-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_13152825-13368515

-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 Augustus_model.g20066.t1
Valid prediction for snap_scaffold_12-snap.2427-T1
Valid prediction for snap_scaffold_12-snap.2459-T1
Valid prediction for snap_scaffold_12-snap.2421-T1
Valid prediction for GlimmerHMM_glimmerT_30311-T1
Valid prediction for GlimmerHMM_glimmerT_30294-T1
Valid prediction for GlimmerHMM_glimmerT_30310-T1
Valid prediction for snap_scaffold_12-snap.2435-T1
Valid prediction for snap_scaffold_12-snap.2443-T1
Valid prediction for Augustus_model.g20073.t1
Valid prediction for snap_scaffold_12-snap.2438-T1
Valid prediction for snap_scaffold_12-snap.2451-T1
Valid prediction for GlimmerHMM_glimmerT_30322-T1
Valid prediction for snap_scaffold_12-snap.2447-T1
Valid prediction for GlimmerHMM_glimmerT_30289-T1
Valid prediction for HiQ_model.g20063.t1
Valid prediction for snap_scaffold_12-snap.2454-T1
Valid prediction for snap_scaffold_12-snap.2458-T1
Valid prediction for snap_scaffold_12-snap.2449-T1
Valid prediction for snap_scaffold_12-snap.2433-T1
Valid prediction for GlimmerHMM_glimmerT_30319-T1
Valid prediction for GlimmerHMM_glimmerT_30317-T1
Valid prediction for snap_scaffold_12-snap.2441-T1
Couldn't classify 76237, 76732
Sorry, prediction pasa_asmbl_8038.p1 fails validation.
(TCC)	 TG	76237-76732	GT	TCG
(TCC)	 AG	76831-76970	GT	TGG
(GCA)	 AG	77137-77220	GT	GGG
(CTG)	 AG	77379-77621	CC	GAC
-recovered pasa_asmbl_8038.p1, terminal, 77379, 77621
-recovered pasa_asmbl_8038.p1, internal, 76831, 76970
-recovered pasa_asmbl_8038.p1, internal, 77137, 77220
Valid prediction for snap_scaffold_12-snap.2444-T1
Valid prediction for snap_scaffold_12-snap.2426-T1
Valid prediction for Augustus_model.g20053.t1
Valid prediction for snap_scaffold_12-snap.2446-T1
Valid prediction for GlimmerHMM_glimmerT_30302-T1
Valid prediction for GlimmerHMM_glimmerT_30296-T1
Valid prediction for snap_scaffold_12-snap.2452-T1
Valid prediction for Augustus_model.g20059.t1
Valid prediction for GlimmerHMM_glimmerT_30293-T1
Valid prediction for GlimmerHMM_glimmerT_30297-T1
Valid prediction for GlimmerHMM_glimmerT_30305-T1
Valid prediction for Augustus_model.g20071.t1
Valid prediction for GlimmerHMM_glimmerT_30292-T1
Valid prediction for snap_scaffold_12-snap.2432-T1
Valid prediction for snap_scaffold_12-snap.2453-T1
Valid prediction for GlimmerHMM_glimmerT_30320-T1
Valid prediction for Augustus_model.g20058.t1
Valid prediction for snap_scaffold_12-snap.2440-T1
Valid prediction for snap_scaffold_12-snap.2428-T1
Valid prediction for GlimmerHMM_glimmerT_30313-T1
Valid prediction for GlimmerHMM_glimmerT_30299-T1
Valid prediction for snap_scaffold_12-snap.2456-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_30298-T1
Valid prediction for GlimmerHMM_glimmerT_30312-T1
Valid prediction for snap_scaffold_12-snap.2436-T1
Valid prediction for GlimmerHMM_glimmerT_30314-T1
Valid prediction for Augustus_model.g20072.t1
Couldn't classify 39305, 39537
Sorry, prediction pasa_asmbl_8936.p1 fails validation.
(AGT)	 AG	39305-39537	GT	AGG
(CGG)	 AG	40409-40565	GT	AGG
(GAA)	 AG	41295-41358	GT	CGG
(GAA)	 AG	42182-42237	GT	AGG
(TCT)	 AG	42623-42679	TA	GAT
-recovered pasa_asmbl_8936.p1, terminal, 42623, 42679
-recovered pasa_asmbl_8936.p1, internal, 39305, 39537
-recovered pasa_asmbl_8936.p1, internal, 40409, 40565
-recovered pasa_asmbl_8936.p1, internal, 41295, 41358
-recovered pasa_asmbl_8936.p1, internal, 42182, 42237
Valid prediction for GlimmerHMM_glimmerT_30321-T1
Valid prediction for snap_scaffold_12-snap.2430-T1
Valid prediction for Augustus_model.g20068.t1
Couldn't classify 129690, 129858
Couldn't classify 131883, 132169
Sorry, prediction pasa_asmbl_8932.p1 fails validation.
(GAT)	 CA	129690-129858	GT	CTG
(CGG)	 AG	130142-130328	GT	AGG
(TGA)	 AG	130787-131009	GT	AGG
(GTC)	 AG	131126-131213	GT	AGG
(GCC)	 AG	131455-131520	GT	TGG
(CCC)	 AG	131883-132169	GT	AGG
-recovered pasa_asmbl_8932.p1, internal, 130142, 130328
-recovered pasa_asmbl_8932.p1, internal, 130787, 131009
-recovered pasa_asmbl_8932.p1, internal, 131126, 131213
-recovered pasa_asmbl_8932.p1, internal, 131455, 131520
-recovered pasa_asmbl_8932.p1, internal, 131883, 132169
Valid prediction for snap_scaffold_12-snap.2439-T1
Valid prediction for snap_scaffold_12-snap.2445-T1
Valid prediction for Augustus_model.g20057.t1
Valid prediction for Augustus_model.g20061.t1
Valid prediction for GlimmerHMM_glimmerT_30316-T1
Valid prediction for GlimmerHMM_glimmerT_30290-T1
Valid prediction for Augustus_model.g20064.t1
Valid prediction for CodingQuarry_transcript_10444-T1
Valid prediction for CodingQuarry_transcript_10446-T1
Valid prediction for snap_scaffold_12-snap.2429-T1
Valid prediction for GlimmerHMM_glimmerT_30303-T1
Valid prediction for snap_scaffold_12-snap.2423-T1
Valid prediction for GlimmerHMM_glimmerT_30315-T1
Valid prediction for snap_scaffold_12-snap.2450-T1
Valid prediction for GlimmerHMM_glimmerT_30307-T1
Valid prediction for GlimmerHMM_glimmerT_30318-T1
Valid prediction for GlimmerHMM_glimmerT_30304-T1
Valid prediction for Augustus_model.g20054.t1
Couldn't classify 89624, 89759
Couldn't classify 91180, 91358
Sorry, prediction pasa_asmbl_9253.p1 fails validation.
(GAC)	 CG	89624-89759	GT	GGG
(GTT)	 AG	91180-91358	AG	CCA
Valid prediction for Augustus_model.g20069.t1
Couldn't classify 133538, 133670
Sorry, prediction pasa_asmbl_8931.p3 fails validation.
(CAG)	 CA	133538-133670	GT	GGG
(GTG)	 AG	134299-134609	GG	GAG
-recovered pasa_asmbl_8931.p3, terminal, 134299, 134609
Valid prediction for GlimmerHMM_glimmerT_30301-T1
Valid prediction for HiQ_model.g20062.t1
Valid prediction for snap_scaffold_12-snap.2424-T1
Valid prediction for Augustus_model.g20060.t1
Valid prediction for Augustus_model.g20065.t1
Valid prediction for snap_scaffold_12-snap.2431-T1
Valid prediction for snap_scaffold_12-snap.2460-T1
Valid prediction for HiQ_model.g20070.t1
Valid prediction for CodingQuarry_transcript_10443-T1
Valid prediction for GlimmerHMM_glimmerT_30295-T1
Valid prediction for HiQ_model.g20055.t1
Valid prediction for pasa_asmbl_8930.p1
Valid prediction for GlimmerHMM_glimmerT_30300-T1
Valid prediction for snap_scaffold_12-snap.2448-T1
Valid prediction for CodingQuarry_transcript_10445-T1
Valid prediction for GlimmerHMM_glimmerT_30308-T1
Valid prediction for snap_scaffold_12-snap.2442-T1
Valid prediction for snap_scaffold_12-snap.2457-T1
Valid prediction for GlimmerHMM_glimmerT_30291-T1
Valid prediction for snap_scaffold_12-snap.2455-T1
Valid prediction for pasa_asmbl_8928.p1
Valid prediction for snap_scaffold_12-snap.2425-T1
Valid prediction for HiQ_model.g20056.t1
Valid prediction for snap_scaffold_12-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_30309-T1
Valid prediction for GlimmerHMM_glimmerT_30306-T1
Valid prediction for snap_scaffold_12-snap.2434-T1
Valid prediction for snap_scaffold_12-snap.2437-T1
Valid prediction for Augustus_model.g20067.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21036, rend_intergenic: 16037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47777, rend_intergenic: 32052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56248, rend_intergenic: 53843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72226, rend_intergenic: 58182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90681, rend_intergenic: 82069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118387, rend_intergenic: 96646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128221, rend_intergenic: 119972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155898, rend_intergenic: 129426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173544, rend_intergenic: 158665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206182, rend_intergenic: 197131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215691
-exon list size: 395


building trellis

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99.0    
99.2    
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99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 21036, rend_intergenic: 16037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47777, rend_intergenic: 32052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56248, rend_intergenic: 53843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72226, rend_intergenic: 58182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90681, rend_intergenic: 82069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118387, rend_intergenic: 96646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128221, rend_intergenic: 119972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155898, rend_intergenic: 129426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173544, rend_intergenic: 158665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206182, rend_intergenic: 197131  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