-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_12374423-12611852

-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 snap_scaffold_13-snap.2359-T1
Valid prediction for snap_scaffold_13-snap.2340-T1
Valid prediction for GeneMark_model.56826_t
Valid prediction for GlimmerHMM_glimmerT_33263-T1
Valid prediction for GeneMark_model.56819_t
Valid prediction for snap_scaffold_13-snap.2349-T1
Valid prediction for GeneMark_model.56802_t
Valid prediction for snap_scaffold_13-snap.2330-T1
Valid prediction for GeneMark_model.56821_t
Valid prediction for snap_scaffold_13-snap.2367-T1
Valid prediction for GlimmerHMM_glimmerT_33264-T1
Valid prediction for GlimmerHMM_glimmerT_33280-T1
Valid prediction for GeneMark_model.56800_t
Valid prediction for Augustus_model.g22371.t1
Valid prediction for GeneMark_model.56779_t
Valid prediction for snap_scaffold_13-snap.2351-T1
Valid prediction for Augustus_model.g22377.t1
Valid prediction for snap_scaffold_13-snap.2336-T1
Valid prediction for snap_scaffold_13-snap.2348-T1
Valid prediction for GlimmerHMM_glimmerT_33268-T1
Valid prediction for GeneMark_model.56786_t
Valid prediction for snap_scaffold_13-snap.2354-T1
Valid prediction for GeneMark_model.56816_t
Valid prediction for GlimmerHMM_glimmerT_33265-T1
Valid prediction for snap_scaffold_13-snap.2339-T1
Valid prediction for snap_scaffold_13-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_33281-T1
Valid prediction for snap_scaffold_13-snap.2368-T1
Valid prediction for snap_scaffold_13-snap.2353-T1
Valid prediction for snap_scaffold_13-snap.2352-T1
Valid prediction for snap_scaffold_13-snap.2355-T1
Valid prediction for Augustus_model.g22367.t1
Valid prediction for GlimmerHMM_glimmerT_33266-T1
Valid prediction for GlimmerHMM_glimmerT_33277-T1
Valid prediction for snap_scaffold_13-snap.2342-T1
Valid prediction for snap_scaffold_13-snap.2334-T1
Valid prediction for Augustus_model.g22365.t1
Valid prediction for GeneMark_model.56797_t
Valid prediction for GeneMark_model.56798_t
Valid prediction for snap_scaffold_13-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_33275-T1
Valid prediction for GeneMark_model.56795_t
Valid prediction for Augustus_model.g22376.t1
Valid prediction for Augustus_model.g22373.t1
Valid prediction for GeneMark_model.56793_t
Valid prediction for snap_scaffold_13-snap.2347-T1
Valid prediction for GlimmerHMM_glimmerT_33262-T1
Valid prediction for GeneMark_model.56804_t
Valid prediction for snap_scaffold_13-snap.2356-T1
Valid prediction for snap_scaffold_13-snap.2335-T1
Valid prediction for snap_scaffold_13-snap.2337-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.56791_t
Valid prediction for snap_scaffold_13-snap.2360-T1
Valid prediction for Augustus_model.g22363.t1
Valid prediction for Augustus_model.g22375.t1
Valid prediction for GeneMark_model.56810_t
Valid prediction for snap_scaffold_13-snap.2366-T1
Valid prediction for Augustus_model.g22359.t1
Valid prediction for GeneMark_model.56808_t
Valid prediction for snap_scaffold_13-snap.2363-T1
Valid prediction for GlimmerHMM_glimmerT_33278-T1
Valid prediction for GeneMark_model.56787_t
Valid prediction for GeneMark_model.56823_t
Valid prediction for GeneMark_model.56827_t
Valid prediction for GeneMark_model.56806_t
Valid prediction for Augustus_model.g22364.t1
Valid prediction for GeneMark_model.56824_t
Valid prediction for snap_scaffold_13-snap.2365-T1
Valid prediction for snap_scaffold_13-snap.2341-T1
Valid prediction for snap_scaffold_13-snap.2331-T1
Valid prediction for snap_scaffold_13-snap.2327-T1
Valid prediction for GlimmerHMM_glimmerT_33257-T1
Valid prediction for snap_scaffold_13-snap.2333-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 GeneMark_model.56813_t
Valid prediction for GlimmerHMM_glimmerT_33267-T1
Valid prediction for Augustus_model.g22366.t1
Valid prediction for GeneMark_model.56783_t
Valid prediction for Augustus_model.g22370.t1
Valid prediction for Augustus_model.g22361.t1
Valid prediction for snap_scaffold_13-snap.2361-T1
Valid prediction for GeneMark_model.56817_t
Valid prediction for snap_scaffold_13-snap.2326-T1
Valid prediction for GeneMark_model.56814_t
Valid prediction for GlimmerHMM_glimmerT_33272-T1
Valid prediction for GeneMark_model.56811_t
Valid prediction for snap_scaffold_13-snap.2344-T1
Valid prediction for GeneMark_model.56818_t
Valid prediction for GeneMark_model.56801_t
Valid prediction for GlimmerHMM_glimmerT_33274-T1
Valid prediction for GeneMark_model.56809_t
Valid prediction for GeneMark_model.56780_t
Valid prediction for GeneMark_model.56792_t
Valid prediction for snap_scaffold_13-snap.2345-T1
Valid prediction for snap_scaffold_13-snap.2364-T1
Valid prediction for Augustus_model.g22369.t1
Valid prediction for GlimmerHMM_glimmerT_33261-T1
Valid prediction for GlimmerHMM_glimmerT_33279-T1
Valid prediction for snap_scaffold_13-snap.2362-T1
Valid prediction for GeneMark_model.56789_t
Valid prediction for GeneMark_model.56807_t
Couldn't classify 140062, 140139
Sorry, prediction pasa_asmbl_10102.p1 fails validation.
(AGG)	 TC	140062-140139	GT	AGG
(CAT)	 AG	142371-142532	GT	AGG
(GAC)	 AG	143611-143742	GT	AGG
(GTC)	 AG	144780-144847	GT	CCG
(GTT)	 AG	146818-146945	GT	AGG
(ATG)	 AG	149117-149202	GT	AGG
(TCT)	 AG	149888-149936	GT	TGG
(ACA)	 AG	150373-150476	GT	AGG
(GCC)	 AG	150911-150960	GT	AGG
(ACC)	 AG	151151-151256	AA	AGA
-recovered pasa_asmbl_10102.p1, initial, 149117, 149202
-recovered pasa_asmbl_10102.p1, terminal, 150911, 150960
-recovered pasa_asmbl_10102.p1, terminal, 151151, 151256
-recovered pasa_asmbl_10102.p1, internal, 142371, 142532
-recovered pasa_asmbl_10102.p1, internal, 143611, 143742
-recovered pasa_asmbl_10102.p1, internal, 144780, 144847
-recovered pasa_asmbl_10102.p1, internal, 146818, 146945
-recovered pasa_asmbl_10102.p1, internal, 149117, 149202
-recovered pasa_asmbl_10102.p1, internal, 149888, 149936
-recovered pasa_asmbl_10102.p1, internal, 150373, 150476
-recovered pasa_asmbl_10102.p1, internal, 150911, 150960
Valid prediction for GeneMark_model.56794_t
Valid prediction for GeneMark_model.56812_t
Valid prediction for GlimmerHMM_glimmerT_33260-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g22362.t1
Valid prediction for Augustus_model.g22360.t1
Valid prediction for snap_scaffold_13-snap.2329-T1
Valid prediction for GlimmerHMM_glimmerT_33270-T1
Valid prediction for snap_scaffold_13-snap.2343-T1
Valid prediction for GeneMark_model.56822_t
Valid prediction for snap_scaffold_13-snap.2350-T1
Valid prediction for GeneMark_model.56825_t
Valid prediction for GeneMark_model.56815_t
Valid prediction for GeneMark_model.56820_t
Valid prediction for GlimmerHMM_glimmerT_33258-T1
Valid prediction for GeneMark_model.56784_t
Valid prediction for GlimmerHMM_glimmerT_33259-T1
Valid prediction for snap_scaffold_13-snap.2358-T1
Valid prediction for GlimmerHMM_glimmerT_33276-T1
Valid prediction for snap_scaffold_13-snap.2338-T1
Valid prediction for GeneMark_model.56781_t
Valid prediction for GeneMark_model.56782_t
Valid prediction for snap_scaffold_13-snap.2332-T1
Valid prediction for GlimmerHMM_glimmerT_33273-T1
Valid prediction for snap_scaffold_13-snap.2328-T1
Valid prediction for GeneMark_model.56785_t
Valid prediction for Augustus_model.g22374.t1
Valid prediction for GeneMark_model.56805_t
Valid prediction for GlimmerHMM_glimmerT_33271-T1
Valid prediction for Augustus_model.g22368.t1
Valid prediction for Augustus_model.g22372.t1
Valid prediction for GeneMark_model.56799_t
Valid prediction for GlimmerHMM_glimmerT_33269-T1
Valid prediction for GeneMark_model.56803_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 65332, rend_intergenic: 64231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109817, rend_intergenic: 98489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120447, rend_intergenic: 113415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126597, rend_intergenic: 120756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237430
-exon list size: 602


building trellis

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93.0    
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95.2    
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96.0    
96.2    
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96.5    
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96.9    
97.0    
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98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 65332, rend_intergenic: 64231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109817, rend_intergenic: 98489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120447, rend_intergenic: 113415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126597, rend_intergenic: 120756  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