-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_1652692-1849998

-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_18625.p1
Valid prediction for Augustus_model.g26518.t1
Couldn't classify 154504, 154537
Couldn't classify 161363, 161488
Sorry, prediction pasa_asmbl_18632.p1 fails validation.
(ACC)	 GC	154504-154537	GT	AGG
(GCC)	 AG	156506-156765	GT	AGG
(GAG)	 AG	156955-157125	GT	AGG
(GAC)	 AG	157544-157673	GT	AGG
(TGC)	 AG	158149-158256	GT	AGG
(GCC)	 AG	159159-159298	GT	TGG
(AAC)	 AG	160223-160383	GT	AGG
(CCC)	 AG	160833-160972	GT	CTG
(GTG)	 AG	161137-161255	GT	AGG
(CTG)	 AG	161363-161488	GT	GGG
-recovered pasa_asmbl_18632.p1, internal, 156506, 156765
-recovered pasa_asmbl_18632.p1, internal, 156955, 157125
-recovered pasa_asmbl_18632.p1, internal, 157544, 157673
-recovered pasa_asmbl_18632.p1, internal, 158149, 158256
-recovered pasa_asmbl_18632.p1, internal, 159159, 159298
-recovered pasa_asmbl_18632.p1, internal, 160223, 160383
-recovered pasa_asmbl_18632.p1, internal, 160833, 160972
-recovered pasa_asmbl_18632.p1, internal, 161137, 161255
-recovered pasa_asmbl_18632.p1, internal, 161363, 161488
Valid prediction for snap_scaffold_17-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_39797-T1
Valid prediction for GlimmerHMM_glimmerT_39801-T1
Valid prediction for CodingQuarry_transcript_21872-T1
Valid prediction for CodingQuarry_transcript_21870-T1
Valid prediction for CodingQuarry_transcript_21868-T1
Valid prediction for CodingQuarry_transcript_21865-T1
Valid prediction for HiQ_model.g26520.t1
Valid prediction for CodingQuarry_transcript_21873-T1
Valid prediction for GlimmerHMM_glimmerT_39791-T1
Valid prediction for GlimmerHMM_glimmerT_39788-T1
Valid prediction for snap_scaffold_17-snap.346-T1
Valid prediction for snap_scaffold_17-snap.355-T1
Valid prediction for GlimmerHMM_glimmerT_39800-T1
Valid prediction for Augustus_model.g26513.t1
Valid prediction for GlimmerHMM_glimmerT_39814-T1
Valid prediction for HiQ_model.g26511.t1
Valid prediction for snap_scaffold_17-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_39811-T1
Valid prediction for snap_scaffold_17-snap.370-T1
Valid prediction for snap_scaffold_17-snap.372-T1
Valid prediction for snap_scaffold_17-snap.367-T1
Valid prediction for snap_scaffold_17-snap.368-T1
Valid prediction for snap_scaffold_17-snap.376-T1
Valid prediction for GlimmerHMM_glimmerT_39798-T1
Valid prediction for Augustus_model.g26515.t1
Valid prediction for CodingQuarry_transcript_21871-T1
Valid prediction for snap_scaffold_17-snap.349-T1
Valid prediction for GlimmerHMM_glimmerT_39815-T1
Valid prediction for snap_scaffold_17-snap.351-T1
Valid prediction for GlimmerHMM_glimmerT_39813-T1
Valid prediction for CodingQuarry_transcript_21869-T1
Valid prediction for snap_scaffold_17-snap.356-T1
Valid prediction for snap_scaffold_17-snap.382-T1
Couldn't classify 154164, 154269
Sorry, prediction pasa_asmbl_18630.p1 fails validation.
(ATG)	 GG	152381-152457	GT	CGG
(GGT)	 AG	152662-152817	GT	AGG
(GCA)	 AG	153009-153105	GT	AGG
(GTC)	 AG	153247-153350	GT	AGG
(ATT)	 AG	153516-153694	GT	TGG
(GAC)	 AG	153836-153995	GT	AGG
(GTA)	 AG	154164-154269	GC	CCG
-recovered pasa_asmbl_18630.p1, initial, 152381, 152457
-recovered pasa_asmbl_18630.p1, terminal, 152662, 152817
-recovered pasa_asmbl_18630.p1, internal, 152662, 152817
-recovered pasa_asmbl_18630.p1, internal, 153009, 153105
-recovered pasa_asmbl_18630.p1, internal, 153247, 153350
-recovered pasa_asmbl_18630.p1, internal, 153516, 153694
-recovered pasa_asmbl_18630.p1, internal, 153836, 153995
-recovered pasa_asmbl_18630.p1, internal, 154164, 154269
Valid prediction for Augustus_model.g26517.t1
Valid prediction for snap_scaffold_17-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_39802-T1
Valid prediction for HiQ_model.g26519.t1
Valid prediction for GlimmerHMM_glimmerT_39808-T1
Valid prediction for HiQ_model.g26505.t1
Valid prediction for pasa_asmbl_18620.p1
Valid prediction for snap_scaffold_17-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_39804-T1
Valid prediction for Augustus_model.g26514.t1
Valid prediction for snap_scaffold_17-snap.366-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 CodingQuarry_transcript_21866-T1
Valid prediction for snap_scaffold_17-snap.347-T1
Valid prediction for pasa_asmbl_17731.p1
Valid prediction for snap_scaffold_17-snap.373-T1
Valid prediction for snap_scaffold_17-snap.361-T1
Valid prediction for snap_scaffold_17-snap.350-T1
Valid prediction for snap_scaffold_17-snap.375-T1
Valid prediction for snap_scaffold_17-snap.360-T1
Valid prediction for snap_scaffold_17-snap.352-T1
Valid prediction for snap_scaffold_17-snap.380-T1
Valid prediction for GlimmerHMM_glimmerT_39795-T1
Valid prediction for GlimmerHMM_glimmerT_39796-T1
Valid prediction for GlimmerHMM_glimmerT_39799-T1
Valid prediction for snap_scaffold_17-snap.354-T1
Valid prediction for GlimmerHMM_glimmerT_39803-T1
Valid prediction for snap_scaffold_17-snap.374-T1
Valid prediction for snap_scaffold_17-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_39787-T1
Couldn't classify 78356, 78536
Couldn't classify 81053, 81690
Sorry, prediction pasa_asmbl_17735.p1 fails validation.
(GAG)	 CA	78356-78536	GT	TGG
(GGC)	 AG	80707-80886	GT	TGG
(GTT)	 AG	81053-81690	GC	TCG
-recovered pasa_asmbl_17735.p1, internal, 80707, 80886
-recovered pasa_asmbl_17735.p1, internal, 81053, 81690
Valid prediction for snap_scaffold_17-snap.348-T1
Valid prediction for snap_scaffold_17-snap.358-T1
Valid prediction for GlimmerHMM_glimmerT_39807-T1
Valid prediction for snap_scaffold_17-snap.345-T1
Valid prediction for GlimmerHMM_glimmerT_39790-T1
Valid prediction for Augustus_model.g26506.t1
Couldn't classify 81874, 82179
Sorry, prediction pasa_asmbl_17734.p1 fails validation.
(AAC)	 CC	81874-82179	GT	CGG
(GCT)	 AG	82498-82597	GT	TGG
(CCA)	 AG	82924-83135	GT	AGG
(TAC)	 AG	83235-83618	TT	GAT
-recovered pasa_asmbl_17734.p1, terminal, 83235, 83618
-recovered pasa_asmbl_17734.p1, internal, 82498, 82597
-recovered pasa_asmbl_17734.p1, internal, 82924, 83135
Valid prediction for snap_scaffold_17-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_39793-T1
Valid prediction for GlimmerHMM_glimmerT_39810-T1
Valid prediction for GlimmerHMM_glimmerT_39812-T1
Valid prediction for snap_scaffold_17-snap.362-T1
Valid prediction for GlimmerHMM_glimmerT_39789-T1
Valid prediction for CodingQuarry_transcript_21867-T1
Couldn't classify 132627, 132742
Sorry, prediction pasa_asmbl_17728.p2 fails validation.
(ATG)	 AG	131331-131495	GT	AGG
(AAG)	 AG	131749-131820	GT	AGG
(GGA)	 AG	131985-132120	GT	CGG
(GTG)	 AG	132269-132391	GT	AGG
(ACA)	 AG	132627-132742	AT	AGA
-recovered pasa_asmbl_17728.p2, initial, 131331, 131495
-recovered pasa_asmbl_17728.p2, internal, 131331, 131495
-recovered pasa_asmbl_17728.p2, internal, 131749, 131820
-recovered pasa_asmbl_17728.p2, internal, 131985, 132120
-recovered pasa_asmbl_17728.p2, internal, 132269, 132391
Valid prediction for snap_scaffold_17-snap.364-T1
Valid prediction for snap_scaffold_17-snap.378-T1
Valid prediction for Augustus_model.g26508.t1
Valid prediction for GlimmerHMM_glimmerT_39806-T1
Valid prediction for Augustus_model.g26516.t1
Valid prediction for HiQ_model.g26512.t1
Valid prediction for snap_scaffold_17-snap.353-T1
Valid prediction for snap_scaffold_17-snap.384-T1
Valid prediction for GlimmerHMM_glimmerT_39792-T1
Valid prediction for GlimmerHMM_glimmerT_39805-T1
Valid prediction for HiQ_model.g26510.t1
Valid prediction for GlimmerHMM_glimmerT_39809-T1
Valid prediction for Augustus_model.g26509.t1
Valid prediction for snap_scaffold_17-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_39794-T1
Valid prediction for Augustus_model.g26507.t1
Valid prediction for snap_scaffold_17-snap.371-T1
Couldn't classify 67417, 67734
Sorry, prediction pasa_asmbl_17736.p2 fails validation.
(ATG)	 GC	67417-67734	CC	AAC
Valid prediction for snap_scaffold_17-snap.381-T1
Valid prediction for snap_scaffold_17-snap.357-T1
Couldn't classify 132847, 132989
Sorry, prediction pasa_asmbl_18477.p1 fails validation.
(TTC)	 CT	132847-132989	GT	GTG
(GAA)	 AG	133157-133321	GT	GAG
(GAT)	 AG	134292-134409	GT	AGG
(CCA)	 AG	135845-135949	GT	TGG
(GGG)	 AG	136182-136215	GT	AAG
(GTA)	 AG	136873-136919	TG	GAT
-recovered pasa_asmbl_18477.p1, terminal, 136873, 136919
-recovered pasa_asmbl_18477.p1, internal, 133157, 133321
-recovered pasa_asmbl_18477.p1, internal, 134292, 134409
-recovered pasa_asmbl_18477.p1, internal, 135845, 135949
-recovered pasa_asmbl_18477.p1, internal, 136182, 136215

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19608, rend_intergenic: 12625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26645, rend_intergenic: 23637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57343, rend_intergenic: 53177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60465, rend_intergenic: 58993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77724, rend_intergenic: 67502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85325, rend_intergenic: 81917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96105, rend_intergenic: 85368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116199, rend_intergenic: 113690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122560, rend_intergenic: 116316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129879, rend_intergenic: 129731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133480, rend_intergenic: 130006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151281, rend_intergenic: 148190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161982, rend_intergenic: 151713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175816, rend_intergenic: 166053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184908, rend_intergenic: 176534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196164, rend_intergenic: 186185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197307
-exon list size: 399


building trellis

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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 19608, rend_intergenic: 12625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26645, rend_intergenic: 23637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57343, rend_intergenic: 53177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60465, rend_intergenic: 58993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77724, rend_intergenic: 67502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85325, rend_intergenic: 81917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96105, rend_intergenic: 85368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116199, rend_intergenic: 113690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122560, rend_intergenic: 116316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129879, rend_intergenic: 129731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133480, rend_intergenic: 130006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151281, rend_intergenic: 148190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161982, rend_intergenic: 151713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175816, rend_intergenic: 166053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184908, rend_intergenic: 176534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196164, rend_intergenic: 186185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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