-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_16137857-16283695

-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_33029-T1
Valid prediction for GlimmerHMM_glimmerT_33024-T1
Valid prediction for snap_scaffold_13-snap.3188-T1
Valid prediction for Augustus_model.g22036.t1
Valid prediction for snap_scaffold_13-snap.3200-T1
Valid prediction for pasa_asmbl_11563.p1
Valid prediction for snap_scaffold_13-snap.3175-T1
Valid prediction for snap_scaffold_13-snap.3186-T1
Valid prediction for snap_scaffold_13-snap.3181-T1
Valid prediction for Augustus_model.g22043.t1
Valid prediction for GlimmerHMM_glimmerT_33026-T1
Valid prediction for snap_scaffold_13-snap.3168-T1
Valid prediction for snap_scaffold_13-snap.3178-T1
Valid prediction for snap_scaffold_13-snap.3192-T1
Valid prediction for HiQ_model.g22046.t1
Valid prediction for HiQ_model.g22049.t1
Valid prediction for GlimmerHMM_glimmerT_33034-T1
Valid prediction for Augustus_model.g22039.t1
Valid prediction for snap_scaffold_13-snap.3202-T1
Valid prediction for CodingQuarry_transcript_13357-T1
Valid prediction for GlimmerHMM_glimmerT_33017-T1
Valid prediction for snap_scaffold_13-snap.3166-T1
Valid prediction for GlimmerHMM_glimmerT_33032-T1
Valid prediction for snap_scaffold_13-snap.3167-T1
Valid prediction for snap_scaffold_13-snap.3198-T1
Valid prediction for snap_scaffold_13-snap.3179-T1
Couldn't classify 4643, 4697
Couldn't classify 7147, 7206
Sorry, prediction pasa_asmbl_11559.p1 fails validation.
(CCG)	 TG	4643-4697	GT	AGG
(TGT)	 AG	4922-5073	GT	GGG
(ATC)	 AG	5608-5686	GT	GGG
(GCA)	 AG	5764-5906	GT	ACG
(GAG)	 AG	7147-7206	GG	TGG
-recovered pasa_asmbl_11559.p1, internal, 4922, 5073
-recovered pasa_asmbl_11559.p1, internal, 5608, 5686
-recovered pasa_asmbl_11559.p1, internal, 5764, 5906
Valid prediction for GlimmerHMM_glimmerT_33036-T1
Valid prediction for GlimmerHMM_glimmerT_33035-T1
Valid prediction for snap_scaffold_13-snap.3170-T1
Valid prediction for snap_scaffold_13-snap.3172-T1
Valid prediction for snap_scaffold_13-snap.3184-T1
Valid prediction for snap_scaffold_13-snap.3185-T1
Valid prediction for GlimmerHMM_glimmerT_33039-T1
Valid prediction for snap_scaffold_13-snap.3194-T1
Valid prediction for Augustus_model.g22033.t1
Valid prediction for CodingQuarry_transcript_13358-T1
Valid prediction for CodingQuarry_transcript_13359-T1
Valid prediction for Augustus_model.g22047.t1
Valid prediction for snap_scaffold_13-snap.3195-T1
Valid prediction for snap_scaffold_13-snap.3173-T1
Valid prediction for snap_scaffold_13-snap.3190-T1
Valid prediction for GlimmerHMM_glimmerT_33028-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_33027-T1
Valid prediction for snap_scaffold_13-snap.3201-T1
Couldn't classify 87533, 87952
Sorry, prediction pasa_asmbl_10280.p1 fails validation.
(GCC)	 CA	87533-87952	GC	AAG
Valid prediction for GlimmerHMM_glimmerT_33020-T1
Valid prediction for GlimmerHMM_glimmerT_33037-T1
Valid prediction for snap_scaffold_13-snap.3191-T1
Valid prediction for Augustus_model.g22045.t1
Valid prediction for GlimmerHMM_glimmerT_33025-T1
Valid prediction for Augustus_model.g22041.t1
Valid prediction for snap_scaffold_13-snap.3187-T1
Valid prediction for HiQ_model.g22034.t1
Valid prediction for GlimmerHMM_glimmerT_33031-T1
Valid prediction for snap_scaffold_13-snap.3180-T1
Valid prediction for snap_scaffold_13-snap.3193-T1
Couldn't classify 104456, 104605
Couldn't classify 106175, 106375
Sorry, prediction pasa_asmbl_10313.p1 fails validation.
(GAC)	 TA	104456-104605	GT	AGG
(GTT)	 AG	105035-105181	GT	AGG
(AAC)	 AG	105434-105533	GT	CGG
(GTA)	 AG	105799-105941	GT	AGG
(CTG)	 AG	106175-106375	TC	GGT
-recovered pasa_asmbl_10313.p1, internal, 105035, 105181
-recovered pasa_asmbl_10313.p1, internal, 105434, 105533
-recovered pasa_asmbl_10313.p1, internal, 105799, 105941
Valid prediction for snap_scaffold_13-snap.3176-T1
Valid prediction for CodingQuarry_transcript_13356-T1
Valid prediction for snap_scaffold_13-snap.3199-T1
Couldn't classify 6585, 6612
Couldn't classify 8887, 8924
Sorry, prediction pasa_asmbl_10288.p1 fails validation.
(CAG)	 AA	6585-6612	GT	AGG
(GAG)	 AG	7216-7338	GT	CAG
(CCC)	 AG	7464-7585	GT	AGG
(GTG)	 AG	7677-7837	GT	AGG
(TCT)	 AG	8073-8179	GT	CGG
(ATG)	 AG	8271-8462	GT	AGG
(ATG)	 AG	8887-8924	CT	CCC
-recovered pasa_asmbl_10288.p1, initial, 8271, 8462
-recovered pasa_asmbl_10288.p1, internal, 7216, 7338
-recovered pasa_asmbl_10288.p1, internal, 7464, 7585
-recovered pasa_asmbl_10288.p1, internal, 7677, 7837
-recovered pasa_asmbl_10288.p1, internal, 8073, 8179
-recovered pasa_asmbl_10288.p1, internal, 8271, 8462
Valid prediction for GlimmerHMM_glimmerT_33040-T1
Valid prediction for CodingQuarry_transcript_13354-T1
Couldn't classify 21443, 22003
Sorry, prediction pasa_asmbl_10283.p1 fails validation.
(CGC)	 GC	21443-22003	CC	CTC
Valid prediction for HiQ_model.g22038.t1
Valid prediction for snap_scaffold_13-snap.3189-T1
Couldn't classify 29656, 29846
Sorry, prediction pasa_asmbl_10384.p1 fails validation.
(ATG)	 AG	29174-29285	GT	AGG
(GTC)	 AG	29656-29846	CC	CCC
-recovered pasa_asmbl_10384.p1, initial, 29174, 29285
-recovered pasa_asmbl_10384.p1, internal, 29174, 29285
Valid prediction for Augustus_model.g22042.t1
Valid prediction for CodingQuarry_transcript_13360-T1
Valid prediction for GlimmerHMM_glimmerT_33030-T1
Valid prediction for Augustus_model.g22051.t1
Valid prediction for Augustus_model.g22048.t1
Valid prediction for snap_scaffold_13-snap.3183-T1
Valid prediction for pasa_asmbl_10274.p1
Valid prediction for GlimmerHMM_glimmerT_33018-T1
Valid prediction for snap_scaffold_13-snap.3174-T1
Valid prediction for Augustus_model.g22052.t1
Valid prediction for snap_scaffold_13-snap.3169-T1
Valid prediction for GlimmerHMM_glimmerT_33019-T1
Couldn't classify 107412, 107519
Couldn't classify 109615, 109827
Sorry, prediction pasa_asmbl_10392.p1 fails validation.
(GGT)	 CA	107412-107519	GT	ATG
(ATC)	 AG	107802-107945	GT	AGG
(GTT)	 AG	108240-108370	GT	AGG
(GAC)	 AG	108457-108664	GT	AGG
(GGT)	 AG	108996-109106	GT	AGG
(TCA)	 AG	109615-109827	AA	GAA
-recovered pasa_asmbl_10392.p1, internal, 107802, 107945
-recovered pasa_asmbl_10392.p1, internal, 108240, 108370
-recovered pasa_asmbl_10392.p1, internal, 108457, 108664
-recovered pasa_asmbl_10392.p1, internal, 108996, 109106
Valid prediction for Augustus_model.g22040.t1
Valid prediction for snap_scaffold_13-snap.3196-T1
Valid prediction for Augustus_model.g22037.t1
Valid prediction for snap_scaffold_13-snap.3177-T1
Valid prediction for CodingQuarry_transcript_13351-T1
Valid prediction for pasa_asmbl_10266.p1
Couldn't classify 119224, 119342
Couldn't classify 119941, 120182
Sorry, prediction pasa_asmbl_10270.p1 fails validation.
(CTG)	 AG	119224-119342	GT	CAG
(TGG)	 AG	119654-119763	GT	TGG
(GTG)	 AG	119941-120182	NN	CTN
-recovered pasa_asmbl_10270.p1, internal, 119224, 119342
-recovered pasa_asmbl_10270.p1, internal, 119654, 119763
Valid prediction for CodingQuarry_transcript_13353-T1
Valid prediction for GlimmerHMM_glimmerT_33038-T1
Valid prediction for GlimmerHMM_glimmerT_33022-T1
Valid prediction for GlimmerHMM_glimmerT_33041-T1
Valid prediction for CodingQuarry_transcript_13352-T1
Valid prediction for GlimmerHMM_glimmerT_33033-T1
Valid prediction for snap_scaffold_13-snap.3165-T1
Valid prediction for snap_scaffold_13-snap.3182-T1
Valid prediction for GlimmerHMM_glimmerT_33021-T1
Valid prediction for Augustus_model.g22044.t1
Valid prediction for GlimmerHMM_glimmerT_33023-T1
Valid prediction for Augustus_model.g22053.t1
Valid prediction for snap_scaffold_13-snap.3171-T1
Valid prediction for HiQ_model.g22050.t1
Valid prediction for snap_scaffold_13-snap.3197-T1
Valid prediction for Augustus_model.g22035.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18555, rend_intergenic: 2810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22097, rend_intergenic: 20933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29814, rend_intergenic: 24138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33860, rend_intergenic: 31230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39711, rend_intergenic: 33995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42871, rend_intergenic: 39906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54720, rend_intergenic: 46489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55883, rend_intergenic: 55159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63212, rend_intergenic: 57888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76973, rend_intergenic: 68493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81885, rend_intergenic: 80236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89841, rend_intergenic: 83165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99314, rend_intergenic: 94272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105937, rend_intergenic: 102698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110571, rend_intergenic: 107676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119598, rend_intergenic: 113981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124538, rend_intergenic: 120703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140659, rend_intergenic: 131976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142134, rend_intergenic: 140755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 57891, rend_intergenic: 57888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 126028, rend_intergenic: 126025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145839
-exon list size: 366


building trellis

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18.8    
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22.6    
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26.6    
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27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
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44.0    
44.3    
44.6    
44.8    
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45.4    
45.7    
45.9    
46.2    
46.5    
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47.0    
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47.8    
48.1    
48.4    
48.6    
48.9    
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49.5    
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50.3    
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51.9    
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88.3    
88.6    
88.9    
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99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 18555, rend_intergenic: 2810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22097, rend_intergenic: 20933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29814, rend_intergenic: 24138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33860, rend_intergenic: 31230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39711, rend_intergenic: 33995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42871, rend_intergenic: 39906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54720, rend_intergenic: 46489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55883, rend_intergenic: 55159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63212, rend_intergenic: 57888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76973, rend_intergenic: 68493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81885, rend_intergenic: 80236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89841, rend_intergenic: 83165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99314, rend_intergenic: 94272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105937, rend_intergenic: 102698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110571, rend_intergenic: 107676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119598, rend_intergenic: 113981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124538, rend_intergenic: 120703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140659, rend_intergenic: 131976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142134, rend_intergenic: 140755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 57891, rend_intergenic: 57888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 126028, rend_intergenic: 126025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support