-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_6645761-6852754

-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 GlimmerHMM_glimmerT_9751-T1
Valid prediction for snap_scaffold_4-snap.1427-T1
Valid prediction for snap_scaffold_4-snap.1437-T1
Valid prediction for GeneMark_model.15872_t
Valid prediction for GeneMark_model.15859_t
Valid prediction for snap_scaffold_4-snap.1418-T1
Valid prediction for GeneMark_model.15875_t
Valid prediction for GeneMark_model.15845_t
Valid prediction for GlimmerHMM_glimmerT_9755-T1
Valid prediction for GeneMark_model.15867_t
Couldn't classify 59922, 59922
Sorry, prediction CodingQuarry_transcript_48923-T1 fails validation.
(ATG)	 AC	56677-56823	GT	CGG
(TCC)	 AG	57398-57475	GT	AGG
(CAG)	 AG	57726-57845	GT	TGG
(AGT)	 AG	58143-58318	GT	TGG
(GCC)	 AG	58438-58563	GT	TAG
(GAG)	 AG	59922-59922	AG	GGA
-recovered CodingQuarry_transcript_48923-T1, initial, 56677, 56823
-recovered CodingQuarry_transcript_48923-T1, internal, 57398, 57475
-recovered CodingQuarry_transcript_48923-T1, internal, 57726, 57845
-recovered CodingQuarry_transcript_48923-T1, internal, 58143, 58318
-recovered CodingQuarry_transcript_48923-T1, internal, 58438, 58563
Valid prediction for GlimmerHMM_glimmerT_9746-T1
Valid prediction for GeneMark_model.15851_t
Valid prediction for GeneMark_model.15844_t
Valid prediction for CodingQuarry_transcript_48921-T1
Valid prediction for Augustus_model.g6382.t1
Couldn't classify 200138, 200202
Sorry, prediction pasa_asmbl_42761.p1 fails validation.
(CTG)	 GT	200138-200202	GT	GGG
(GGT)	 AG	200593-200730	GT	AGG
(GGC)	 AG	200935-201049	GT	AGG
(CTG)	 AG	201723-201869	GT	AGG
(GTT)	 AG	202011-202199	GT	GCG
(GAG)	 AG	202366-202515	GT	AGG
(GCT)	 AG	202693-202827	GT	TCG
(ATC)	 AG	203078-203180	GT	AGG
(GCT)	 AG	203755-203820	GT	AGG
(GTC)	 AG	203924-204000	GA	AAG
add_exon() Sorry, pasa_asmbl_42761.p1 203078-203180-terminal-3 is invalid.
-recovered pasa_asmbl_42761.p1, terminal, 203078, 203180
-recovered pasa_asmbl_42761.p1, terminal, 203924, 204000
-recovered pasa_asmbl_42761.p1, internal, 200593, 200730
-recovered pasa_asmbl_42761.p1, internal, 200935, 201049
-recovered pasa_asmbl_42761.p1, internal, 201723, 201869
-recovered pasa_asmbl_42761.p1, internal, 202011, 202199
-recovered pasa_asmbl_42761.p1, internal, 202366, 202515
-recovered pasa_asmbl_42761.p1, internal, 202693, 202827
-recovered pasa_asmbl_42761.p1, internal, 203078, 203180
-recovered pasa_asmbl_42761.p1, internal, 203755, 203820
Valid prediction for CodingQuarry_transcript_48922-T1
Valid prediction for GlimmerHMM_glimmerT_9758-T1
Couldn't classify 59485, 59637
Sorry, prediction pasa_asmbl_42755.p1 fails validation.
(GGT)	 TG	59485-59637	GT	TGG
(GAG)	 AG	59922-60092	AC	GAA
-recovered pasa_asmbl_42755.p1, terminal, 59922, 60092
Valid prediction for GlimmerHMM_glimmerT_9754-T1
Valid prediction for snap_scaffold_4-snap.1421-T1
Valid prediction for GeneMark_model.15848_t
Valid prediction for snap_scaffold_4-snap.1442-T1
Valid prediction for GeneMark_model.15860_t
Valid prediction for GeneMark_model.15874_t
Valid prediction for pasa_asmbl_42752.p1
Valid prediction for GeneMark_model.15839_t
Valid prediction for pasa_asmbl_42751.p1
Valid prediction for GeneMark_model.15858_t
Valid prediction for Augustus_model.g6378.t1
Valid prediction for Augustus_model.g6385.t1
Valid prediction for GlimmerHMM_glimmerT_9763-T1
Valid prediction for snap_scaffold_4-snap.1404-T1
Couldn't classify 163934, 164260
Sorry, prediction pasa_asmbl_41438.p1 fails validation.
(TTC)	 TC	163934-164260	AA	GAA
Valid prediction for snap_scaffold_4-snap.1426-T1
Valid prediction for GeneMark_model.15870_t
Valid prediction for snap_scaffold_4-snap.1423-T1
Valid prediction for snap_scaffold_4-snap.1415-T1
Valid prediction for Augustus_model.g6390.t1
Valid prediction for GeneMark_model.15854_t
Valid prediction for GlimmerHMM_glimmerT_9760-T1
Valid prediction for GlimmerHMM_glimmerT_9750-T1
Valid prediction for GeneMark_model.15869_t
Valid prediction for HiQ_model.g6379.t1
Valid prediction for GeneMark_model.15856_t
Valid prediction for snap_scaffold_4-snap.1438-T1
Valid prediction for Augustus_model.g6377.t1
Valid prediction for snap_scaffold_4-snap.1422-T1
Couldn't classify 193186, 193218
Couldn't classify 197083, 197131
Sorry, prediction pasa_asmbl_42758.p1 fails validation.
(AAG)	 TC	193186-193218	GT	AAG
(GAT)	 AG	193434-193580	GT	AGG
(GTT)	 AG	195184-195210	GT	AGG
(GAC)	 AG	196391-196513	GT	TGG
(GAC)	 AG	196699-196778	GT	ATG
(TAA)	 AG	197083-197131	AC	GGA
-recovered pasa_asmbl_42758.p1, internal, 193434, 193580
-recovered pasa_asmbl_42758.p1, internal, 195184, 195210
-recovered pasa_asmbl_42758.p1, internal, 196391, 196513
-recovered pasa_asmbl_42758.p1, internal, 196699, 196778
Valid prediction for GlimmerHMM_glimmerT_9748-T1
Valid prediction for GlimmerHMM_glimmerT_9752-T1
Valid prediction for HiQ_model.g6374.t1
Valid prediction for GlimmerHMM_glimmerT_9747-T1
Valid prediction for Augustus_model.g6383.t1
Valid prediction for snap_scaffold_4-snap.1416-T1
Valid prediction for GeneMark_model.15843_t
Couldn't classify 197371, 197433
Couldn't classify 198469, 198677
Sorry, prediction pasa_asmbl_42760.p1 fails validation.
(CAG)	 AC	197371-197433	GT	AGG
(CAC)	 AG	197669-197773	GT	AGG
(AAC)	 AG	198137-198272	GT	GGG
(GGT)	 AG	198469-198677	CA	CCC
-recovered pasa_asmbl_42760.p1, internal, 197669, 197773
-recovered pasa_asmbl_42760.p1, internal, 198137, 198272
Valid prediction for GeneMark_model.15865_t
Valid prediction for snap_scaffold_4-snap.1434-T1
Valid prediction for GeneMark_model.15862_t
Valid prediction for Augustus_model.g6392.t1
Valid prediction for snap_scaffold_4-snap.1424-T1
Valid prediction for snap_scaffold_4-snap.1440-T1
Valid prediction for snap_scaffold_4-snap.1425-T1
Valid prediction for GeneMark_model.15837_t
Valid prediction for GeneMark_model.15841_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: -)Valid prediction for GlimmerHMM_glimmerT_9744-T1
Valid prediction for Augustus_model.g6387.t1
Valid prediction for snap_scaffold_4-snap.1431-T1
Valid prediction for Augustus_model.g6384.t1
Valid prediction for snap_scaffold_4-snap.1435-T1
Valid prediction for snap_scaffold_4-snap.1412-T1
Valid prediction for GeneMark_model.15852_t
Valid prediction for snap_scaffold_4-snap.1430-T1
Valid prediction for GlimmerHMM_glimmerT_9756-T1
Valid prediction for snap_scaffold_4-snap.1407-T1
Valid prediction for GlimmerHMM_glimmerT_9762-T1
Valid prediction for snap_scaffold_4-snap.1428-T1
Valid prediction for GlimmerHMM_glimmerT_9749-T1
Valid prediction for snap_scaffold_4-snap.1429-T1
Valid prediction for snap_scaffold_4-snap.1417-T1
Couldn't classify 194152, 194282
Sorry, prediction pasa_asmbl_41431.p1 fails validation.
(ATA)	 GG	194152-194282	GT	CAG
(GTA)	 AG	194820-194973	GT	ACG
(AGG)	 AG	196098-196268	TC	GAT
-recovered pasa_asmbl_41431.p1, terminal, 196098, 196268
-recovered pasa_asmbl_41431.p1, internal, 194820, 194973
Valid prediction for GlimmerHMM_glimmerT_9759-T1
Valid prediction for GlimmerHMM_glimmerT_9753-T1
Valid prediction for GlimmerHMM_glimmerT_9757-T1
Valid prediction for Augustus_model.g6386.t1
Valid prediction for GeneMark_model.15855_t
Valid prediction for GeneMark_model.15846_t
Valid prediction for snap_scaffold_4-snap.1439-T1
Valid prediction for GlimmerHMM_glimmerT_9761-T1
Valid prediction for GeneMark_model.15873_t
Valid prediction for snap_scaffold_4-snap.1410-T1
Valid prediction for Augustus_model.g6380.t1
Valid prediction for GeneMark_model.15850_t
Valid prediction for Augustus_model.g6381.t1
Valid prediction for GlimmerHMM_glimmerT_9745-T1
Valid prediction for GeneMark_model.15842_t
Valid prediction for GeneMark_model.15838_t
Valid prediction for snap_scaffold_4-snap.1441-T1
Valid prediction for snap_scaffold_4-snap.1408-T1
Valid prediction for Augustus_model.g6375.t1
Valid prediction for Augustus_model.g6388.t1
Valid prediction for snap_scaffold_4-snap.1405-T1
Valid prediction for snap_scaffold_4-snap.1419-T1
Valid prediction for Augustus_model.g6391.t1
Valid prediction for snap_scaffold_4-snap.1432-T1
Valid prediction for GeneMark_model.15847_t
Valid prediction for GeneMark_model.15866_t
Valid prediction for Augustus_model.g6376.t1
Valid prediction for GlimmerHMM_glimmerT_9743-T1
Valid prediction for GeneMark_model.15861_t
Valid prediction for Augustus_model.g6389.t1
Valid prediction for GeneMark_model.15871_t
Valid prediction for snap_scaffold_4-snap.1411-T1
Valid prediction for GeneMark_model.15868_t
Valid prediction for GeneMark_model.15864_t
Valid prediction for snap_scaffold_4-snap.1420-T1
Valid prediction for snap_scaffold_4-snap.1414-T1
Valid prediction for GeneMark_model.15863_t
Valid prediction for snap_scaffold_4-snap.1436-T1
Valid prediction for snap_scaffold_4-snap.1406-T1
Valid prediction for GeneMark_model.15849_t
Valid prediction for GeneMark_model.15840_t
Couldn't classify 164186, 164326
Couldn't classify 171758, 171947
Sorry, prediction pasa_asmbl_41436.p1 fails validation.
(GGC)	 GC	164186-164326	GT	AGG
(GTG)	 AG	164803-164987	GT	AGG
(CAC)	 AG	165131-165244	GT	TGG
(GGC)	 AG	166694-166793	GT	AGG
(GAG)	 AG	167073-167158	GT	AAG
(CCC)	 AG	168284-168419	GT	AGG
(GTG)	 AG	168835-168989	GT	GTG
(AGA)	 AG	169219-169333	GT	TGG
(GGT)	 AG	170341-170450	GT	CGG
(AAA)	 AG	170593-170658	GT	GAG
(CGC)	 AG	171758-171947	AT	ACA
-recovered pasa_asmbl_41436.p1, internal, 164803, 164987
-recovered pasa_asmbl_41436.p1, internal, 165131, 165244
-recovered pasa_asmbl_41436.p1, internal, 166694, 166793
-recovered pasa_asmbl_41436.p1, internal, 167073, 167158
-recovered pasa_asmbl_41436.p1, internal, 168284, 168419
-recovered pasa_asmbl_41436.p1, internal, 168835, 168989
-recovered pasa_asmbl_41436.p1, internal, 169219, 169333
-recovered pasa_asmbl_41436.p1, internal, 170341, 170450
-recovered pasa_asmbl_41436.p1, internal, 170593, 170658
Valid prediction for snap_scaffold_4-snap.1409-T1
Valid prediction for snap_scaffold_4-snap.1433-T1
Valid prediction for GeneMark_model.15853_t
Valid prediction for pasa_asmbl_41432.p2
Valid prediction for GeneMark_model.15857_t
Valid prediction for snap_scaffold_4-snap.1413-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69951, rend_intergenic: 67291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83284, rend_intergenic: 79632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92983, rend_intergenic: 85614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166841, rend_intergenic: 166469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197475, rend_intergenic: 192002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199430, rend_intergenic: 197651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206994
-exon list size: 550


building trellis

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99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 69951, rend_intergenic: 67291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83284, rend_intergenic: 79632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92983, rend_intergenic: 85614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166841, rend_intergenic: 166469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197475, rend_intergenic: 192002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199430, rend_intergenic: 197651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support