-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_7083294-7301080

-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 GeneMark_model.11460_t
Valid prediction for snap_scaffold_3-snap.1465-T1
Valid prediction for snap_scaffold_3-snap.1464-T1
Valid prediction for GeneMark_model.11449_t
Valid prediction for Augustus_model.g4540.t1
Valid prediction for GlimmerHMM_glimmerT_6923-T1
Valid prediction for GeneMark_model.11429_t
Valid prediction for Augustus_model.g4528.t1
Valid prediction for GlimmerHMM_glimmerT_6902-T1
Valid prediction for snap_scaffold_3-snap.1447-T1
Valid prediction for GeneMark_model.11442_t
Valid prediction for Augustus_model.g4527.t1
Valid prediction for Augustus_model.g4530.t1
Valid prediction for GeneMark_model.11428_t
Valid prediction for GlimmerHMM_glimmerT_6919-T1
Valid prediction for GeneMark_model.11457_t
Valid prediction for snap_scaffold_3-snap.1456-T1
Valid prediction for snap_scaffold_3-snap.1472-T1
Couldn't classify 115496, 115724
Sorry, prediction pasa_asmbl_40109.p1 fails validation.
(AGC)	 AC	115496-115724	GT	AGG
(CTC)	 AG	115921-116006	GT	GAG
(GGT)	 AG	116201-116375	GT	AGG
(ACA)	 AG	116496-116565	GT	AGG
(GAT)	 AG	116695-116809	GT	AGG
(ATC)	 AG	116945-117043	TC	GAT
add_exon() Sorry, pasa_asmbl_40109.p1 116201-116375-terminal-3 is invalid.
-recovered pasa_asmbl_40109.p1, terminal, 116201, 116375
-recovered pasa_asmbl_40109.p1, terminal, 116945, 117043
-recovered pasa_asmbl_40109.p1, internal, 115921, 116006
-recovered pasa_asmbl_40109.p1, internal, 116201, 116375
-recovered pasa_asmbl_40109.p1, internal, 116496, 116565
-recovered pasa_asmbl_40109.p1, internal, 116695, 116809
Valid prediction for GeneMark_model.11434_t
Valid prediction for GlimmerHMM_glimmerT_6904-T1
Valid prediction for snap_scaffold_3-snap.1451-T1
Valid prediction for snap_scaffold_3-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_6914-T1
Valid prediction for snap_scaffold_3-snap.1475-T1
Valid prediction for GeneMark_model.11458_t
Valid prediction for Augustus_model.g4524.t1
Valid prediction for GlimmerHMM_glimmerT_6901-T1
Valid prediction for GlimmerHMM_glimmerT_6903-T1
Valid prediction for GeneMark_model.11447_t
Valid prediction for Augustus_model.g4539.t1
Valid prediction for GeneMark_model.11440_t
Valid prediction for snap_scaffold_3-snap.1473-T1
Valid prediction for Augustus_model.g4522.t1
Valid prediction for GeneMark_model.11450_t
Valid prediction for GeneMark_model.11433_t
Valid prediction for snap_scaffold_3-snap.1450-T1
Valid prediction for GeneMark_model.11455_t
Valid prediction for Augustus_model.g4529.t1
Valid prediction for GeneMark_model.11426_t
Valid prediction for GlimmerHMM_glimmerT_6927-T1
Valid prediction for HiQ_model.g4535.t1
Valid prediction for GeneMark_model.11432_t
Valid prediction for GeneMark_model.11452_t
Valid prediction for GlimmerHMM_glimmerT_6922-T1
Valid prediction for snap_scaffold_3-snap.1457-T1
Valid prediction for GeneMark_model.11427_t
Valid prediction for snap_scaffold_3-snap.1467-T1
Couldn't classify 13576, 13661
Couldn't classify 14499, 14504
Sorry, prediction pasa_asmbl_40107.p1 fails validation.
(GAG)	 TA	13576-13661	GT	GAG
(TTT)	 AG	13793-13862	GT	ACG
(GAG)	 AG	13971-14057	GT	TGG
(GGC)	 AG	14147-14239	GT	AGG
(GAC)	 AG	14338-14388	GT	AGG
(AAA)	 AG	14499-14504	GT	CGG
-recovered pasa_asmbl_40107.p1, internal, 13793, 13862
-recovered pasa_asmbl_40107.p1, internal, 13971, 14057
-recovered pasa_asmbl_40107.p1, internal, 14147, 14239
-recovered pasa_asmbl_40107.p1, internal, 14338, 14388
-recovered pasa_asmbl_40107.p1, internal, 14499, 14504
Valid prediction for GlimmerHMM_glimmerT_6912-T1
Valid prediction for GlimmerHMM_glimmerT_6915-T1
Valid prediction for Augustus_model.g4523.t1
Valid prediction for snap_scaffold_3-snap.1471-T1
Valid prediction for GeneMark_model.11454_t
Valid prediction for GeneMark_model.11437_t
Valid prediction for Augustus_model.g4544.t1
Valid prediction for snap_scaffold_3-snap.1445-T1
Valid prediction for snap_scaffold_3-snap.1453-T1
Valid prediction for GeneMark_model.11443_t
Valid prediction for GlimmerHMM_glimmerT_6905-T1
Valid prediction for snap_scaffold_3-snap.1448-T1
Valid prediction for Augustus_model.g4536.t1
Valid prediction for Augustus_model.g4525.t1
Valid prediction for snap_scaffold_3-snap.1483-T1
Valid prediction for Augustus_model.g4526.t1
Valid prediction for GlimmerHMM_glimmerT_6916-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_6917-T1
Valid prediction for Augustus_model.g4531.t1
Valid prediction for snap_scaffold_3-snap.1454-T1
Valid prediction for snap_scaffold_3-snap.1470-T1
Valid prediction for snap_scaffold_3-snap.1469-T1
Valid prediction for GlimmerHMM_glimmerT_6907-T1
Valid prediction for Augustus_model.g4541.t1
Valid prediction for GlimmerHMM_glimmerT_6918-T1
Valid prediction for GeneMark_model.11435_t
Valid prediction for snap_scaffold_3-snap.1460-T1
Valid prediction for snap_scaffold_3-snap.1468-T1
Valid prediction for snap_scaffold_3-snap.1481-T1
Valid prediction for snap_scaffold_3-snap.1455-T1
Valid prediction for GlimmerHMM_glimmerT_6921-T1
Valid prediction for snap_scaffold_3-snap.1458-T1
Valid prediction for Augustus_model.g4538.t1
Valid prediction for GeneMark_model.11456_t
Valid prediction for Augustus_model.g4533.t1
Valid prediction for GlimmerHMM_glimmerT_6925-T1
Valid prediction for snap_scaffold_3-snap.1482-T1
Valid prediction for GeneMark_model.11430_t
Valid prediction for GlimmerHMM_glimmerT_6910-T1
Valid prediction for GeneMark_model.11446_t
Valid prediction for snap_scaffold_3-snap.1474-T1
Valid prediction for GeneMark_model.11448_t
Valid prediction for Augustus_model.g4543.t1
Valid prediction for GeneMark_model.11451_t
Valid prediction for snap_scaffold_3-snap.1446-T1
Valid prediction for GeneMark_model.11441_t
Valid prediction for GeneMark_model.11453_t
Valid prediction for snap_scaffold_3-snap.1476-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1459-T1
Valid prediction for snap_scaffold_3-snap.1461-T1
Valid prediction for GlimmerHMM_glimmerT_6908-T1
Valid prediction for snap_scaffold_3-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_6913-T1
Valid prediction for GlimmerHMM_glimmerT_6924-T1
Valid prediction for GlimmerHMM_glimmerT_6906-T1
Couldn't classify 79995, 80073
Sorry, prediction pasa_asmbl_38909.p1 fails validation.
(AAC)	 TA	79995-80073	GT	GGG
(GCA)	 AG	80248-80343	GT	GGG
(GTG)	 AG	80456-80628	GT	AAG
(GAT)	 AG	80821-80919	GT	AGG
(GAT)	 AG	81006-81068	TT	GAT
-recovered pasa_asmbl_38909.p1, terminal, 81006, 81068
-recovered pasa_asmbl_38909.p1, internal, 80248, 80343
-recovered pasa_asmbl_38909.p1, internal, 80456, 80628
-recovered pasa_asmbl_38909.p1, internal, 80821, 80919
Valid prediction for GlimmerHMM_glimmerT_6926-T1
Valid prediction for Augustus_model.g4537.t1
Valid prediction for GeneMark_model.11445_t
Valid prediction for GeneMark_model.11425_t
Valid prediction for snap_scaffold_3-snap.1480-T1
Valid prediction for GlimmerHMM_glimmerT_6909-T1
Valid prediction for GeneMark_model.11438_t
Valid prediction for snap_scaffold_3-snap.1478-T1
Valid prediction for snap_scaffold_3-snap.1466-T1
Valid prediction for GlimmerHMM_glimmerT_6920-T1
Valid prediction for pasa_asmbl_38907.p1
Valid prediction for Augustus_model.g4542.t1
Valid prediction for GlimmerHMM_glimmerT_6911-T1
Valid prediction for snap_scaffold_3-snap.1479-T1
Valid prediction for Augustus_model.g4534.t1
Valid prediction for snap_scaffold_3-snap.1477-T1
Valid prediction for GeneMark_model.11439_t
Valid prediction for GeneMark_model.11431_t
Valid prediction for CodingQuarry_transcript_46088-T1
Valid prediction for GeneMark_model.11459_t
Valid prediction for Augustus_model.g4532.t1
Valid prediction for pasa_asmbl_38914.p1
Valid prediction for CodingQuarry_transcript_46087-T1
Valid prediction for GeneMark_model.11444_t
Valid prediction for snap_scaffold_3-snap.1462-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1452-T1
Valid prediction for GeneMark_model.11436_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8940, rend_intergenic: 7716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56105, rend_intergenic: 50933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127257, rend_intergenic: 122917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166193, rend_intergenic: 161539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217787
-exon list size: 502


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 8940, rend_intergenic: 7716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56105, rend_intergenic: 50933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127257, rend_intergenic: 122917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166193, rend_intergenic: 161539  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