-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_1422725-1598750

-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_58160-T1
Valid prediction for CodingQuarry_transcript_43536-T1
Valid prediction for Augustus_model.g38507.t1
Valid prediction for snap_scaffold_28-snap.366-T1
Valid prediction for snap_scaffold_28-snap.342-T1
Valid prediction for snap_scaffold_28-snap.352-T1
Valid prediction for snap_scaffold_28-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_58158-T1
Valid prediction for snap_scaffold_28-snap.351-T1
Valid prediction for Augustus_model.g38510.t1
Valid prediction for snap_scaffold_28-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_58146-T1
Valid prediction for snap_scaffold_28-snap.354-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.357-T1
Valid prediction for CodingQuarry_transcript_43534-T1
Valid prediction for GlimmerHMM_glimmerT_58150-T1
Valid prediction for snap_scaffold_28-snap.344-T1
Valid prediction for GlimmerHMM_glimmerT_58154-T1
Valid prediction for snap_scaffold_28-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_58162-T1
Valid prediction for GlimmerHMM_glimmerT_58152-T1
Valid prediction for GlimmerHMM_glimmerT_58161-T1
Valid prediction for snap_scaffold_28-snap.340-T1
Valid prediction for GlimmerHMM_glimmerT_58148-T1
Valid prediction for snap_scaffold_28-snap.346-T1
Valid prediction for snap_scaffold_28-snap.359-T1
Valid prediction for pasa_asmbl_37310.p1
Valid prediction for snap_scaffold_28-snap.328-T1
Valid prediction for snap_scaffold_28-snap.349-T1
Valid prediction for Augustus_model.g38504.t1
Valid prediction for HiQ_model.g38512.t1
Valid prediction for snap_scaffold_28-snap.335-T1
Valid prediction for snap_scaffold_28-snap.369-T1
Valid prediction for snap_scaffold_28-snap.338-T1
Valid prediction for snap_scaffold_28-snap.358-T1
Valid prediction for GlimmerHMM_glimmerT_58166-T1
Valid prediction for Augustus_model.g38509.t1
Couldn't classify 158282, 158537
Couldn't classify 160748, 160812
Sorry, prediction pasa_asmbl_37313.p1 fails validation.
(CCG)	 CT	158282-158537	GT	AGG
(ACA)	 AG	158699-158896	GT	AGG
(AGT)	 AG	159057-159158	GT	TGG
(AGA)	 AG	159267-159365	GT	TGG
(CTC)	 AG	159751-159833	GT	AGG
(TAT)	 AG	160162-160262	GT	AGG
(AAA)	 AG	160459-160565	GT	GTG
(GCA)	 AG	160748-160812	AC	CCA
-recovered pasa_asmbl_37313.p1, internal, 158699, 158896
-recovered pasa_asmbl_37313.p1, internal, 159057, 159158
-recovered pasa_asmbl_37313.p1, internal, 159267, 159365
-recovered pasa_asmbl_37313.p1, internal, 159751, 159833
-recovered pasa_asmbl_37313.p1, internal, 160162, 160262
-recovered pasa_asmbl_37313.p1, internal, 160459, 160565
Valid prediction for CodingQuarry_transcript_43535-T1
Valid prediction for GlimmerHMM_glimmerT_58164-T1
Valid prediction for snap_scaffold_28-snap.327-T1
Valid prediction for Augustus_model.g38506.t1
Valid prediction for GlimmerHMM_glimmerT_58167-T1
Valid prediction for Augustus_model.g38498.t1
Valid prediction for pasa_asmbl_37315.p1
Valid prediction for snap_scaffold_28-snap.336-T1
Valid prediction for snap_scaffold_28-snap.333-T1
Couldn't classify 156646, 157083
Couldn't classify 157372, 157524
Sorry, prediction pasa_asmbl_37312.p1 fails validation.
(CGC)	 CC	156646-157083	GT	AGG
(GAG)	 AG	157372-157524	AC	AGA
Valid prediction for GlimmerHMM_glimmerT_58170-T1
Valid prediction for snap_scaffold_28-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_58151-T1
Valid prediction for snap_scaffold_28-snap.348-T1
Valid prediction for GlimmerHMM_glimmerT_58147-T1
Valid prediction for snap_scaffold_28-snap.331-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 Augustus_model.g38499.t1
Valid prediction for GlimmerHMM_glimmerT_58165-T1
Valid prediction for snap_scaffold_28-snap.325-T1
Valid prediction for snap_scaffold_28-snap.350-T1
Valid prediction for snap_scaffold_28-snap.367-T1
Valid prediction for Augustus_model.g38500.t1
Valid prediction for snap_scaffold_28-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_58143-T1
Valid prediction for snap_scaffold_28-snap.329-T1
Couldn't classify 142602, 142727
Couldn't classify 145609, 145679
Sorry, prediction pasa_asmbl_37992.p1 fails validation.
(TCC)	 GC	142602-142727	GT	AGG
(TCA)	 AG	143232-143403	GT	AGG
(GCC)	 AG	145609-145679	GG	AAG
-recovered pasa_asmbl_37992.p1, internal, 143232, 143403
Valid prediction for GlimmerHMM_glimmerT_58169-T1
Valid prediction for snap_scaffold_28-snap.362-T1
Valid prediction for GlimmerHMM_glimmerT_58157-T1
Valid prediction for snap_scaffold_28-snap.339-T1
Couldn't classify 171089, 171167
Couldn't classify 173627, 173683
Sorry, prediction pasa_asmbl_37988.p1 fails validation.
(AAC)	 AC	171089-171167	GT	AGG
(GGA)	 AG	171487-171552	GT	AGG
(CTG)	 AG	171715-171771	GT	AGG
(GCA)	 AG	171914-172058	GT	TGG
(GTC)	 AG	172687-172761	GT	AAG
(GAA)	 AG	173373-173451	GT	AGG
(ACG)	 AG	173627-173683	AC	CCA
-recovered pasa_asmbl_37988.p1, internal, 171487, 171552
-recovered pasa_asmbl_37988.p1, internal, 171715, 171771
-recovered pasa_asmbl_37988.p1, internal, 171914, 172058
-recovered pasa_asmbl_37988.p1, internal, 172687, 172761
-recovered pasa_asmbl_37988.p1, internal, 173373, 173451
Couldn't classify 159681, 159800
Sorry, prediction pasa_asmbl_37989.p1 fails validation.
(CTG)	 AG	159681-159800	GT	CCG
(TGG)	 AG	161205-161355	GT	CGG
(GAA)	 AG	161515-161707	GT	AGG
(CCA)	 AG	162955-163066	GT	AGG
(CCC)	 AG	163246-163333	GT	AGG
(ATG)	 AG	164530-164621	GT	AGG
(GAT)	 AG	167065-167070	TC	AAT
add_exon() Sorry, pasa_asmbl_37989.p1 164530-164621-initial-1 is invalid.
-recovered pasa_asmbl_37989.p1, initial, 164530, 164621
-recovered pasa_asmbl_37989.p1, terminal, 167065, 167070
-recovered pasa_asmbl_37989.p1, internal, 159681, 159800
-recovered pasa_asmbl_37989.p1, internal, 161205, 161355
-recovered pasa_asmbl_37989.p1, internal, 161515, 161707
-recovered pasa_asmbl_37989.p1, internal, 162955, 163066
-recovered pasa_asmbl_37989.p1, internal, 163246, 163333
-recovered pasa_asmbl_37989.p1, internal, 164530, 164621
Valid prediction for snap_scaffold_28-snap.324-T1
Valid prediction for snap_scaffold_28-snap.347-T1
Valid prediction for pasa_asmbl_37994.p1
Valid prediction for Augustus_model.g38494.t1
Valid prediction for snap_scaffold_28-snap.337-T1
Valid prediction for snap_scaffold_28-snap.345-T1
Valid prediction for Augustus_model.g38508.t1
Valid prediction for Augustus_model.g38495.t1
Valid prediction for Augustus_model.g38505.t1
Valid prediction for Augustus_model.g38502.t1
Valid prediction for GlimmerHMM_glimmerT_58159-T1
Valid prediction for Augustus_model.g38493.t1
Valid prediction for snap_scaffold_28-snap.330-T1
Valid prediction for Augustus_model.g38491.t1
Valid prediction for HiQ_model.g38511.t1
Valid prediction for Augustus_model.g38490.t1
Valid prediction for GlimmerHMM_glimmerT_58163-T1
Valid prediction for snap_scaffold_28-snap.364-T1
Valid prediction for GlimmerHMM_glimmerT_58153-T1
Valid prediction for snap_scaffold_28-snap.341-T1
Valid prediction for GlimmerHMM_glimmerT_58156-T1
Valid prediction for Augustus_model.g38496.t1
Valid prediction for Augustus_model.g38497.t1
Valid prediction for snap_scaffold_28-snap.323-T1
Valid prediction for snap_scaffold_28-snap.334-T1
Valid prediction for snap_scaffold_28-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_58168-T1
Valid prediction for snap_scaffold_28-snap.355-T1
Valid prediction for Augustus_model.g38503.t1
Valid prediction for snap_scaffold_28-snap.368-T1
Couldn't classify 125470, 125895
Sorry, prediction pasa_asmbl_37993.p1 fails validation.
(GCC)	 AC	125470-125895	CG	ACC
Valid prediction for snap_scaffold_28-snap.332-T1
Valid prediction for Augustus_model.g38492.t1
Valid prediction for snap_scaffold_28-snap.326-T1
Valid prediction for GlimmerHMM_glimmerT_58145-T1
Valid prediction for GlimmerHMM_glimmerT_58144-T1
Valid prediction for GlimmerHMM_glimmerT_58142-T1
Valid prediction for Augustus_model.g38501.t1
Valid prediction for GlimmerHMM_glimmerT_58149-T1
Valid prediction for snap_scaffold_28-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_58155-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25826, rend_intergenic: 22384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31599, rend_intergenic: 30168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40042, rend_intergenic: 33819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41536, rend_intergenic: 40405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45652, rend_intergenic: 43011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55327, rend_intergenic: 46371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63685, rend_intergenic: 55655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69522, rend_intergenic: 65286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70597, rend_intergenic: 70368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78031, rend_intergenic: 76116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81421, rend_intergenic: 78663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85061, rend_intergenic: 82672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90070, rend_intergenic: 85752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104507, rend_intergenic: 101603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110313, rend_intergenic: 107986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121306, rend_intergenic: 114060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161581, rend_intergenic: 158068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176026
-exon list size: 395


building trellis

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17.9    
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19.6    
19.9    
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20.4    
20.7    
20.9    
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24.9    
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25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
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29.2    
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30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
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50.4    
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53.9    
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55.4    
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74.1    
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75.3    
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82.1    
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88.4    
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89.4    
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91.4    
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91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.5    
93.7    
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95.0    
95.2    
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96.0    
96.2    
96.5    
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97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 25826, rend_intergenic: 22384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31599, rend_intergenic: 30168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40042, rend_intergenic: 33819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41536, rend_intergenic: 40405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45652, rend_intergenic: 43011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55327, rend_intergenic: 46371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63685, rend_intergenic: 55655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69522, rend_intergenic: 65286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70597, rend_intergenic: 70368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78031, rend_intergenic: 76116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81421, rend_intergenic: 78663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85061, rend_intergenic: 82672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90070, rend_intergenic: 85752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104507, rend_intergenic: 101603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110313, rend_intergenic: 107986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121306, rend_intergenic: 114060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161581, rend_intergenic: 158068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support