-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_3763104-3862052

-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 GeneMark_model.38415_t
Valid prediction for GeneMark_model.38417_t
Valid prediction for Augustus_model.g14988.t1
Valid prediction for GeneMark_model.38399_t
Valid prediction for GeneMark_model.38404_t
Valid prediction for GeneMark_model.38406_t
Valid prediction for snap_scaffold_9-snap.810-T1
Valid prediction for Augustus_model.g14984.t1
Valid prediction for snap_scaffold_9-snap.823-T1
Valid prediction for snap_scaffold_9-snap.816-T1
Valid prediction for GlimmerHMM_glimmerT_22398-T1
Valid prediction for GeneMark_model.38422_t
Valid prediction for snap_scaffold_9-snap.826-T1
Valid prediction for GlimmerHMM_glimmerT_22402-T1
Valid prediction for snap_scaffold_9-snap.830-T1
Valid prediction for GeneMark_model.38419_t
Couldn't classify 29002, 29070
Sorry, prediction pasa_asmbl_53900.p1 fails validation.
(ATG)	 CC	25370-25372	GT	TGG
(TCT)	 AG	26224-26328	GT	AGG
(GAA)	 AG	27591-27740	GT	GGG
(GAC)	 AG	29002-29070	GC	AGG
-recovered pasa_asmbl_53900.p1, initial, 25370, 25372
-recovered pasa_asmbl_53900.p1, internal, 26224, 26328
-recovered pasa_asmbl_53900.p1, internal, 27591, 27740
-recovered pasa_asmbl_53900.p1, internal, 29002, 29070
Valid prediction for snap_scaffold_9-snap.818-T1
Valid prediction for GeneMark_model.38407_t
Valid prediction for GeneMark_model.38408_t
Valid prediction for GeneMark_model.38395_t
Couldn't classify 34179, 34560
Couldn't classify 34662, 34777
Sorry, prediction pasa_asmbl_53902.p1 fails validation.
(CCC)	 CC	34179-34560	GT	AGG
(TGG)	 AG	34662-34777	GC	AGG
-recovered pasa_asmbl_53902.p1, internal, 34662, 34777
Valid prediction for GeneMark_model.38401_t
Valid prediction for GeneMark_model.38394_t
Valid prediction for GeneMark_model.38397_t
Valid prediction for GlimmerHMM_glimmerT_22408-T1
Valid prediction for Augustus_model.g14983.t1
Valid prediction for CodingQuarry_transcript_61982-T1
Valid prediction for snap_scaffold_9-snap.837-T1
Valid prediction for GeneMark_model.38414_t
Valid prediction for Augustus_model.g14987.t1
Valid prediction for snap_scaffold_9-snap.824-T1
Valid prediction for Augustus_model.g14986.t1
Valid prediction for snap_scaffold_9-snap.812-T1
Valid prediction for GlimmerHMM_glimmerT_22399-T1
Valid prediction for GlimmerHMM_glimmerT_22400-T1
Valid prediction for snap_scaffold_9-snap.828-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.819-T1
Valid prediction for snap_scaffold_9-snap.833-T1
Valid prediction for GlimmerHMM_glimmerT_22409-T1
Valid prediction for GeneMark_model.38425_t
Valid prediction for GeneMark_model.38390_t
Valid prediction for GeneMark_model.38410_t
Valid prediction for GlimmerHMM_glimmerT_22397-T1
Valid prediction for GlimmerHMM_glimmerT_22404-T1
Valid prediction for GeneMark_model.38387_t
Valid prediction for GlimmerHMM_glimmerT_22407-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.832-T1
Valid prediction for snap_scaffold_9-snap.821-T1
Couldn't classify 63506, 63613
Couldn't classify 65528, 65635
Sorry, prediction pasa_asmbl_53907.p1 fails validation.
(TCC)	 GC	63506-63613	GT	AGG
(GTG)	 AG	64012-64145	GT	AGG
(GAT)	 AG	64425-64551	GT	GAG
(GTG)	 AG	65528-65635	CT	GCC
-recovered pasa_asmbl_53907.p1, internal, 64012, 64145
-recovered pasa_asmbl_53907.p1, internal, 64425, 64551
Valid prediction for snap_scaffold_9-snap.815-T1
Valid prediction for snap_scaffold_9-snap.825-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.38389_t
Valid prediction for GeneMark_model.38392_t
Valid prediction for snap_scaffold_9-snap.835-T1
Couldn't classify 30829, 30912
Couldn't classify 33639, 33684
Sorry, prediction pasa_asmbl_53901.p2 fails validation.
(GAG)	 AG	30829-30912	GT	GGG
(GGA)	 AG	31228-31392	GT	GTG
(AGT)	 AG	31814-31992	GT	ATG
(GTT)	 AG	32682-32743	GC	AGG
(ATG)	 AG	33368-33485	GT	AGG
(CAT)	 AG	33639-33684	AG	AGA
-recovered pasa_asmbl_53901.p2, initial, 33368, 33485
-recovered pasa_asmbl_53901.p2, internal, 30829, 30912
-recovered pasa_asmbl_53901.p2, internal, 31228, 31392
-recovered pasa_asmbl_53901.p2, internal, 31814, 31992
-recovered pasa_asmbl_53901.p2, internal, 32682, 32743
-recovered pasa_asmbl_53901.p2, internal, 33368, 33485
Valid prediction for GlimmerHMM_glimmerT_22403-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.g14990.t1
Valid prediction for snap_scaffold_9-snap.817-T1
Valid prediction for snap_scaffold_9-snap.838-T1
Couldn't classify 13572, 13679
Sorry, prediction pasa_asmbl_54907.p1 fails validation.
(GCC)	 TA	13572-13679	GT	AGG
(GTG)	 AG	14019-14194	GT	AGG
(GGT)	 AG	14573-14679	GT	CCG
(TTC)	 AG	15083-15230	GT	AGG
(TGT)	 AG	15572-15786	GT	AGG
(ACT)	 AG	16007-16173	GT	TGG
(CCT)	 AG	16563-16604	CG	AAC
-recovered pasa_asmbl_54907.p1, terminal, 16563, 16604
-recovered pasa_asmbl_54907.p1, internal, 14019, 14194
-recovered pasa_asmbl_54907.p1, internal, 14573, 14679
-recovered pasa_asmbl_54907.p1, internal, 15083, 15230
-recovered pasa_asmbl_54907.p1, internal, 15572, 15786
-recovered pasa_asmbl_54907.p1, internal, 16007, 16173
Valid prediction for GlimmerHMM_glimmerT_22395-T1
Valid prediction for snap_scaffold_9-snap.809-T1
Valid prediction for pasa_asmbl_55705.p1
Valid prediction for Augustus_model.g14982.t1
Valid prediction for GeneMark_model.38412_t
Valid prediction for HiQ_model.g14989.t1
Valid prediction for snap_scaffold_9-snap.834-T1
Valid prediction for Augustus_model.g14991.t1
Valid prediction for GeneMark_model.38426_t
Valid prediction for GeneMark_model.38396_t
Valid prediction for snap_scaffold_9-snap.811-T1
Valid prediction for GlimmerHMM_glimmerT_22401-T1
Valid prediction for snap_scaffold_9-snap.829-T1
Valid prediction for snap_scaffold_9-snap.836-T1
Couldn't classify 10461, 10650
Couldn't classify 10744, 10919
Sorry, prediction pasa_asmbl_54910.p1 fails validation.
(TCC)	 GG	10461-10650	GT	AGG
(GTA)	 AG	10744-10919	GT	AGG
-recovered pasa_asmbl_54910.p1, internal, 10744, 10919
Valid prediction for GeneMark_model.38402_t
Valid prediction for GlimmerHMM_glimmerT_22405-T1
Valid prediction for CodingQuarry_transcript_61985-T1
Valid prediction for GeneMark_model.38413_t
Valid prediction for GeneMark_model.38418_t
Valid prediction for snap_scaffold_9-snap.822-T1
Valid prediction for Augustus_model.g14992.t1
Valid prediction for GeneMark_model.38398_t
Valid prediction for snap_scaffold_9-snap.831-T1
Valid prediction for snap_scaffold_9-snap.814-T1
Valid prediction for GlimmerHMM_glimmerT_22396-T1
Valid prediction for GlimmerHMM_glimmerT_22406-T1
Valid prediction for Augustus_model.g14985.t1
Valid prediction for GeneMark_model.38403_t
Valid prediction for GeneMark_model.38400_t
Valid prediction for GeneMark_model.38405_t
Valid prediction for snap_scaffold_9-snap.827-T1
Valid prediction for GeneMark_model.38420_t
Valid prediction for GeneMark_model.38421_t
Valid prediction for GeneMark_model.38391_t
Valid prediction for GeneMark_model.38424_t
Valid prediction for GeneMark_model.38423_t
Valid prediction for GeneMark_model.38393_t
Valid prediction for GeneMark_model.38416_t
Valid prediction for GeneMark_model.38388_t
Valid prediction for snap_scaffold_9-snap.820-T1
Valid prediction for snap_scaffold_9-snap.813-T1
Valid prediction for GeneMark_model.38411_t
Valid prediction for GeneMark_model.38409_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12968, rend_intergenic: 3480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19876, rend_intergenic: 17051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22595, rend_intergenic: 20495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30059, rend_intergenic: 25370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31996, rend_intergenic: 31162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33525, rend_intergenic: 32498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39441, rend_intergenic: 35637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40019, rend_intergenic: 39578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41278, rend_intergenic: 40947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42756, rend_intergenic: 41297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55157, rend_intergenic: 54008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59556, rend_intergenic: 59514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63516, rend_intergenic: 59575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67072, rend_intergenic: 63952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79010, rend_intergenic: 75270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84198, rend_intergenic: 80691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86703, rend_intergenic: 84218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 98949
-exon list size: 499


building trellis

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27.9    
28.1    
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28.9    
29.1    
29.3    
29.5    
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29.9    
30.1    
30.3    
30.5    
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30.9    
31.1    
31.3    
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31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
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35.9    
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36.3    
36.5    
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37.5    
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37.9    
38.1    
38.3    
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38.7    
38.9    
39.1    
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98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 12968, rend_intergenic: 3480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19876, rend_intergenic: 17051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22595, rend_intergenic: 20495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30059, rend_intergenic: 25370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31996, rend_intergenic: 31162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33525, rend_intergenic: 32498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39441, rend_intergenic: 35637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40019, rend_intergenic: 39578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41278, rend_intergenic: 40947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42756, rend_intergenic: 41297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55157, rend_intergenic: 54008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59556, rend_intergenic: 59514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63516, rend_intergenic: 59575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67072, rend_intergenic: 63952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79010, rend_intergenic: 75270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84198, rend_intergenic: 80691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86703, rend_intergenic: 84218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support