-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_13341610-13580046

-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_34997-T1
Valid prediction for snap_scaffold_14-snap.2756-T1
Valid prediction for HiQ_model.g23410.t1
Valid prediction for snap_scaffold_14-snap.2785-T1
Valid prediction for GlimmerHMM_glimmerT_35014-T1
Valid prediction for snap_scaffold_14-snap.2772-T1
Valid prediction for snap_scaffold_14-snap.2776-T1
Valid prediction for snap_scaffold_14-snap.2780-T1
Valid prediction for snap_scaffold_14-snap.2743-T1
Couldn't classify 96464, 96946
Couldn't classify 98161, 98198
Sorry, prediction pasa_asmbl_12476.p1 fails validation.
(AGT)	 AC	96464-96946	GT	CGG
(TTG)	 AG	97137-97410	GT	AGG
(ACC)	 AG	98161-98198	GG	GGG
-recovered pasa_asmbl_12476.p1, internal, 97137, 97410
Valid prediction for GlimmerHMM_glimmerT_34996-T1
Valid prediction for snap_scaffold_14-snap.2783-T1
Valid prediction for snap_scaffold_14-snap.2775-T1
Valid prediction for snap_scaffold_14-snap.2753-T1
Valid prediction for snap_scaffold_14-snap.2765-T1
Valid prediction for Augustus_model.g23415.t1
Valid prediction for snap_scaffold_14-snap.2768-T1
Valid prediction for snap_scaffold_14-snap.2769-T1
Valid prediction for snap_scaffold_14-snap.2786-T1
Valid prediction for pasa_asmbl_12480.p1
Valid prediction for snap_scaffold_14-snap.2762-T1
Valid prediction for Augustus_model.g23403.t1
Valid prediction for snap_scaffold_14-snap.2778-T1
Valid prediction for GlimmerHMM_glimmerT_35000-T1
Valid prediction for GlimmerHMM_glimmerT_35005-T1
Valid prediction for GlimmerHMM_glimmerT_34995-T1
Valid prediction for Augustus_model.g23408.t1
Valid prediction for GlimmerHMM_glimmerT_35011-T1
Valid prediction for GlimmerHMM_glimmerT_35009-T1
Valid prediction for GlimmerHMM_glimmerT_34998-T1
Couldn't classify 154998, 155148
Couldn't classify 156063, 156168
Sorry, prediction pasa_asmbl_12744.p1 fails validation.
(CCT)	 TC	154998-155148	GT	AGG
(GAG)	 AG	155342-155465	GT	CGG
(AGG)	 AG	156063-156168	AC	GAA
-recovered pasa_asmbl_12744.p1, internal, 155342, 155465
Valid prediction for Augustus_model.g23409.t1
Valid prediction for GlimmerHMM_glimmerT_35007-T1
Valid prediction for snap_scaffold_14-snap.2790-T1
Valid prediction for snap_scaffold_14-snap.2770-T1
Valid prediction for snap_scaffold_14-snap.2746-T1
Valid prediction for Augustus_model.g23412.t1
Valid prediction for snap_scaffold_14-snap.2794-T1
Valid prediction for snap_scaffold_14-snap.2763-T1
Valid prediction for GlimmerHMM_glimmerT_35001-T1
Valid prediction for snap_scaffold_14-snap.2787-T1
Couldn't classify 98280, 98356
Sorry, prediction pasa_asmbl_12477.p1 fails validation.
(CTG)	 TG	98280-98356	GT	AGG
(GTC)	 AG	98923-99107	GT	AAG
(ACT)	 AG	99411-99506	GT	GGG
(GGG)	 AG	99701-99859	GT	AGG
(AGT)	 AG	100670-100763	GT	AGG
(GCG)	 AG	100911-100974	CC	AAC
-recovered pasa_asmbl_12477.p1, terminal, 100911, 100974
-recovered pasa_asmbl_12477.p1, internal, 98923, 99107
-recovered pasa_asmbl_12477.p1, internal, 99411, 99506
-recovered pasa_asmbl_12477.p1, internal, 99701, 99859
-recovered pasa_asmbl_12477.p1, internal, 100670, 100763
Valid prediction for GlimmerHMM_glimmerT_35003-T1
Valid prediction for snap_scaffold_14-snap.2793-T1
Valid prediction for GlimmerHMM_glimmerT_34988-T1
Valid prediction for GlimmerHMM_glimmerT_35002-T1
Valid prediction for GlimmerHMM_glimmerT_34993-T1
Valid prediction for Augustus_model.g23406.t1
Valid prediction for CodingQuarry_transcript_15911-T1
Valid prediction for Augustus_model.g23413.t1
Valid prediction for CodingQuarry_transcript_15909-T1
Valid prediction for Augustus_model.g23405.t1
Valid prediction for snap_scaffold_14-snap.2766-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_34986-T1
Valid prediction for CodingQuarry_transcript_15908-T1
Valid prediction for snap_scaffold_14-snap.2758-T1
Valid prediction for GlimmerHMM_glimmerT_34999-T1
Valid prediction for Augustus_model.g23397.t1
Valid prediction for snap_scaffold_14-snap.2748-T1
Valid prediction for pasa_asmbl_13637.p1
Valid prediction for snap_scaffold_14-snap.2751-T1
Valid prediction for snap_scaffold_14-snap.2744-T1
Valid prediction for snap_scaffold_14-snap.2760-T1
Valid prediction for snap_scaffold_14-snap.2779-T1
Valid prediction for Augustus_model.g23398.t1
Valid prediction for snap_scaffold_14-snap.2788-T1
Valid prediction for snap_scaffold_14-snap.2782-T1
Valid prediction for snap_scaffold_14-snap.2774-T1
Valid prediction for snap_scaffold_14-snap.2764-T1
Valid prediction for snap_scaffold_14-snap.2742-T1
Couldn't classify 192733, 192758
Sorry, prediction pasa_asmbl_13844.p1 fails validation.
(ATG)	 CA	191276-191340	GT	AAG
(GAA)	 AG	191631-191749	GT	AGG
(GGG)	 AG	191914-192069	GT	AGG
(AGG)	 AG	192172-192276	GT	AGG
(GTC)	 AG	192381-192593	GC	AGG
(GAA)	 AG	192733-192758	CA	TGC
-recovered pasa_asmbl_13844.p1, initial, 191276, 191340
add_exon() Sorry, pasa_asmbl_13844.p1 192172-192276-terminal-1 is invalid.
-recovered pasa_asmbl_13844.p1, terminal, 192172, 192276
-recovered pasa_asmbl_13844.p1, internal, 191631, 191749
-recovered pasa_asmbl_13844.p1, internal, 191914, 192069
-recovered pasa_asmbl_13844.p1, internal, 192172, 192276
-recovered pasa_asmbl_13844.p1, internal, 192381, 192593
Valid prediction for snap_scaffold_14-snap.2781-T1
Valid prediction for Augustus_model.g23399.t1
Valid prediction for GlimmerHMM_glimmerT_35006-T1
Valid prediction for HiQ_model.g23402.t1
Valid prediction for snap_scaffold_14-snap.2777-T1
Valid prediction for Augustus_model.g23414.t1
Valid prediction for snap_scaffold_14-snap.2747-T1
Valid prediction for snap_scaffold_14-snap.2752-T1
Valid prediction for snap_scaffold_14-snap.2757-T1
Valid prediction for GlimmerHMM_glimmerT_34989-T1
Couldn't classify 237095, 237423
Sorry, prediction pasa_asmbl_13635.p1 fails validation.
(ACA)	 TC	237095-237423	GT	AGG
(CAA)	 AG	237686-238004	AA	AAA
-recovered pasa_asmbl_13635.p1, terminal, 237686, 238004
Valid prediction for snap_scaffold_14-snap.2755-T1
Valid prediction for CodingQuarry_transcript_15906-T1
Valid prediction for Augustus_model.g23404.t1
Valid prediction for HiQ_model.g23407.t1
Valid prediction for GlimmerHMM_glimmerT_34987-T1
Valid prediction for GlimmerHMM_glimmerT_35004-T1
Couldn't classify 192759, 192834
Sorry, prediction pasa_asmbl_13819.p1 fails validation.
(CAC)	 TG	192759-192834	GT	GAG
(GTC)	 AG	193277-193629	CT	AAC
-recovered pasa_asmbl_13819.p1, terminal, 193277, 193629
Valid prediction for GlimmerHMM_glimmerT_34991-T1
Valid prediction for snap_scaffold_14-snap.2791-T1
Valid prediction for snap_scaffold_14-snap.2771-T1
Valid prediction for pasa_asmbl_13640.p1
Valid prediction for snap_scaffold_14-snap.2759-T1
Valid prediction for CodingQuarry_transcript_15907-T1
Valid prediction for snap_scaffold_14-snap.2745-T1
Valid prediction for snap_scaffold_14-snap.2749-T1
Valid prediction for GlimmerHMM_glimmerT_35008-T1
Valid prediction for snap_scaffold_14-snap.2789-T1
Valid prediction for GlimmerHMM_glimmerT_34990-T1
Valid prediction for snap_scaffold_14-snap.2767-T1
Valid prediction for HiQ_model.g23401.t1
Valid prediction for snap_scaffold_14-snap.2773-T1
Valid prediction for snap_scaffold_14-snap.2754-T1
Valid prediction for GlimmerHMM_glimmerT_34994-T1
Valid prediction for GlimmerHMM_glimmerT_35010-T1
Valid prediction for Augustus_model.g23411.t1
Valid prediction for GlimmerHMM_glimmerT_35013-T1
Valid prediction for snap_scaffold_14-snap.2761-T1
Valid prediction for GlimmerHMM_glimmerT_34992-T1
Valid prediction for snap_scaffold_14-snap.2750-T1
Valid prediction for snap_scaffold_14-snap.2792-T1
Valid prediction for GlimmerHMM_glimmerT_35012-T1
Valid prediction for CodingQuarry_transcript_15910-T1
Valid prediction for snap_scaffold_14-snap.2784-T1
Valid prediction for Augustus_model.g23400.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10554, rend_intergenic: 6971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18600, rend_intergenic: 10994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52407, rend_intergenic: 51121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54463, rend_intergenic: 52819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60045, rend_intergenic: 56242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101202, rend_intergenic: 97133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141659, rend_intergenic: 138649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159114, rend_intergenic: 143689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173628, rend_intergenic: 167728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191860, rend_intergenic: 183963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204341, rend_intergenic: 200427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210238, rend_intergenic: 204757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218167, rend_intergenic: 211874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222909, rend_intergenic: 218828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 238437
-exon list size: 455


building trellis

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99.3    
99.6    
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-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 10554, rend_intergenic: 6971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18600, rend_intergenic: 10994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52407, rend_intergenic: 51121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54463, rend_intergenic: 52819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60045, rend_intergenic: 56242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101202, rend_intergenic: 97133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141659, rend_intergenic: 138649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159114, rend_intergenic: 143689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173628, rend_intergenic: 167728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191860, rend_intergenic: 183963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204341, rend_intergenic: 200427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210238, rend_intergenic: 204757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218167, rend_intergenic: 211874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222909, rend_intergenic: 218828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support