM_glimmerT_24557-T1
Valid prediction for GlimmerHMM_glimmerT_24559-T1
Valid prediction for CodingQuarry_transcript_5358-T1
Valid prediction for Augustus_model.g16348.t1
Valid prediction for snap_scaffold_10-snap.914-T1
Valid prediction for snap_scaffold_10-snap.894-T1
Couldn't classify 157205, 157323
Sorry, prediction pasa_asmbl_4268.p1 fails validation.
(ATG)	 GG	153914-154144	GT	AGG
(GTT)	 AG	154263-154380	GT	AGG
(GCG)	 AG	155118-155351	GT	TGG
(CCA)	 AG	155715-155890	GT	AGG
(GTG)	 AG	156534-156734	GT	AGG
(CTC)	 AG	156941-157073	GT	AGG
(AGG)	 AG	157205-157323	GT	AGG
-recovered pasa_asmbl_4268.p1, initial, 153914, 154144
-recovered pasa_asmbl_4268.p1, internal, 154263, 154380
-recovered pasa_asmbl_4268.p1, internal, 155118, 155351
-recovered pasa_asmbl_4268.p1, internal, 155715, 155890
-recovered pasa_asmbl_4268.p1, internal, 156534, 156734
-recovered pasa_asmbl_4268.p1, internal, 156941, 157073
-recovered pasa_asmbl_4268.p1, internal, 157205, 157323
Valid prediction for snap_scaffold_10-snap.893-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g16361.t1
Valid prediction for snap_scaffold_10-snap.915-T1
Valid prediction for CodingQuarry_transcript_5355-T1
Valid prediction for CodingQuarry_transcript_5356-T1
Valid prediction for Augustus_model.g16356.t1
Valid prediction for Augustus_model.g16362.t1
Couldn't classify 174494, 174703
Couldn't classify 175554, 175594
Sorry, prediction pasa_asmbl_4264.p1 fails validation.
(GGA)	 TA	174494-174703	GT	CGG
(GCT)	 AG	175242-175404	GT	GAG
(GTC)	 AG	175554-175594	GA	CCG
add_exon() Sorry, pasa_asmbl_4264.p1 175242-175404-terminal-3 is invalid.
-recovered pasa_asmbl_4264.p1, terminal, 175242, 175404
-recovered pasa_asmbl_4264.p1, internal, 175242, 175404
Valid prediction for pasa_asmbl_4278.p1
Valid prediction for snap_scaffold_10-snap.932-T1
Valid prediction for Augustus_model.g16347.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24818, rend_intergenic: 19503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29416, rend_intergenic: 24852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49674, rend_intergenic: 42686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52921, rend_intergenic: 49774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58210, rend_intergenic: 53131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64936, rend_intergenic: 62049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103096, rend_intergenic: 97099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113655, rend_intergenic: 110816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123968, rend_intergenic: 118818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129141, rend_intergenic: 128240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135743, rend_intergenic: 132801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149397, rend_intergenic: 144797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167802, rend_intergenic: 164866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168649, rend_intergenic: 168404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171668, rend_intergenic: 169124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178405, rend_intergenic: 171707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183191
-exon list size: 448


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 24818, rend_intergenic: 19503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29416, rend_intergenic: 24852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49674, rend_intergenic: 42686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52921, rend_intergenic: 49774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58210, rend_intergenic: 53131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64936, rend_intergenic: 62049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103096, rend_intergenic: 97099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113655, rend_intergenic: 110816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123968, rend_intergenic: 118818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129141, rend_intergenic: 128240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135743, rend_intergenic: 132801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149397, rend_intergenic: 144797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167802, rend_intergenic: 164866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168649, rend_intergenic: 168404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171668, rend_intergenic: 169124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178405, rend_intergenic: 171707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support