-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_15158755-15396041

-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_57727-T1
Valid prediction for HiQ_model.g12531.t1
Valid prediction for snap_scaffold_7-snap.2868-T1
Valid prediction for snap_scaffold_7-snap.2859-T1
Couldn't classify 82951, 83023
Couldn't classify 84263, 84408
Sorry, prediction pasa_asmbl_50565.p1 fails validation.
(CCT)	 GC	82951-83023	GT	TGG
(AGC)	 AG	83431-83562	GT	GAG
(CGG)	 AG	84263-84408	AA	GTA
-recovered pasa_asmbl_50565.p1, internal, 83431, 83562
Valid prediction for snap_scaffold_7-snap.2889-T1
Valid prediction for Augustus_model.g12529.t1
Valid prediction for Augustus_model.g12528.t1
Valid prediction for GlimmerHMM_glimmerT_18590-T1
Valid prediction for snap_scaffold_7-snap.2883-T1
Valid prediction for CodingQuarry_transcript_57729-T1
Valid prediction for snap_scaffold_7-snap.2857-T1
Couldn't classify 86749, 87917
Sorry, prediction pasa_asmbl_50421.p1 fails validation.
(GAC)	 CC	86749-87917	GT	AGG
(CCA)	 AG	88163-88349	GT	AGG
(GGA)	 AG	89183-89266	GT	AAG
(GTC)	 AG	89368-89490	GT	AGG
(CCT)	 AG	90202-90273	GA	AGG
-recovered pasa_asmbl_50421.p1, terminal, 90202, 90273
-recovered pasa_asmbl_50421.p1, internal, 88163, 88349
-recovered pasa_asmbl_50421.p1, internal, 89183, 89266
-recovered pasa_asmbl_50421.p1, internal, 89368, 89490
Couldn't classify 42381, 42479
Couldn't classify 43445, 43552
Sorry, prediction pasa_asmbl_50596.p2 fails validation.
(AAC)	 AG	42381-42479	GT	AGG
(GAC)	 AG	42923-43021	GT	AGG
(AAC)	 AG	43445-43552	AC	TGA
-recovered pasa_asmbl_50596.p2, internal, 42381, 42479
-recovered pasa_asmbl_50596.p2, internal, 42923, 43021
Valid prediction for snap_scaffold_7-snap.2878-T1
Valid prediction for snap_scaffold_7-snap.2881-T1
Valid prediction for snap_scaffold_7-snap.2871-T1
Valid prediction for GlimmerHMM_glimmerT_18600-T1
Valid prediction for snap_scaffold_7-snap.2867-T1
Valid prediction for pasa_asmbl_50428.p1
Valid prediction for snap_scaffold_7-snap.2870-T1
Valid prediction for snap_scaffold_7-snap.2863-T1
Valid prediction for GlimmerHMM_glimmerT_18598-T1
Valid prediction for GlimmerHMM_glimmerT_18593-T1
Valid prediction for Augustus_model.g12533.t1
Valid prediction for Augustus_model.g12541.t1
Valid prediction for GlimmerHMM_glimmerT_18599-T1
Valid prediction for snap_scaffold_7-snap.2876-T1
Couldn't classify 73766, 74191
Sorry, prediction pasa_asmbl_50416.p1 fails validation.
(ATG)	 TG	63505-63540	GT	CAG
(CAC)	 AG	65434-65540	GT	GGG
(GTT)	 AG	68079-68303	GT	GGG
(CCC)	 AG	68576-68730	GT	GGG
(AGC)	 AG	69070-69281	GT	AGG
(GCC)	 AG	69695-69902	GC	AGG
(GAG)	 AG	70240-70336	GT	AGG
(GTT)	 AG	71560-71788	GT	AGG
(GTC)	 AG	71949-72074	GT	AGG
(GTC)	 AG	72278-72400	GT	AGG
(GAC)	 AG	72927-72953	GT	AGG
(ACT)	 AG	73766-74191	TC	CAT
-recovered pasa_asmbl_50416.p1, initial, 63505, 63540
-recovered pasa_asmbl_50416.p1, internal, 65434, 65540
-recovered pasa_asmbl_50416.p1, internal, 68079, 68303
-recovered pasa_asmbl_50416.p1, internal, 68576, 68730
-recovered pasa_asmbl_50416.p1, internal, 69070, 69281
-recovered pasa_asmbl_50416.p1, internal, 69695, 69902
-recovered pasa_asmbl_50416.p1, internal, 70240, 70336
-recovered pasa_asmbl_50416.p1, internal, 71560, 71788
-recovered pasa_asmbl_50416.p1, internal, 71949, 72074
-recovered pasa_asmbl_50416.p1, internal, 72278, 72400
-recovered pasa_asmbl_50416.p1, internal, 72927, 72953
Couldn't classify 129891, 129943
Sorry, prediction pasa_asmbl_50442.p1 fails validation.
(TTC)	 GC	129891-129943	GT	ATG
(GGC)	 AG	130182-130323	GT	GGG
(CCG)	 AG	131066-131147	GT	AGG
(ACC)	 AG	131410-131615	GT	AGG
(GAG)	 AG	131816-131899	GT	CGG
(AGC)	 AG	132030-132134	GT	TCG
(GAG)	 AG	132229-132452	GT	AGG
(ATG)	 AG	132605-132706	GT	CGG
(GAG)	 AG	133137-133260	GT	GAG
add_exon() Sorry, pasa_asmbl_50442.p1 132605-132706-initial-1 is invalid.
-recovered pasa_asmbl_50442.p1, initial, 132605, 132706
-recovered pasa_asmbl_50442.p1, terminal, 133137, 133260
-recovered pasa_asmbl_50442.p1, internal, 130182, 130323
-recovered pasa_asmbl_50442.p1, internal, 131066, 131147
-recovered pasa_asmbl_50442.p1, internal, 131410, 131615
-recovered pasa_asmbl_50442.p1, internal, 131816, 131899
-recovered pasa_asmbl_50442.p1, internal, 132030, 132134
-recovered pasa_asmbl_50442.p1, internal, 132229, 132452
-recovered pasa_asmbl_50442.p1, internal, 132605, 132706
-recovered pasa_asmbl_50442.p1, internal, 133137, 133260
Valid prediction for GlimmerHMM_glimmerT_18594-T1
Valid prediction for snap_scaffold_7-snap.2885-T1
Valid prediction for snap_scaffold_7-snap.2855-T1
Valid prediction for GlimmerHMM_glimmerT_18597-T1
Valid prediction for CodingQuarry_transcript_57725-T1
Valid prediction for Augustus_model.g12534.t1
Valid prediction for GlimmerHMM_glimmerT_18604-T1
Valid prediction for GlimmerHMM_glimmerT_18592-T1
Valid prediction for snap_scaffold_7-snap.2866-T1
Valid prediction for CodingQuarry_transcript_57730-T1
Couldn't classify 125839, 125945
Couldn't classify 128745, 128927
Sorry, prediction pasa_asmbl_50436.p2 fails validation.
(CAG)	 AC	125839-125945	GT	AGG
(AGT)	 AG	126933-126984	GT	AGG
(GAG)	 AG	127434-127490	GT	ATG
(AGC)	 AG	128745-128927	CA	CAC
-recovered pasa_asmbl_50436.p2, internal, 126933, 126984
-recovered pasa_asmbl_50436.p2, internal, 127434, 127490
Valid prediction for Augustus_model.g12530.t1
Valid prediction for GlimmerHMM_glimmerT_18609-T1
Valid prediction for CodingQuarry_transcript_57726-T1
Valid prediction for Augustus_model.g12532.t1
Valid prediction for GlimmerHMM_glimmerT_18596-T1
Valid prediction for CodingQuarry_transcript_57724-T1
Valid prediction for snap_scaffold_7-snap.2869-T1
Valid prediction for snap_scaffold_7-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_18601-T1
Valid prediction for snap_scaffold_7-snap.2890-T1
Valid prediction for snap_scaffold_7-snap.2873-T1
Valid prediction for GlimmerHMM_glimmerT_18605-T1
Couldn't classify 81729, 82031
Sorry, prediction pasa_asmbl_50580.p1 fails validation.
(AGC)	 TT	81729-82031	AA	AAA
Valid prediction for snap_scaffold_7-snap.2891-T1
Valid prediction for pasa_asmbl_50424.p1
Valid prediction for Augustus_model.g12526.t1
Valid prediction for snap_scaffold_7-snap.2884-T1
Couldn't classify 54407, 54475
Couldn't classify 56151, 56209
Sorry, prediction pasa_asmbl_50414.p1 fails validation.
(CAG)	 CG	54407-54475	GT	TGG
(AAT)	 AG	54809-54904	GT	TGG
(ACT)	 AG	55893-55965	GT	AGG
(TCA)	 AG	56151-56209	AT	GTA
-recovered pasa_asmbl_50414.p1, internal, 54809, 54904
-recovered pasa_asmbl_50414.p1, internal, 55893, 55965
Valid prediction for snap_scaffold_7-snap.2892-T1
Valid prediction for CodingQuarry_transcript_57728-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 snap_scaffold_7-snap.2880-T1
Valid prediction for Augustus_model.g12535.t1
Valid prediction for snap_scaffold_7-snap.2879-T1
Valid prediction for snap_scaffold_7-snap.2882-T1
Valid prediction for Augustus_model.g12538.t1
Valid prediction for GlimmerHMM_glimmerT_18595-T1
Valid prediction for Augustus_model.g12536.t1
Couldn't classify 70260, 70313
Couldn't classify 75819, 75937
Sorry, prediction pasa_asmbl_51372.p1 fails validation.
(TAC)	 TC	70260-70313	GT	AGG
(AGG)	 AG	72017-72268	GT	TGG
(GGC)	 AG	73812-73943	GT	AGG
(TCT)	 AG	74665-74860	GT	GGG
(GTC)	 AG	75819-75937	CC	CCC
-recovered pasa_asmbl_51372.p1, internal, 72017, 72268
-recovered pasa_asmbl_51372.p1, internal, 73812, 73943
-recovered pasa_asmbl_51372.p1, internal, 74665, 74860
Valid prediction for GlimmerHMM_glimmerT_18606-T1
Valid prediction for snap_scaffold_7-snap.2854-T1
Valid prediction for snap_scaffold_7-snap.2861-T1
Valid prediction for HiQ_model.g12539.t1
Valid prediction for GlimmerHMM_glimmerT_18591-T1
Valid prediction for pasa_asmbl_51373.p1
Couldn't classify 81167, 81322
Sorry, prediction pasa_asmbl_51369.p1 fails validation.
(CTT)	 AG	81167-81322	GT	AGG
(ATT)	 AG	82217-82316	GT	AGG
(AAC)	 AG	84226-84353	AC	AGA
-recovered pasa_asmbl_51369.p1, terminal, 84226, 84353
-recovered pasa_asmbl_51369.p1, internal, 81167, 81322
-recovered pasa_asmbl_51369.p1, internal, 82217, 82316
Valid prediction for snap_scaffold_7-snap.2860-T1
Valid prediction for GlimmerHMM_glimmerT_18608-T1
Valid prediction for GlimmerHMM_glimmerT_18607-T1
Valid prediction for snap_scaffold_7-snap.2877-T1
Valid prediction for snap_scaffold_7-snap.2887-T1
Valid prediction for snap_scaffold_7-snap.2874-T1
Valid prediction for snap_scaffold_7-snap.2862-T1
Valid prediction for snap_scaffold_7-snap.2856-T1
Valid prediction for snap_scaffold_7-snap.2865-T1
Valid prediction for snap_scaffold_7-snap.2864-T1
Valid prediction for snap_scaffold_7-snap.2886-T1
Valid prediction for snap_scaffold_7-snap.2858-T1
Valid prediction for CodingQuarry_transcript_57731-T1
Valid prediction for snap_scaffold_7-snap.2875-T1
Valid prediction for Augustus_model.g12537.t1
Valid prediction for snap_scaffold_7-snap.2872-T1
Valid prediction for Augustus_model.g12527.t1
Valid prediction for Augustus_model.g12540.t1
Valid prediction for snap_scaffold_7-snap.2888-T1
Valid prediction for GlimmerHMM_glimmerT_18603-T1
Valid prediction for GlimmerHMM_glimmerT_18602-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11563, rend_intergenic: 7362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16163, rend_intergenic: 15511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23561, rend_intergenic: 17136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30376, rend_intergenic: 24379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40347, rend_intergenic: 35624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57477, rend_intergenic: 42854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72145, rend_intergenic: 63547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129217, rend_intergenic: 118044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133260, rend_intergenic: 131178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158198, rend_intergenic: 154571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163894, rend_intergenic: 158846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167247, rend_intergenic: 164924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179075, rend_intergenic: 176983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188707, rend_intergenic: 182087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237287
-exon list size: 410


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 11563, rend_intergenic: 7362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16163, rend_intergenic: 15511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23561, rend_intergenic: 17136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30376, rend_intergenic: 24379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40347, rend_intergenic: 35624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57477, rend_intergenic: 42854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72145, rend_intergenic: 63547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129217, rend_intergenic: 118044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133260, rend_intergenic: 131178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158198, rend_intergenic: 154571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163894, rend_intergenic: 158846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167247, rend_intergenic: 164924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179075, rend_intergenic: 176983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188707, rend_intergenic: 182087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support