-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_13374076-13592482

-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_4789-T1
Valid prediction for Augustus_model.g3221.t1
Valid prediction for GlimmerHMM_glimmerT_4801-T1
Couldn't classify 2076, 2155
Sorry, prediction pasa_asmbl_24840.p1 fails validation.
(GGT)	 AA	2076-2155	GT	AGG
(AGT)	 AG	2589-2727	GT	AGG
(GAA)	 AG	2963-3070	GT	AGG
(GAG)	 AG	3393-3551	GT	AGG
(GAG)	 AG	3691-3820	GT	GGG
(GTG)	 AG	3955-4166	CA	GAC
-recovered pasa_asmbl_24840.p1, terminal, 3955, 4166
-recovered pasa_asmbl_24840.p1, internal, 2589, 2727
-recovered pasa_asmbl_24840.p1, internal, 2963, 3070
-recovered pasa_asmbl_24840.p1, internal, 3393, 3551
-recovered pasa_asmbl_24840.p1, internal, 3691, 3820
Valid prediction for snap_scaffold_2-snap.2563-T1
Valid prediction for GlimmerHMM_glimmerT_4799-T1
Valid prediction for snap_scaffold_2-snap.2603-T1
Valid prediction for snap_scaffold_2-snap.2608-T1
Valid prediction for snap_scaffold_2-snap.2588-T1
Valid prediction for Augustus_model.g3229.t1
Valid prediction for snap_scaffold_2-snap.2568-T1
Valid prediction for snap_scaffold_2-snap.2582-T1
Valid prediction for GlimmerHMM_glimmerT_4807-T1
Valid prediction for Augustus_model.g3220.t1
Valid prediction for snap_scaffold_2-snap.2575-T1
Valid prediction for snap_scaffold_2-snap.2592-T1
Valid prediction for snap_scaffold_2-snap.2610-T1
Valid prediction for snap_scaffold_2-snap.2584-T1
Valid prediction for GlimmerHMM_glimmerT_4803-T1
Valid prediction for Augustus_model.g3223.t1
Valid prediction for GlimmerHMM_glimmerT_4796-T1
Valid prediction for HiQ_model.g3219.t1
Valid prediction for snap_scaffold_2-snap.2595-T1
Valid prediction for GlimmerHMM_glimmerT_4815-T1
Valid prediction for snap_scaffold_2-snap.2606-T1
Valid prediction for GlimmerHMM_glimmerT_4788-T1
Valid prediction for snap_scaffold_2-snap.2598-T1
Valid prediction for Augustus_model.g3225.t1
Valid prediction for snap_scaffold_2-snap.2571-T1
Valid prediction for Augustus_model.g3216.t1
Valid prediction for GlimmerHMM_glimmerT_4817-T1
Valid prediction for snap_scaffold_2-snap.2612-T1
Valid prediction for snap_scaffold_2-snap.2578-T1
Valid prediction for snap_scaffold_2-snap.2594-T1
Valid prediction for snap_scaffold_2-snap.2572-T1
Valid prediction for snap_scaffold_2-snap.2599-T1
Valid prediction for GlimmerHMM_glimmerT_4818-T1
Valid prediction for GlimmerHMM_glimmerT_4794-T1
Couldn't classify 90441, 90553
Sorry, prediction pasa_asmbl_24856.p1 fails validation.
(GAC)	 AG	90441-90553	GT	CAG
(GTA)	 AG	90700-90856	GT	AGG
(AGC)	 AG	91025-91177	GT	AGG
(AGC)	 AG	93308-93853	GA	GAG
-recovered pasa_asmbl_24856.p1, terminal, 93308, 93853
-recovered pasa_asmbl_24856.p1, internal, 90441, 90553
-recovered pasa_asmbl_24856.p1, internal, 90700, 90856
-recovered pasa_asmbl_24856.p1, internal, 91025, 91177
Valid prediction for snap_scaffold_2-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_4792-T1
Valid prediction for Augustus_model.g3218.t1
Valid prediction for GlimmerHMM_glimmerT_4805-T1
Valid prediction for snap_scaffold_2-snap.2574-T1
Couldn't classify 69217, 69283
Couldn't classify 69573, 69697
Sorry, prediction CodingQuarry_transcript_28699-T1 fails validation.
(ATG)	 CC	68836-68880	GT	TGG
(GTC)	 AG	69217-69283	AT	AAA
(TTG)	 AC	69573-69697	AG	AAA
-recovered CodingQuarry_transcript_28699-T1, initial, 68836, 68880
Valid prediction for GlimmerHMM_glimmerT_4812-T1
Valid prediction for snap_scaffold_2-snap.2583-T1
Valid prediction for snap_scaffold_2-snap.2591-T1
Valid prediction for Augustus_model.g3211.t1
Valid prediction for GlimmerHMM_glimmerT_4795-T1
Valid prediction for snap_scaffold_2-snap.2580-T1
Valid prediction for snap_scaffold_2-snap.2573-T1
Valid prediction for snap_scaffold_2-snap.2585-T1
Valid prediction for CodingQuarry_transcript_28697-T1
Valid prediction for snap_scaffold_2-snap.2570-T1
Valid prediction for GlimmerHMM_glimmerT_4819-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_2-snap.2589-T1
Valid prediction for GlimmerHMM_glimmerT_4809-T1
Couldn't classify 89808, 90039
Couldn't classify 91315, 91535
Sorry, prediction pasa_asmbl_23523.p2 fails validation.
(AGC)	 GC	89808-90039	GT	CAG
(ACA)	 AG	91315-91535	TG	CCT
Couldn't classify 207845, 207855
Sorry, prediction pasa_asmbl_23506.p1 fails validation.
(GTG)	 AG	207845-207855	GT	AAG
(TCT)	 AG	207994-208087	GT	ATG
(GTT)	 AG	208210-208243	GT	AGG
(CAA)	 AG	208331-208505	GT	CGG
(ATT)	 AG	208651-208839	GT	GGG
(AGA)	 AG	209061-209484	CA	AAC
-recovered pasa_asmbl_23506.p1, terminal, 209061, 209484
-recovered pasa_asmbl_23506.p1, internal, 207845, 207855
-recovered pasa_asmbl_23506.p1, internal, 207994, 208087
-recovered pasa_asmbl_23506.p1, internal, 208210, 208243
-recovered pasa_asmbl_23506.p1, internal, 208331, 208505
-recovered pasa_asmbl_23506.p1, internal, 208651, 208839
Valid prediction for Augustus_model.g3227.t1
Couldn't classify 198819, 199128
Sorry, prediction pasa_asmbl_23510.p1 fails validation.
(GAG)	 AG	198819-199128	GT	GTG
(TGA)	 AG	199393-199486	GT	AGG
(AGC)	 AG	199584-199671	GT	AGG
(GAC)	 AG	199779-200079	GT	AAG
(TGA)	 AG	200317-200410	GT	AAG
(AGC)	 AG	200527-200614	GT	AGG
(GAC)	 AG	200763-201374	AT	AGA
-recovered pasa_asmbl_23510.p1, terminal, 200763, 201374
-recovered pasa_asmbl_23510.p1, internal, 198819, 199128
-recovered pasa_asmbl_23510.p1, internal, 199393, 199486
-recovered pasa_asmbl_23510.p1, internal, 199584, 199671
-recovered pasa_asmbl_23510.p1, internal, 199779, 200079
-recovered pasa_asmbl_23510.p1, internal, 200317, 200410
-recovered pasa_asmbl_23510.p1, internal, 200527, 200614
Valid prediction for snap_scaffold_2-snap.2566-T1
Valid prediction for snap_scaffold_2-snap.2576-T1
Couldn't classify 132878, 132906
Couldn't classify 136108, 136159
Sorry, prediction pasa_asmbl_23521.p1 fails validation.
(GAA)	 AC	132878-132906	GT	AGG
(TTT)	 AG	135310-135399	GT	ACG
(GGT)	 AG	135497-135584	GT	AGG
(AAG)	 AG	135788-135915	GT	TGG
(GTG)	 AG	136108-136159	AG	ATA
-recovered pasa_asmbl_23521.p1, internal, 135310, 135399
-recovered pasa_asmbl_23521.p1, internal, 135497, 135584
-recovered pasa_asmbl_23521.p1, internal, 135788, 135915
Valid prediction for snap_scaffold_2-snap.2565-T1
Valid prediction for GlimmerHMM_glimmerT_4813-T1
Valid prediction for GlimmerHMM_glimmerT_4800-T1
Valid prediction for GlimmerHMM_glimmerT_4816-T1
Valid prediction for CodingQuarry_transcript_28696-T1
Valid prediction for Augustus_model.g3222.t1
Valid prediction for snap_scaffold_2-snap.2590-T1
Valid prediction for snap_scaffold_2-snap.2605-T1
Valid prediction for snap_scaffold_2-snap.2593-T1
Valid prediction for HiQ_model.g3215.t1
Valid prediction for snap_scaffold_2-snap.2601-T1
Valid prediction for snap_scaffold_2-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_4808-T1
Valid prediction for snap_scaffold_2-snap.2567-T1
Valid prediction for snap_scaffold_2-snap.2577-T1
Couldn't classify 198624, 198702
Sorry, prediction pasa_asmbl_23511.p1 fails validation.
(ATG)	 AA	196329-196380	GT	AAG
(TGA)	 AG	197295-197388	GT	AAG
(TAC)	 AG	197491-197578	GT	AGG
(GAT)	 AG	197746-198103	GT	AAG
(TGA)	 AG	198250-198343	GT	AGG
(AGC)	 AG	198624-198702	AG	GGA
-recovered pasa_asmbl_23511.p1, initial, 196329, 196380
-recovered pasa_asmbl_23511.p1, internal, 197295, 197388
-recovered pasa_asmbl_23511.p1, internal, 197491, 197578
-recovered pasa_asmbl_23511.p1, internal, 197746, 198103
-recovered pasa_asmbl_23511.p1, internal, 198250, 198343
Valid prediction for HiQ_model.g3217.t1
Valid prediction for GlimmerHMM_glimmerT_4798-T1
Valid prediction for snap_scaffold_2-snap.2611-T1
Valid prediction for snap_scaffold_2-snap.2607-T1
Valid prediction for GlimmerHMM_glimmerT_4810-T1
Valid prediction for snap_scaffold_2-snap.2586-T1
Valid prediction for snap_scaffold_2-snap.2569-T1
Valid prediction for GlimmerHMM_glimmerT_4793-T1
Valid prediction for GlimmerHMM_glimmerT_4804-T1
Valid prediction for snap_scaffold_2-snap.2581-T1
Valid prediction for Augustus_model.g3224.t1
Valid prediction for snap_scaffold_2-snap.2600-T1
Valid prediction for GlimmerHMM_glimmerT_4802-T1
Valid prediction for Augustus_model.g3213.t1
Valid prediction for snap_scaffold_2-snap.2604-T1
Valid prediction for snap_scaffold_2-snap.2596-T1
Valid prediction for pasa_asmbl_23515.p1
Valid prediction for Augustus_model.g3228.t1
Valid prediction for GlimmerHMM_glimmerT_4790-T1
Valid prediction for GlimmerHMM_glimmerT_4811-T1
Couldn't classify 207994, 207997
Sorry, prediction pasa_asmbl_23507.p2 fails validation.
(ATG)	 AA	206550-206645	GT	ATG
(GTC)	 AG	207432-207635	GT	AGG
(GTG)	 AG	207743-207855	GT	AAG
(TCT)	 AG	207994-207997	GG	TAG
-recovered pasa_asmbl_23507.p2, initial, 206550, 206645
-recovered pasa_asmbl_23507.p2, internal, 207432, 207635
-recovered pasa_asmbl_23507.p2, internal, 207743, 207855
Valid prediction for GlimmerHMM_glimmerT_4806-T1
Valid prediction for pasa_asmbl_23513.p1
Valid prediction for GlimmerHMM_glimmerT_4797-T1
Couldn't classify 68581, 68724
Couldn't classify 68985, 69239
Sorry, prediction pasa_asmbl_23926.p1 fails validation.
(GTC)	 TG	68581-68724	GT	AGG
(CCT)	 AG	68985-69239	TG	GGT
Valid prediction for snap_scaffold_2-snap.2564-T1
Valid prediction for GlimmerHMM_glimmerT_4814-T1
Valid prediction for HiQ_model.g3214.t1
Valid prediction for snap_scaffold_2-snap.2609-T1
Valid prediction for Augustus_model.g3212.t1
Valid prediction for snap_scaffold_2-snap.2579-T1
Valid prediction for GlimmerHMM_glimmerT_4791-T1
Valid prediction for CodingQuarry_transcript_28698-T1
Couldn't classify 144120, 144251
Sorry, prediction pasa_asmbl_23517.p1 fails validation.
(TGT)	 GC	144120-144251	GT	ATG
(ACA)	 AG	145977-146091	GT	CAG
(TGA)	 AG	146292-146419	GT	AAG
(ATT)	 AG	146535-146629	GT	GCG
(GGT)	 AG	146737-146886	GT	TGG
(GTG)	 AG	147065-147167	CA	AAC
-recovered pasa_asmbl_23517.p1, terminal, 147065, 147167
-recovered pasa_asmbl_23517.p1, internal, 145977, 146091
-recovered pasa_asmbl_23517.p1, internal, 146292, 146419
-recovered pasa_asmbl_23517.p1, internal, 146535, 146629
-recovered pasa_asmbl_23517.p1, internal, 146737, 146886
Valid prediction for Augustus_model.g3226.t1
Valid prediction for snap_scaffold_2-snap.2587-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4809, rend_intergenic: 2952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73347, rend_intergenic: 71361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76802, rend_intergenic: 73610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85602, rend_intergenic: 76907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106699, rend_intergenic: 104652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120415, rend_intergenic: 115925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129452, rend_intergenic: 121088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137434, rend_intergenic: 133027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149854, rend_intergenic: 141806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155056, rend_intergenic: 152224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161843, rend_intergenic: 159285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166785, rend_intergenic: 162589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173877, rend_intergenic: 168125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192951, rend_intergenic: 183718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194502, rend_intergenic: 193582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207783, rend_intergenic: 205047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218367, rend_intergenic: 210767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218407
-exon list size: 393


building trellis

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99.5    
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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 4809, rend_intergenic: 2952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73347, rend_intergenic: 71361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76802, rend_intergenic: 73610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85602, rend_intergenic: 76907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106699, rend_intergenic: 104652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120415, rend_intergenic: 115925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129452, rend_intergenic: 121088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137434, rend_intergenic: 133027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149854, rend_intergenic: 141806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155056, rend_intergenic: 152224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161843, rend_intergenic: 159285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166785, rend_intergenic: 162589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173877, rend_intergenic: 168125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192951, rend_intergenic: 183718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194502, rend_intergenic: 193582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207783, rend_intergenic: 205047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218367, rend_intergenic: 210767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support