-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_17891053-18057072

-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_3-snap.3525-T1
Valid prediction for Augustus_model.g5620.t1
Couldn't classify 16991, 17725
Sorry, prediction pasa_asmbl_40675.p1 fails validation.
(ATG)	 AA	16128-16196	GT	AGG
(GAC)	 AG	16366-16455	GT	TGG
(ACA)	 AG	16991-17725	GC	ACG
-recovered pasa_asmbl_40675.p1, initial, 16128, 16196
-recovered pasa_asmbl_40675.p1, internal, 16366, 16455
-recovered pasa_asmbl_40675.p1, internal, 16991, 17725
Valid prediction for snap_scaffold_3-snap.3541-T1
Valid prediction for GeneMark_model.13743_t
Valid prediction for snap_scaffold_3-snap.3538-T1
Valid prediction for GeneMark_model.13753_t
Valid prediction for GlimmerHMM_glimmerT_8453-T1
Valid prediction for snap_scaffold_3-snap.3507-T1
Valid prediction for snap_scaffold_3-snap.3514-T1
Valid prediction for GeneMark_model.13736_t
Valid prediction for snap_scaffold_3-snap.3506-T1
Couldn't classify 3323, 3462
Couldn't classify 6655, 6777
Sorry, prediction pasa_asmbl_40755.p1 fails validation.
(TTG)	 GG	3323-3462	GT	AGG
(TGT)	 AG	4063-4159	GT	GAG
(AAA)	 AG	6655-6777	GT	AGG
-recovered pasa_asmbl_40755.p1, internal, 4063, 4159
-recovered pasa_asmbl_40755.p1, internal, 6655, 6777
Valid prediction for GlimmerHMM_glimmerT_8468-T1
Valid prediction for GlimmerHMM_glimmerT_8449-T1
Valid prediction for snap_scaffold_3-snap.3505-T1
Valid prediction for GeneMark_model.13733_t
Valid prediction for GlimmerHMM_glimmerT_8452-T1
Valid prediction for GlimmerHMM_glimmerT_8465-T1
Valid prediction for snap_scaffold_3-snap.3524-T1
Valid prediction for snap_scaffold_3-snap.3518-T1
Valid prediction for Augustus_model.g5610.t1
Valid prediction for GeneMark_model.13751_t
Valid prediction for GeneMark_model.13731_t
Valid prediction for GeneMark_model.13744_t
Valid prediction for GlimmerHMM_glimmerT_8464-T1
Couldn't classify 137983, 138027
Couldn't classify 139286, 139351
Sorry, prediction pasa_asmbl_40680.p1 fails validation.
(AAT)	 CC	137983-138027	GT	AGG
(ACT)	 AG	138847-139035	GT	AGG
(GCG)	 AG	139286-139351	CC	ATC
-recovered pasa_asmbl_40680.p1, internal, 138847, 139035
Couldn't classify 129438, 129496
Couldn't classify 135223, 135457
Sorry, prediction pasa_asmbl_40679.p1 fails validation.
(AAA)	 AG	129438-129496	GT	AGG
(AAT)	 AG	129878-129982	GT	AGG
(CTT)	 AG	130670-130796	GT	AGG
(GAG)	 AG	132228-132365	GT	AGG
(CTC)	 AG	132449-132502	GT	AGG
(CTG)	 AG	132661-132890	GT	AAG
(GGA)	 AG	133191-133287	GT	GGG
(CTA)	 AG	133447-133570	GT	AGG
(AAG)	 AG	133959-134110	GT	AGG
(GAT)	 AG	134256-134607	GT	AGG
(ATG)	 AG	134807-134864	GT	GGG
(GGG)	 AG	134942-135013	GT	AGG
(GGG)	 AG	135223-135457	AC	ACA
-recovered pasa_asmbl_40679.p1, initial, 134807, 134864
-recovered pasa_asmbl_40679.p1, internal, 129438, 129496
-recovered pasa_asmbl_40679.p1, internal, 129878, 129982
-recovered pasa_asmbl_40679.p1, internal, 130670, 130796
-recovered pasa_asmbl_40679.p1, internal, 132228, 132365
-recovered pasa_asmbl_40679.p1, internal, 132449, 132502
-recovered pasa_asmbl_40679.p1, internal, 132661, 132890
-recovered pasa_asmbl_40679.p1, internal, 133191, 133287
-recovered pasa_asmbl_40679.p1, internal, 133447, 133570
-recovered pasa_asmbl_40679.p1, internal, 133959, 134110
-recovered pasa_asmbl_40679.p1, internal, 134256, 134607
-recovered pasa_asmbl_40679.p1, internal, 134807, 134864
-recovered pasa_asmbl_40679.p1, internal, 134942, 135013
Valid prediction for snap_scaffold_3-snap.3510-T1
Valid prediction for GlimmerHMM_glimmerT_8470-T1
Valid prediction for Augustus_model.g5622.t1
Valid prediction for snap_scaffold_3-snap.3531-T1
Valid prediction for GlimmerHMM_glimmerT_8450-T1
Valid prediction for pasa_asmbl_40676.p1
Valid prediction for snap_scaffold_3-snap.3513-T1
Valid prediction for snap_scaffold_3-snap.3530-T1
Valid prediction for Augustus_model.g5611.t1
Couldn't classify 117268, 118770
Sorry, prediction pasa_asmbl_40678.p1 fails validation.
(GCC)	 AC	117268-118770	AA	TCA
Valid prediction for GlimmerHMM_glimmerT_8467-T1
Valid prediction for Augustus_model.g5619.t1
Valid prediction for GlimmerHMM_glimmerT_8462-T1
Valid prediction for GeneMark_model.13749_t
Valid prediction for snap_scaffold_3-snap.3526-T1
Valid prediction for snap_scaffold_3-snap.3508-T1
Valid prediction for snap_scaffold_3-snap.3511-T1
Valid prediction for GeneMark_model.13746_t
Valid prediction for GlimmerHMM_glimmerT_8448-T1
Valid prediction for snap_scaffold_3-snap.3533-T1
Valid prediction for GeneMark_model.13732_t

-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 snap_scaffold_3-snap.3528-T1
Valid prediction for GeneMark_model.13758_t
Valid prediction for GeneMark_model.13755_t
Valid prediction for GlimmerHMM_glimmerT_8469-T1
Couldn't classify 8437, 8554
Couldn't classify 9740, 9751
Sorry, prediction pasa_asmbl_39534.p1 fails validation.
(ATC)	 AC	8437-8554	GT	AGG
(ACA)	 AG	8663-8757	GT	AGG
(ATC)	 AG	8895-9022	GT	AGG
(GTC)	 AG	9130-9219	GT	TGG
(TTT)	 AG	9324-9385	GT	GAG
(CGA)	 AG	9478-9647	GT	AGG
(GAG)	 AG	9740-9751	GA	GAG
add_exon() Sorry, pasa_asmbl_39534.p1 9324-9385-terminal-2 is invalid.
-recovered pasa_asmbl_39534.p1, terminal, 9324, 9385
-recovered pasa_asmbl_39534.p1, internal, 8663, 8757
-recovered pasa_asmbl_39534.p1, internal, 8895, 9022
-recovered pasa_asmbl_39534.p1, internal, 9130, 9219
-recovered pasa_asmbl_39534.p1, internal, 9324, 9385
-recovered pasa_asmbl_39534.p1, internal, 9478, 9647
Valid prediction for Augustus_model.g5618.t1
Valid prediction for snap_scaffold_3-snap.3516-T1
Valid prediction for snap_scaffold_3-snap.3522-T1
Valid prediction for GeneMark_model.13739_t
Valid prediction for GlimmerHMM_glimmerT_8463-T1
Valid prediction for snap_scaffold_3-snap.3537-T1
Valid prediction for snap_scaffold_3-snap.3536-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.13735_t
Valid prediction for snap_scaffold_3-snap.3521-T1
Valid prediction for GeneMark_model.13742_t
Valid prediction for GeneMark_model.13750_t
Valid prediction for GlimmerHMM_glimmerT_8460-T1
Valid prediction for GeneMark_model.13738_t
Couldn't classify 88395, 88432
Couldn't classify 90174, 90193
Sorry, prediction pasa_asmbl_39531.p1 fails validation.
(GTT)	 GT	88395-88432	GT	CAG
(CTG)	 AG	88698-88788	GT	AGG
(AAA)	 AG	88878-88928	GT	TGG
(GAC)	 AG	89173-89260	GT	AGG
(ACG)	 AG	89591-89655	GT	TGG
(CGT)	 AG	89751-89805	GT	CAG
(TTG)	 AG	90174-90193	AG	CCA
-recovered pasa_asmbl_39531.p1, internal, 88698, 88788
-recovered pasa_asmbl_39531.p1, internal, 88878, 88928
-recovered pasa_asmbl_39531.p1, internal, 89173, 89260
-recovered pasa_asmbl_39531.p1, internal, 89591, 89655
-recovered pasa_asmbl_39531.p1, internal, 89751, 89805
Valid prediction for snap_scaffold_3-snap.3512-T1
Couldn't classify 98362, 98467
Sorry, prediction pasa_asmbl_39527.p1 fails validation.
(ACA)	 TT	98362-98467	GT	AGG
(GAA)	 AG	99020-99085	GT	TGG
(TGG)	 AG	99273-99301	GT	AGG
(ATC)	 AG	99409-99546	GT	TGG
(GTG)	 AG	100871-100957	GT	AGG
(AGA)	 AG	101138-101212	GT	AGG
(GAG)	 AG	101315-101421	GT	AGG
(GTG)	 AG	103107-103242	GT	CGG
(CTC)	 AG	105205-105528	AG	AGA
-recovered pasa_asmbl_39527.p1, terminal, 105205, 105528
-recovered pasa_asmbl_39527.p1, internal, 99020, 99085
-recovered pasa_asmbl_39527.p1, internal, 99273, 99301
-recovered pasa_asmbl_39527.p1, internal, 99409, 99546
-recovered pasa_asmbl_39527.p1, internal, 100871, 100957
-recovered pasa_asmbl_39527.p1, internal, 101138, 101212
-recovered pasa_asmbl_39527.p1, internal, 101315, 101421
-recovered pasa_asmbl_39527.p1, internal, 103107, 103242
Valid prediction for GlimmerHMM_glimmerT_8461-T1
Valid prediction for GlimmerHMM_glimmerT_8459-T1
Valid prediction for GeneMark_model.13737_t
Valid prediction for GeneMark_model.13734_t
Valid prediction for GeneMark_model.13745_t
Couldn't classify 5772, 5877
Couldn't classify 7300, 7370
Sorry, prediction pasa_asmbl_39535.p1 fails validation.
(GCT)	 GA	5772-5877	GT	AGG
(AGG)	 AG	6173-6252	GT	TGG
(ACG)	 AG	6519-6780	GT	AGG
(GCA)	 AG	7300-7370	GT	AGG
-recovered pasa_asmbl_39535.p1, internal, 6173, 6252
-recovered pasa_asmbl_39535.p1, internal, 6519, 6780
-recovered pasa_asmbl_39535.p1, internal, 7300, 7370
Valid prediction for snap_scaffold_3-snap.3509-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.13752_t
Valid prediction for GlimmerHMM_glimmerT_8471-T1
Valid prediction for snap_scaffold_3-snap.3527-T1
Valid prediction for CodingQuarry_transcript_46353-T1
Valid prediction for snap_scaffold_3-snap.3535-T1
Valid prediction for pasa_asmbl_39532.p1
Valid prediction for snap_scaffold_3-snap.3532-T1
Valid prediction for GeneMark_model.13740_t
Valid prediction for GlimmerHMM_glimmerT_8458-T1
Valid prediction for Augustus_model.g5623.t1
Valid prediction for Augustus_model.g5616.t1
Valid prediction for snap_scaffold_3-snap.3534-T1
Valid prediction for GeneMark_model.13748_t
Valid prediction for GlimmerHMM_glimmerT_8451-T1
Valid prediction for snap_scaffold_3-snap.3523-T1
Valid prediction for CodingQuarry_transcript_46356-T1
Valid prediction for pasa_asmbl_39526.p1
Valid prediction for Augustus_model.g5614.t1
Valid prediction for GlimmerHMM_glimmerT_8455-T1
Valid prediction for snap_scaffold_3-snap.3504-T1
Valid prediction for snap_scaffold_3-snap.3519-T1
Valid prediction for GlimmerHMM_glimmerT_8454-T1
Valid prediction for snap_scaffold_3-snap.3540-T1
Valid prediction for snap_scaffold_3-snap.3529-T1
Valid prediction for GlimmerHMM_glimmerT_8456-T1
Valid prediction for Augustus_model.g5612.t1
Valid prediction for Augustus_model.g5615.t1
Valid prediction for snap_scaffold_3-snap.3539-T1
Valid prediction for GeneMark_model.13757_t
Valid prediction for CodingQuarry_transcript_46354-T1
Valid prediction for snap_scaffold_3-snap.3515-T1
Valid prediction for GeneMark_model.13747_t
Valid prediction for GeneMark_model.13754_t
Valid prediction for snap_scaffold_3-snap.3520-T1
Valid prediction for snap_scaffold_3-snap.3517-T1
Valid prediction for GlimmerHMM_glimmerT_8466-T1
Couldn't classify 11659, 11748
Couldn't classify 12051, 12140
Sorry, prediction pasa_asmbl_39652.p1 fails validation.
(AAC)	 CA	11659-11748	GT	TGG
(ATG)	 AG	11837-11953	GT	AGG
(AAT)	 AG	12051-12140	GA	CCG
-recovered pasa_asmbl_39652.p1, initial, 11837, 11953
-recovered pasa_asmbl_39652.p1, internal, 11837, 11953
Valid prediction for Augustus_model.g5613.t1
Valid prediction for Augustus_model.g5617.t1
Valid prediction for HiQ_model.g5621.t1
Valid prediction for GeneMark_model.13741_t
Valid prediction for GlimmerHMM_glimmerT_8457-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4410, rend_intergenic: 2621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102860, rend_intergenic: 81652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112926, rend_intergenic: 111330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139387, rend_intergenic: 126264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166020
-exon list size: 553


building trellis

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97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 4410, rend_intergenic: 2621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102860, rend_intergenic: 81652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112926, rend_intergenic: 111330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139387, rend_intergenic: 126264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support