-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_7454748-7695269

-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: +)Couldn't classify 26275, 26619
Sorry, prediction pasa_asmbl_19971.p2 fails validation.
(GCC)	 AG	26275-26619	GA	CCG
Valid prediction for HiQ_model.g29242.t1
Valid prediction for Augustus_model.g29250.t1
Valid prediction for CodingQuarry_transcript_23769-T1
Valid prediction for snap_scaffold_18-snap.1597-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_23763-T1
Valid prediction for snap_scaffold_18-snap.1572-T1
Valid prediction for GeneMark_model.75380_t
Couldn't classify 167779, 168426
Couldn't classify 168548, 168685
Sorry, prediction pasa_asmbl_20782.p1 fails validation.
(GGG)	 CA	167779-168426	GT	ACG
(TAT)	 AG	168548-168685	AG	CCA
Valid prediction for GeneMark_model.75379_t
Valid prediction for GeneMark_model.75404_t
Valid prediction for CodingQuarry_transcript_23762-T1
Couldn't classify 2976, 3101
Sorry, prediction pasa_asmbl_20771.p1 fails validation.
(CAA)	 AG	2976-3101	GT	ACG
(TAT)	 AG	5698-5769	GT	GGG
(AAA)	 AG	7268-7354	GT	AGG
(AAC)	 AG	7574-7711	GT	TGG
(AAC)	 AG	7827-8024	CC	AAC
-recovered pasa_asmbl_20771.p1, terminal, 7827, 8024
-recovered pasa_asmbl_20771.p1, internal, 2976, 3101
-recovered pasa_asmbl_20771.p1, internal, 5698, 5769
-recovered pasa_asmbl_20771.p1, internal, 7268, 7354
-recovered pasa_asmbl_20771.p1, internal, 7574, 7711
Valid prediction for GeneMark_model.75402_t
Valid prediction for snap_scaffold_18-snap.1588-T1
Valid prediction for GeneMark_model.75382_t
Valid prediction for CodingQuarry_transcript_23770-T1
Valid prediction for CodingQuarry_transcript_23767-T1
Valid prediction for GlimmerHMM_glimmerT_43659-T1
Valid prediction for GeneMark_model.75408_t
Valid prediction for pasa_asmbl_20806.p1
Valid prediction for GeneMark_model.75373_t
Valid prediction for HiQ_model.g29259.t1
Valid prediction for GlimmerHMM_glimmerT_43670-T1
Valid prediction for GeneMark_model.75389_t
Couldn't classify 73441, 73491
Couldn't classify 74374, 74429
Sorry, prediction CodingQuarry_transcript_23765-T1 fails validation.
(ATG)	 AC	73441-73491	AA	GTA
(GAG)	 TG	74374-74429	GT	GGG
(TGA)	 AG	75331-75503	GT	AGG
(TTA)	 AG	75775-75860	GT	CGG
(GAT)	 AG	78090-78186	GT	TGG
(TGT)	 AG	78282-78392	GT	AGG
(GTA)	 AG	80521-80651	GT	AGG
(TCT)	 AG	80834-80901	GT	AGG
(GAA)	 AG	81388-81484	GT	AGG
(GTT)	 AG	82442-82503	GT	AAG
(GTC)	 AG	83149-83260	GT	TGG
(GCA)	 AG	83355-83445	GT	AGG
(GTT)	 AG	83576-83697	GT	TGG
(GGT)	 AG	85068-85173	GT	AGG
(TGG)	 AG	85289-85380	AG	AGA
add_exon() Sorry, CodingQuarry_transcript_23765-T1 82442-82503-terminal-2 is invalid.
-recovered CodingQuarry_transcript_23765-T1, terminal, 82442, 82503
-recovered CodingQuarry_transcript_23765-T1, terminal, 85289, 85380
-recovered CodingQuarry_transcript_23765-T1, internal, 75331, 75503
-recovered CodingQuarry_transcript_23765-T1, internal, 75775, 75860
-recovered CodingQuarry_transcript_23765-T1, internal, 78090, 78186
-recovered CodingQuarry_transcript_23765-T1, internal, 78282, 78392
-recovered CodingQuarry_transcript_23765-T1, internal, 80521, 80651
-recovered CodingQuarry_transcript_23765-T1, internal, 80834, 80901
-recovered CodingQuarry_transcript_23765-T1, internal, 81388, 81484
-recovered CodingQuarry_transcript_23765-T1, internal, 82442, 82503
-recovered CodingQuarry_transcript_23765-T1, internal, 83149, 83260
-recovered CodingQuarry_transcript_23765-T1, internal, 83355, 83445
-recovered CodingQuarry_transcript_23765-T1, internal, 83576, 83697
-recovered CodingQuarry_transcript_23765-T1, internal, 85068, 85173
Valid prediction for snap_scaffold_18-snap.1587-T1
Valid prediction for GeneMark_model.75399_t
Valid prediction for GeneMark_model.75387_t
Valid prediction for snap_scaffold_18-snap.1594-T1
Valid prediction for Augustus_model.g29252.t1
Valid prediction for snap_scaffold_18-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_43657-T1
Valid prediction for HiQ_model.g29258.t1
Valid prediction for GlimmerHMM_glimmerT_43665-T1
Valid prediction for CodingQuarry_transcript_23766-T1
Valid prediction for GeneMark_model.75397_t
Valid prediction for GeneMark_model.75375_t
Valid prediction for snap_scaffold_18-snap.1599-T1
Valid prediction for GlimmerHMM_glimmerT_43668-T1
Valid prediction for GeneMark_model.75383_t
Valid prediction for snap_scaffold_18-snap.1595-T1
Valid prediction for snap_scaffold_18-snap.1569-T1
Valid prediction for snap_scaffold_18-snap.1601-T1
Valid prediction for GeneMark_model.75406_t
Valid prediction for pasa_asmbl_20777.p1
Valid prediction for GeneMark_model.75409_t
Valid prediction for GeneMark_model.75376_t
Valid prediction for snap_scaffold_18-snap.1576-T1
Valid prediction for pasa_asmbl_20783.p1
Valid prediction for HiQ_model.g29254.t1
Valid prediction for snap_scaffold_18-snap.1596-T1
Valid prediction for CodingQuarry_transcript_23771-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_43655-T1
Valid prediction for GlimmerHMM_glimmerT_43658-T1
Valid prediction for GeneMark_model.75401_t
Valid prediction for pasa_asmbl_19996.p1
Valid prediction for GeneMark_model.75374_t
Valid prediction for Augustus_model.g29238.t1
Valid prediction for GeneMark_model.75378_t
Couldn't classify 184522, 184535
Sorry, prediction pasa_asmbl_19985.p1 fails validation.
(ATG)	 GG	183304-183441	GT	AGG
(CCT)	 AG	183804-183993	GT	AGG
(TCC)	 AG	184213-184410	GT	TGG
(AGT)	 AG	184522-184535	GG	GGG
-recovered pasa_asmbl_19985.p1, initial, 183304, 183441
-recovered pasa_asmbl_19985.p1, internal, 183804, 183993
-recovered pasa_asmbl_19985.p1, internal, 184213, 184410
Valid prediction for snap_scaffold_18-snap.1577-T1
Valid prediction for GeneMark_model.75405_t
Valid prediction for Augustus_model.g29257.t1
Valid prediction for snap_scaffold_18-snap.1573-T1
Valid prediction for GlimmerHMM_glimmerT_43656-T1
Valid prediction for Augustus_model.g29253.t1
Valid prediction for GeneMark_model.75386_t
Valid prediction for Augustus_model.g29248.t1
Valid prediction for GlimmerHMM_glimmerT_43661-T1
Valid prediction for snap_scaffold_18-snap.1574-T1
Valid prediction for snap_scaffold_18-snap.1580-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43666-T1
Valid prediction for GlimmerHMM_glimmerT_43664-T1
Couldn't classify 150746, 151357
Sorry, prediction pasa_asmbl_21105.p1 fails validation.
(TCG)	 TG	150746-151357	CT	TGC
Couldn't classify 141023, 141024
Sorry, prediction pasa_asmbl_19990.p1 fails validation.
(ATG)	 TA	141023-141024	GT	ATG
(GGA)	 AG	141127-141194	GT	AGG
(ATA)	 AG	141381-141636	GT	ATG
(AAA)	 AG	141716-141894	GT	TGG
(GAA)	 AG	142514-142736	GT	AAG
(CAT)	 AG	144994-145160	GT	AGG
(ATA)	 AG	145332-145581	GT	AGG
(ATT)	 AG	145733-145872	GT	GGG
(AGG)	 AG	147546-147798	GT	AAG
(GAA)	 AG	147995-148125	GT	TGG
(ACA)	 AG	148237-148480	GT	AAG
(AAA)	 AG	148560-148683	AG	GAA
add_exon() Sorry, pasa_asmbl_19990.p1 144994-145160-terminal-2 is invalid.
-recovered pasa_asmbl_19990.p1, terminal, 144994, 145160
-recovered pasa_asmbl_19990.p1, terminal, 148560, 148683
-recovered pasa_asmbl_19990.p1, internal, 141127, 141194
-recovered pasa_asmbl_19990.p1, internal, 141381, 141636
-recovered pasa_asmbl_19990.p1, internal, 141716, 141894
-recovered pasa_asmbl_19990.p1, internal, 142514, 142736
-recovered pasa_asmbl_19990.p1, internal, 144994, 145160
-recovered pasa_asmbl_19990.p1, internal, 145332, 145581
-recovered pasa_asmbl_19990.p1, internal, 145733, 145872
-recovered pasa_asmbl_19990.p1, internal, 147546, 147798
-recovered pasa_asmbl_19990.p1, internal, 147995, 148125
-recovered pasa_asmbl_19990.p1, internal, 148237, 148480
Valid prediction for GeneMark_model.75396_t
Valid prediction for Augustus_model.g29243.t1
Valid prediction for GeneMark_model.75398_t
Valid prediction for GeneMark_model.75385_t
Valid prediction for GlimmerHMM_glimmerT_43671-T1
Valid prediction for GeneMark_model.75407_t
Valid prediction for GeneMark_model.75393_t
Valid prediction for GeneMark_model.75390_t
Valid prediction for GlimmerHMM_glimmerT_43669-T1
Valid prediction for GeneMark_model.75400_t
Valid prediction for GeneMark_model.75381_t
Valid prediction for GlimmerHMM_glimmerT_43674-T1
Valid prediction for GlimmerHMM_glimmerT_43653-T1
Couldn't classify 187383, 187463
Couldn't classify 192307, 192432
Sorry, prediction pasa_asmbl_19980.p1 fails validation.
(CAC)	 CA	187383-187463	GT	GGG
(GTG)	 AG	187773-187898	GT	AGG
(GTG)	 AG	188448-188588	GT	AGG
(TTG)	 AG	188679-188804	GT	AGG
(CTG)	 AG	189083-189241	GT	TTG
(GTG)	 AG	190894-191022	GT	AGG
(CTG)	 AG	191224-191349	GT	GGG
(CTG)	 AG	191936-192061	GT	AGG
(GTG)	 AG	192307-192432	GT	AGG
-recovered pasa_asmbl_19980.p1, internal, 187773, 187898
-recovered pasa_asmbl_19980.p1, internal, 188448, 188588
-recovered pasa_asmbl_19980.p1, internal, 188679, 188804
-recovered pasa_asmbl_19980.p1, internal, 189083, 189241
-recovered pasa_asmbl_19980.p1, internal, 190894, 191022
-recovered pasa_asmbl_19980.p1, internal, 191224, 191349
-recovered pasa_asmbl_19980.p1, internal, 191936, 192061
-recovered pasa_asmbl_19980.p1, internal, 192307, 192432
Valid prediction for HiQ_model.g29240.t1
Valid prediction for Augustus_model.g29251.t1
Valid prediction for GeneMark_model.75388_t
Valid prediction for snap_scaffold_18-snap.1578-T1
Valid prediction for snap_scaffold_18-snap.1575-T1
Valid prediction for pasa_asmbl_19977.p1
Valid prediction for Augustus_model.g29239.t1
Valid prediction for CodingQuarry_transcript_23764-T1
Couldn't classify 204235, 204546
Sorry, prediction pasa_asmbl_19975.p1 fails validation.
(CTC)	 AC	204235-204546	TA	AAT
Valid prediction for GlimmerHMM_glimmerT_43673-T1
Valid prediction for GeneMark_model.75391_t
Valid prediction for HiQ_model.g29245.t1
Valid prediction for snap_scaffold_18-snap.1600-T1
Valid prediction for Augustus_model.g29244.t1
Valid prediction for snap_scaffold_18-snap.1581-T1
Couldn't classify 185112, 185151
Sorry, prediction pasa_asmbl_19984.p1 fails validation.
(CTG)	 AA	185112-185151	GT	AGG
(GTT)	 AG	185323-185561	GT	AGG
(GTT)	 AG	185882-186088	CA	AGC
-recovered pasa_asmbl_19984.p1, terminal, 185882, 186088
-recovered pasa_asmbl_19984.p1, internal, 185323, 185561
Valid prediction for snap_scaffold_18-snap.1590-T1
Valid prediction for Augustus_model.g29256.t1
Valid prediction for snap_scaffold_18-snap.1598-T1
Valid prediction for snap_scaffold_18-snap.1570-T1
Valid prediction for snap_scaffold_18-snap.1579-T1
Valid prediction for GlimmerHMM_glimmerT_43667-T1
Valid prediction for snap_scaffold_18-snap.1584-T1
Valid prediction for snap_scaffold_18-snap.1583-T1
Valid prediction for snap_scaffold_18-snap.1585-T1
Valid prediction for Augustus_model.g29241.t1
Valid prediction for Augustus_model.g29246.t1
Couldn't classify 36320, 37180
Sorry, prediction pasa_asmbl_20790.p1 fails validation.
(ATG)	 CT	36320-37180	TG	CGT
Valid prediction for GeneMark_model.75395_t
Valid prediction for GlimmerHMM_glimmerT_43654-T1
Valid prediction for Augustus_model.g29247.t1
Valid prediction for snap_scaffold_18-snap.1593-T1
Couldn't classify 174071, 174159
Couldn't classify 175837, 175919
Sorry, prediction pasa_asmbl_19988.p1 fails validation.
(GGA)	 CA	174071-174159	GT	CGG
(AAA)	 AG	174335-174417	GT	AGG
(AAA)	 AG	174739-174834	GT	TGG
(ATG)	 AG	175837-175919	AG	GCA
-recovered pasa_asmbl_19988.p1, internal, 174335, 174417
-recovered pasa_asmbl_19988.p1, internal, 174739, 174834
Valid prediction for snap_scaffold_18-snap.1582-T1
Valid prediction for snap_scaffold_18-snap.1571-T1
Valid prediction for snap_scaffold_18-snap.1591-T1
Valid prediction for GlimmerHMM_glimmerT_43663-T1
Valid prediction for GlimmerHMM_glimmerT_43660-T1
Valid prediction for GeneMark_model.75384_t
Valid prediction for GlimmerHMM_glimmerT_43672-T1
Valid prediction for GeneMark_model.75403_t
Valid prediction for snap_scaffold_18-snap.1589-T1
Valid prediction for Augustus_model.g29249.t1
Valid prediction for HiQ_model.g29255.t1
Valid prediction for snap_scaffold_18-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_43662-T1
Valid prediction for GeneMark_model.75394_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 226618, rend_intergenic: 225273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240522
-exon list size: 485


building trellis

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97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 226618, rend_intergenic: 225273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support