-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_1853754-2017979

-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 pasa_asmbl_31369.p1
Valid prediction for snap_scaffold_23-snap.348-T1
Valid prediction for GlimmerHMM_glimmerT_50558-T1
Valid prediction for snap_scaffold_23-snap.343-T1
Valid prediction for snap_scaffold_23-snap.326-T1
Valid prediction for snap_scaffold_23-snap.361-T1
Valid prediction for Augustus_model.g33786.t1
Valid prediction for snap_scaffold_23-snap.351-T1
Valid prediction for GlimmerHMM_glimmerT_50563-T1
Valid prediction for snap_scaffold_23-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_50584-T1
Valid prediction for snap_scaffold_23-snap.341-T1
Valid prediction for Augustus_model.g33788.t1
Valid prediction for GlimmerHMM_glimmerT_50585-T1
Valid prediction for HiQ_model.g33778.t1
Valid prediction for GlimmerHMM_glimmerT_50586-T1
Valid prediction for snap_scaffold_23-snap.339-T1
Valid prediction for snap_scaffold_23-snap.337-T1
Valid prediction for snap_scaffold_23-snap.334-T1
Valid prediction for snap_scaffold_23-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_50560-T1
Valid prediction for GlimmerHMM_glimmerT_50572-T1
Valid prediction for GlimmerHMM_glimmerT_50559-T1
Valid prediction for snap_scaffold_23-snap.332-T1
Valid prediction for Augustus_model.g33782.t1
Valid prediction for GlimmerHMM_glimmerT_50579-T1
Valid prediction for GlimmerHMM_glimmerT_50569-T1
Valid prediction for snap_scaffold_23-snap.358-T1
Valid prediction for snap_scaffold_23-snap.362-T1
Couldn't classify 137868, 137966
Couldn't classify 138811, 138917
Sorry, prediction pasa_asmbl_31367.p1 fails validation.
(GAG)	 AC	137868-137966	GT	AGG
(AGG)	 AG	138077-138165	GT	ATG
(ATA)	 AG	138421-138528	GT	AGG
(GTC)	 AG	138647-138729	GT	CGG
(GAA)	 AG	138811-138917	AA	GCA
add_exon() Sorry, pasa_asmbl_31367.p1 138421-138528-terminal-1 is invalid.
-recovered pasa_asmbl_31367.p1, terminal, 138421, 138528
-recovered pasa_asmbl_31367.p1, internal, 138077, 138165
-recovered pasa_asmbl_31367.p1, internal, 138421, 138528
-recovered pasa_asmbl_31367.p1, internal, 138647, 138729
Valid prediction for GlimmerHMM_glimmerT_50567-T1
Valid prediction for snap_scaffold_23-snap.329-T1
Couldn't classify 8452, 8518
Sorry, prediction pasa_asmbl_31363.p1 fails validation.
(ATG)	 TG	5806-5817	GT	AAG
(CCA)	 AG	6132-6247	GT	AGG
(GTG)	 AG	6331-6406	GT	AGG
(TCA)	 AG	6562-6693	GT	CGG
(GAT)	 AG	6782-6905	GT	CGG
(AGA)	 AG	7134-7194	GT	AGG
(GTA)	 AG	7278-7324	GT	GTG
(TGT)	 AG	8032-8107	GT	AGG
(TAA)	 AG	8234-8341	GT	GTG
(GAC)	 AG	8452-8518	CA	CGC
-recovered pasa_asmbl_31363.p1, initial, 5806, 5817
-recovered pasa_asmbl_31363.p1, internal, 6132, 6247
-recovered pasa_asmbl_31363.p1, internal, 6331, 6406
-recovered pasa_asmbl_31363.p1, internal, 6562, 6693
-recovered pasa_asmbl_31363.p1, internal, 6782, 6905
-recovered pasa_asmbl_31363.p1, internal, 7134, 7194
-recovered pasa_asmbl_31363.p1, internal, 7278, 7324
-recovered pasa_asmbl_31363.p1, internal, 8032, 8107
-recovered pasa_asmbl_31363.p1, internal, 8234, 8341
Couldn't classify 134323, 134457
Couldn't classify 135497, 135591
Sorry, prediction pasa_asmbl_31366.p1 fails validation.
(CCC)	 AT	134323-134457	GT	AGG
(CAT)	 AG	134729-134901	GT	CGG
(GGA)	 AG	135049-135242	GT	GGG
(GCC)	 AG	135497-135591	TT	AAT
-recovered pasa_asmbl_31366.p1, internal, 134729, 134901
-recovered pasa_asmbl_31366.p1, internal, 135049, 135242
Valid prediction for snap_scaffold_23-snap.355-T1
Valid prediction for GlimmerHMM_glimmerT_50561-T1
Valid prediction for Augustus_model.g33784.t1
Valid prediction for GlimmerHMM_glimmerT_50573-T1
Valid prediction for CodingQuarry_transcript_35568-T1
Valid prediction for Augustus_model.g33790.t1
Valid prediction for snap_scaffold_23-snap.347-T1
Valid prediction for HiQ_model.g33779.t1
Valid prediction for GlimmerHMM_glimmerT_50581-T1
Valid prediction for GlimmerHMM_glimmerT_50577-T1
Valid prediction for GlimmerHMM_glimmerT_50588-T1
Valid prediction for snap_scaffold_23-snap.335-T1
Valid prediction for snap_scaffold_23-snap.345-T1
Valid prediction for snap_scaffold_23-snap.324-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_50576-T1
Valid prediction for snap_scaffold_23-snap.333-T1
Valid prediction for snap_scaffold_23-snap.356-T1
Valid prediction for snap_scaffold_23-snap.323-T1
Valid prediction for GlimmerHMM_glimmerT_50565-T1
Valid prediction for GlimmerHMM_glimmerT_50580-T1
Valid prediction for snap_scaffold_23-snap.340-T1
Valid prediction for HiQ_model.g33791.t1
Valid prediction for snap_scaffold_23-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_50587-T1
Valid prediction for GlimmerHMM_glimmerT_50578-T1
Valid prediction for snap_scaffold_23-snap.325-T1
Valid prediction for snap_scaffold_23-snap.338-T1
Valid prediction for snap_scaffold_23-snap.322-T1
Valid prediction for snap_scaffold_23-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_50566-T1
Valid prediction for snap_scaffold_23-snap.357-T1
Valid prediction for GlimmerHMM_glimmerT_50568-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50574-T1
Valid prediction for HiQ_model.g33789.t1
Valid prediction for GlimmerHMM_glimmerT_50575-T1
Valid prediction for snap_scaffold_23-snap.349-T1
Valid prediction for snap_scaffold_23-snap.354-T1
Valid prediction for CodingQuarry_transcript_35569-T1
Valid prediction for GlimmerHMM_glimmerT_50557-T1
Valid prediction for snap_scaffold_23-snap.346-T1
Valid prediction for Augustus_model.g33783.t1
Valid prediction for snap_scaffold_23-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_50583-T1
Valid prediction for snap_scaffold_23-snap.327-T1
Valid prediction for Augustus_model.g33787.t1
Valid prediction for snap_scaffold_23-snap.328-T1
Valid prediction for Augustus_model.g33780.t1
Valid prediction for GlimmerHMM_glimmerT_50589-T1
Valid prediction for GlimmerHMM_glimmerT_50582-T1
Valid prediction for snap_scaffold_23-snap.342-T1
Valid prediction for snap_scaffold_23-snap.350-T1
Valid prediction for GlimmerHMM_glimmerT_50571-T1
Valid prediction for snap_scaffold_23-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_50562-T1
Valid prediction for Augustus_model.g33777.t1
Valid prediction for CodingQuarry_transcript_35570-T1
Valid prediction for Augustus_model.g33785.t1
Valid prediction for GlimmerHMM_glimmerT_50570-T1
Couldn't classify 19756, 19800
Sorry, prediction pasa_asmbl_30680.p1 fails validation.
(CGG)	 CA	19756-19800	GT	TGG
(GGA)	 AG	20340-20405	GT	ACG
(CAA)	 AG	20513-20572	GT	ACG
(CTC)	 AG	20695-20835	GT	AGG
(AGG)	 AG	20999-21110	GT	CGG
(CGA)	 AG	21202-21293	CC	AGC
-recovered pasa_asmbl_30680.p1, terminal, 21202, 21293
-recovered pasa_asmbl_30680.p1, internal, 20340, 20405
-recovered pasa_asmbl_30680.p1, internal, 20513, 20572
-recovered pasa_asmbl_30680.p1, internal, 20695, 20835
-recovered pasa_asmbl_30680.p1, internal, 20999, 21110
Valid prediction for snap_scaffold_23-snap.352-T1
Valid prediction for snap_scaffold_23-snap.344-T1
Valid prediction for GlimmerHMM_glimmerT_50564-T1
Valid prediction for Augustus_model.g33781.t1
Couldn't classify 9451, 9620
Sorry, prediction pasa_asmbl_30682.p1 fails validation.
(ATG)	 GG	1587-1638	GT	AGG
(CCG)	 AG	3770-3967	GT	AGG
(TAT)	 AG	4084-4208	GT	AGG
(TGC)	 AG	5017-5128	GT	GTG
(GTA)	 AG	5320-5465	GT	AGG
(CTG)	 AG	5606-5745	GT	AGG
(TTA)	 AG	5874-5951	GT	GGG
(GTA)	 AG	6167-6261	GT	AGG
(CGG)	 AG	6381-6506	GT	AGG
(TGA)	 AG	6719-6796	GT	GGG
(GTG)	 AG	7594-7678	GT	AGG
(AGA)	 AG	7820-7917	GT	CGG
(CCA)	 AG	9451-9620	AA	CCA
-recovered pasa_asmbl_30682.p1, initial, 1587, 1638
-recovered pasa_asmbl_30682.p1, internal, 3770, 3967
-recovered pasa_asmbl_30682.p1, internal, 4084, 4208
-recovered pasa_asmbl_30682.p1, internal, 5017, 5128
-recovered pasa_asmbl_30682.p1, internal, 5320, 5465
-recovered pasa_asmbl_30682.p1, internal, 5606, 5745
-recovered pasa_asmbl_30682.p1, internal, 5874, 5951
-recovered pasa_asmbl_30682.p1, internal, 6167, 6261
-recovered pasa_asmbl_30682.p1, internal, 6381, 6506
-recovered pasa_asmbl_30682.p1, internal, 6719, 6796
-recovered pasa_asmbl_30682.p1, internal, 7594, 7678
-recovered pasa_asmbl_30682.p1, internal, 7820, 7917

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8896, rend_intergenic: 6562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21090, rend_intergenic: 10134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22348, rend_intergenic: 21270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27504, rend_intergenic: 23932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42252, rend_intergenic: 27984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44284, rend_intergenic: 42867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52036, rend_intergenic: 45396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54424, rend_intergenic: 52287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59122, rend_intergenic: 55804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61609, rend_intergenic: 59247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64425, rend_intergenic: 61610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64980, rend_intergenic: 64437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66468, rend_intergenic: 65429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85020, rend_intergenic: 67026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88806, rend_intergenic: 88473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93867, rend_intergenic: 89306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98696, rend_intergenic: 93922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101355, rend_intergenic: 100291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109325, rend_intergenic: 104644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112912, rend_intergenic: 109405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119262, rend_intergenic: 113173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120318, rend_intergenic: 119450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128848, rend_intergenic: 122541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151407, rend_intergenic: 146659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161497, rend_intergenic: 154967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164226
-exon list size: 424


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 8896, rend_intergenic: 6562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21090, rend_intergenic: 10134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22348, rend_intergenic: 21270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27504, rend_intergenic: 23932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42252, rend_intergenic: 27984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44284, rend_intergenic: 42867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52036, rend_intergenic: 45396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54424, rend_intergenic: 52287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59122, rend_intergenic: 55804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61609, rend_intergenic: 59247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64425, rend_intergenic: 61610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64980, rend_intergenic: 64437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66468, rend_intergenic: 65429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85020, rend_intergenic: 67026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88806, rend_intergenic: 88473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93867, rend_intergenic: 89306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98696, rend_intergenic: 93922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101355, rend_intergenic: 100291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109325, rend_intergenic: 104644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112912, rend_intergenic: 109405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119262, rend_intergenic: 113173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120318, rend_intergenic: 119450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128848, rend_intergenic: 122541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151407, rend_intergenic: 146659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161497, rend_intergenic: 154967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support