-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_6588877-6899469

-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_62211-T1
Valid prediction for snap_scaffold_9-snap.1412-T1
Valid prediction for GlimmerHMM_glimmerT_22353-T1
Valid prediction for GlimmerHMM_glimmerT_22348-T1
Valid prediction for snap_scaffold_9-snap.1408-T1
Valid prediction for Augustus_model.g14866.t1
Valid prediction for snap_scaffold_9-snap.1405-T1
Valid prediction for GlimmerHMM_glimmerT_22360-T1
Valid prediction for pasa_asmbl_54107.p1
Valid prediction for GlimmerHMM_glimmerT_22342-T1
Valid prediction for pasa_asmbl_54099.p1
Valid prediction for snap_scaffold_9-snap.1385-T1
Valid prediction for Augustus_model.g14854.t1
Valid prediction for CodingQuarry_transcript_62216-T1
Valid prediction for snap_scaffold_9-snap.1380-T1
Valid prediction for snap_scaffold_9-snap.1392-T1
Valid prediction for GlimmerHMM_glimmerT_22350-T1
Couldn't classify 247393, 247692
Sorry, prediction pasa_asmbl_54104.p2 fails validation.
(GGC)	 GA	247393-247692	CA	GAC
Valid prediction for snap_scaffold_9-snap.1388-T1
Valid prediction for snap_scaffold_9-snap.1376-T1
Valid prediction for snap_scaffold_9-snap.1373-T1
Valid prediction for GlimmerHMM_glimmerT_22356-T1
Valid prediction for snap_scaffold_9-snap.1407-T1
Valid prediction for GlimmerHMM_glimmerT_22355-T1
Valid prediction for GlimmerHMM_glimmerT_22352-T1
Valid prediction for snap_scaffold_9-snap.1389-T1
Valid prediction for GlimmerHMM_glimmerT_22343-T1
Valid prediction for CodingQuarry_transcript_62219-T1
Valid prediction for snap_scaffold_9-snap.1377-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1378-T1
Valid prediction for HiQ_model.g14873.t1
Valid prediction for GlimmerHMM_glimmerT_22347-T1
Valid prediction for GlimmerHMM_glimmerT_22366-T1
Valid prediction for GlimmerHMM_glimmerT_22357-T1
Valid prediction for snap_scaffold_9-snap.1399-T1
Valid prediction for GlimmerHMM_glimmerT_22354-T1
Valid prediction for CodingQuarry_transcript_62214-T1
Valid prediction for Augustus_model.g14875.t1
Valid prediction for HiQ_model.g14880.t1
Valid prediction for snap_scaffold_9-snap.1403-T1
Valid prediction for Augustus_model.g14865.t1
Valid prediction for HiQ_model.g14871.t1
Valid prediction for Augustus_model.g14861.t1
Valid prediction for snap_scaffold_9-snap.1391-T1
Valid prediction for Augustus_model.g14858.t1
Valid prediction for snap_scaffold_9-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_22345-T1
Valid prediction for GlimmerHMM_glimmerT_22358-T1
Valid prediction for CodingQuarry_transcript_62215-T1
Couldn't classify 225530, 225561
Couldn't classify 226632, 227071
Sorry, prediction pasa_asmbl_54100.p1 fails validation.
(GCT)	 TG	225530-225561	GT	CGG
(ATG)	 AG	226020-226140	GT	CGG
(AGC)	 AG	226230-226337	GT	TGG
(ACA)	 AG	226488-226524	GT	ATG
(TGG)	 AG	226632-227071	CT	ATC
add_exon() Sorry, pasa_asmbl_54100.p1 226020-226140-initial-1 is invalid.
-recovered pasa_asmbl_54100.p1, initial, 226020, 226140
-recovered pasa_asmbl_54100.p1, internal, 226020, 226140
-recovered pasa_asmbl_54100.p1, internal, 226230, 226337
-recovered pasa_asmbl_54100.p1, internal, 226488, 226524
Valid prediction for GlimmerHMM_glimmerT_22363-T1
Valid prediction for snap_scaffold_9-snap.1409-T1
Valid prediction for Augustus_model.g14869.t1
Couldn't classify 238068, 238221
Sorry, prediction pasa_asmbl_54103.p1 fails validation.
(GGA)	 CA	238068-238221	GT	GGG
(AGT)	 AG	238351-238425	GT	TGG
(TAA)	 AG	238534-238654	GT	AGG
(CTT)	 AG	238779-238917	GT	AGG
(GGT)	 AG	239010-239134	GT	AGG
(ATA)	 AG	239233-239665	AC	AAA
-recovered pasa_asmbl_54103.p1, terminal, 239233, 239665
-recovered pasa_asmbl_54103.p1, internal, 238351, 238425
-recovered pasa_asmbl_54103.p1, internal, 238534, 238654
-recovered pasa_asmbl_54103.p1, internal, 238779, 238917
-recovered pasa_asmbl_54103.p1, internal, 239010, 239134
Valid prediction for snap_scaffold_9-snap.1396-T1
Valid prediction for GlimmerHMM_glimmerT_22361-T1
Valid prediction for Augustus_model.g14859.t1
Valid prediction for snap_scaffold_9-snap.1415-T1
Valid prediction for pasa_asmbl_54106.p1
Valid prediction for Augustus_model.g14864.t1
Valid prediction for snap_scaffold_9-snap.1414-T1
Valid prediction for snap_scaffold_9-snap.1394-T1
Valid prediction for HiQ_model.g14867.t1
Valid prediction for snap_scaffold_9-snap.1404-T1
Valid prediction for snap_scaffold_9-snap.1406-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1411-T1
Valid prediction for Augustus_model.g14872.t1
Valid prediction for CodingQuarry_transcript_62209-T1
Valid prediction for pasa_asmbl_54098.p1
Valid prediction for Augustus_model.g14878.t1
Valid prediction for snap_scaffold_9-snap.1402-T1
Valid prediction for pasa_asmbl_54768.p1
Valid prediction for Augustus_model.g14868.t1
Valid prediction for HiQ_model.g14856.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 pasa_asmbl_55068.p1
Valid prediction for snap_scaffold_9-snap.1387-T1
Valid prediction for Augustus_model.g14882.t1
Valid prediction for GlimmerHMM_glimmerT_22368-T1
Valid prediction for Augustus_model.g14870.t1
Valid prediction for GlimmerHMM_glimmerT_22341-T1
Valid prediction for snap_scaffold_9-snap.1419-T1
Valid prediction for snap_scaffold_9-snap.1386-T1
Couldn't classify 149948, 150088
Sorry, prediction pasa_asmbl_55072.p1 fails validation.
(CTG)	 AC	149948-150088	GT	AGG
(CGT)	 AG	150279-150354	GT	AGG
(GCT)	 AG	150501-150603	GT	GGG
(GGT)	 AG	150884-150977	GT	ATG
(GTC)	 AG	151209-151320	GT	AGG
(AAA)	 AG	151551-151657	GT	AGG
(CAA)	 AG	151805-151846	GT	AAG
(GCT)	 AG	153184-153269	GT	AGG
(GGC)	 AG	153429-153552	GT	AGG
(GAA)	 AG	153696-153829	GT	GGG
(TGC)	 AG	153971-154071	GT	AGG
(GAT)	 AG	155678-155788	GT	TGG
(ATA)	 AG	155901-156023	GT	CAG
(ATC)	 AG	156252-156282	GT	AAG
(TGA)	 AG	156406-156505	GT	TGG
(CCT)	 AG	156667-156726	GT	TGG
(CCC)	 AG	156869-156973	GT	AGG
(ATG)	 AG	158251-158265	TA	AAT
add_exon() Sorry, pasa_asmbl_55072.p1 151209-151320-terminal-3 is invalid.
-recovered pasa_asmbl_55072.p1, terminal, 151209, 151320
-recovered pasa_asmbl_55072.p1, terminal, 158251, 158265
-recovered pasa_asmbl_55072.p1, internal, 150279, 150354
-recovered pasa_asmbl_55072.p1, internal, 150501, 150603
-recovered pasa_asmbl_55072.p1, internal, 150884, 150977
-recovered pasa_asmbl_55072.p1, internal, 151209, 151320
-recovered pasa_asmbl_55072.p1, internal, 151551, 151657
-recovered pasa_asmbl_55072.p1, internal, 151805, 151846
-recovered pasa_asmbl_55072.p1, internal, 153184, 153269
-recovered pasa_asmbl_55072.p1, internal, 153429, 153552
-recovered pasa_asmbl_55072.p1, internal, 153696, 153829
-recovered pasa_asmbl_55072.p1, internal, 153971, 154071
-recovered pasa_asmbl_55072.p1, internal, 155678, 155788
-recovered pasa_asmbl_55072.p1, internal, 155901, 156023
-recovered pasa_asmbl_55072.p1, internal, 156252, 156282
-recovered pasa_asmbl_55072.p1, internal, 156406, 156505
-recovered pasa_asmbl_55072.p1, internal, 156667, 156726
-recovered pasa_asmbl_55072.p1, internal, 156869, 156973
Valid prediction for snap_scaffold_9-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_22369-T1
Valid prediction for snap_scaffold_9-snap.1382-T1
Valid prediction for snap_scaffold_9-snap.1418-T1
Valid prediction for Augustus_model.g14862.t1
Valid prediction for HiQ_model.g14863.t1
Valid prediction for snap_scaffold_9-snap.1400-T1
Valid prediction for CodingQuarry_transcript_62213-T1
Valid prediction for pasa_asmbl_55086.p2
Valid prediction for CodingQuarry_transcript_62210-T1
Couldn't classify 51150, 51311
Sorry, prediction pasa_asmbl_55080.p1 fails validation.
(CAT)	 CC	51150-51311	GT	AGG
(GCT)	 AG	51520-51613	GT	AGG
(GAT)	 AG	51860-52006	GT	AGG
(GCC)	 AG	52553-52648	GT	TGG
(GTG)	 AG	52990-53132	AC	AAA
add_exon() Sorry, pasa_asmbl_55080.p1 51520-51613-terminal-3 is invalid.
-recovered pasa_asmbl_55080.p1, terminal, 51520, 51613
-recovered pasa_asmbl_55080.p1, terminal, 52990, 53132
-recovered pasa_asmbl_55080.p1, internal, 51520, 51613
-recovered pasa_asmbl_55080.p1, internal, 51860, 52006
-recovered pasa_asmbl_55080.p1, internal, 52553, 52648
Valid prediction for snap_scaffold_9-snap.1410-T1
Valid prediction for HiQ_model.g14860.t1
Valid prediction for snap_scaffold_9-snap.1422-T1
Valid prediction for snap_scaffold_9-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_22346-T1
Valid prediction for Augustus_model.g14855.t1
Valid prediction for snap_scaffold_9-snap.1416-T1
Valid prediction for CodingQuarry_transcript_62212-T1
Valid prediction for HiQ_model.g14874.t1
Valid prediction for GlimmerHMM_glimmerT_22344-T1
Valid prediction for CodingQuarry_transcript_62218-T1
Valid prediction for snap_scaffold_9-snap.1371-T1
Valid prediction for GlimmerHMM_glimmerT_22340-T1
Valid prediction for GlimmerHMM_glimmerT_22359-T1
Couldn't classify 251259, 251348
Sorry, prediction pasa_asmbl_55066.p1 fails validation.
(CGC)	 CT	251259-251348	GT	AAG
(GTT)	 AG	251432-251527	GT	TGG
(GTG)	 AG	251622-251772	GT	TGG
(AGG)	 AG	251860-251906	AA	GAA
-recovered pasa_asmbl_55066.p1, terminal, 251860, 251906
-recovered pasa_asmbl_55066.p1, internal, 251432, 251527
-recovered pasa_asmbl_55066.p1, internal, 251622, 251772
Valid prediction for CodingQuarry_transcript_62217-T1
Valid prediction for pasa_asmbl_55083.p1
Valid prediction for Augustus_model.g14879.t1
Valid prediction for snap_scaffold_9-snap.1390-T1
Valid prediction for Augustus_model.g14853.t1
Valid prediction for Augustus_model.g14857.t1
Valid prediction for Augustus_model.g14881.t1
Couldn't classify 170957, 171058
Couldn't classify 171690, 171774
Sorry, prediction pasa_asmbl_55749.p1 fails validation.
(GAC)	 AC	170957-171058	GT	GGG
(CCC)	 AG	171264-171342	GT	CAG
(GTG)	 AG	171466-171571	GT	TGG
(TTT)	 AG	171690-171774	AT	CCA
-recovered pasa_asmbl_55749.p1, internal, 171264, 171342
-recovered pasa_asmbl_55749.p1, internal, 171466, 171571
Valid prediction for snap_scaffold_9-snap.1417-T1
Valid prediction for Augustus_model.g14876.t1
Valid prediction for snap_scaffold_9-snap.1398-T1
Valid prediction for snap_scaffold_9-snap.1383-T1
Valid prediction for snap_scaffold_9-snap.1375-T1
Valid prediction for snap_scaffold_9-snap.1393-T1
Valid prediction for GlimmerHMM_glimmerT_22362-T1
Valid prediction for GlimmerHMM_glimmerT_22351-T1
Valid prediction for HiQ_model.g14877.t1
Valid prediction for snap_scaffold_9-snap.1379-T1
Valid prediction for snap_scaffold_9-snap.1421-T1
Valid prediction for GlimmerHMM_glimmerT_22365-T1
Valid prediction for snap_scaffold_9-snap.1381-T1
Valid prediction for snap_scaffold_9-snap.1413-T1
Valid prediction for snap_scaffold_9-snap.1384-T1
Valid prediction for GlimmerHMM_glimmerT_22349-T1
Valid prediction for snap_scaffold_9-snap.1401-T1
Valid prediction for snap_scaffold_9-snap.1395-T1
Valid prediction for snap_scaffold_9-snap.1372-T1
Valid prediction for GlimmerHMM_glimmerT_22367-T1
Valid prediction for GlimmerHMM_glimmerT_22364-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19473, rend_intergenic: 18204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78875, rend_intergenic: 76024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112014, rend_intergenic: 107736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117394, rend_intergenic: 113502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147432, rend_intergenic: 141880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 310593
-exon list size: 568


building trellis

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89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 19473, rend_intergenic: 18204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78875, rend_intergenic: 76024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112014, rend_intergenic: 107736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117394, rend_intergenic: 113502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147432, rend_intergenic: 141880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support