-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_10036239-10298646

-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_22-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_50110-T1
Valid prediction for Augustus_model.g33432.t1
Couldn't classify 21733, 21896
Sorry, prediction pasa_asmbl_30342.p1 fails validation.
(TTG)	 GT	21733-21896	GT	AGG
(TAA)	 AG	23050-23081	GT	CCG
(CGT)	 AG	23827-24011	GT	AGG
(GTC)	 AG	24316-24420	CA	GAC
-recovered pasa_asmbl_30342.p1, terminal, 24316, 24420
-recovered pasa_asmbl_30342.p1, internal, 23050, 23081
-recovered pasa_asmbl_30342.p1, internal, 23827, 24011
Valid prediction for snap_scaffold_22-snap.2098-T1
Valid prediction for snap_scaffold_22-snap.2099-T1
Valid prediction for snap_scaffold_22-snap.2108-T1
Couldn't classify 79536, 79560
Couldn't classify 82372, 82486
Sorry, prediction pasa_asmbl_30533.p1 fails validation.
(GAC)	 AC	79536-79560	GT	AGG
(GGC)	 AG	79879-79914	GT	TGG
(ACC)	 AG	80408-80517	GT	AGG
(GTG)	 AG	81457-81566	GT	AAG
(TGT)	 AG	82372-82486	AA	ACA
-recovered pasa_asmbl_30533.p1, internal, 79879, 79914
-recovered pasa_asmbl_30533.p1, internal, 80408, 80517
-recovered pasa_asmbl_30533.p1, internal, 81457, 81566
Valid prediction for GlimmerHMM_glimmerT_50112-T1
Valid prediction for GlimmerHMM_glimmerT_50101-T1
Valid prediction for HiQ_model.g33429.t1
Valid prediction for GlimmerHMM_glimmerT_50099-T1
Valid prediction for snap_scaffold_22-snap.2094-T1
Valid prediction for Augustus_model.g33438.t1
Valid prediction for Augustus_model.g33433.t1
Couldn't classify 72095, 72242
Couldn't classify 73705, 73789
Sorry, prediction pasa_asmbl_30349.p1 fails validation.
(CTG)	 AG	72095-72242	GT	CGG
(ATT)	 AG	72353-72454	GT	TGG
(GAG)	 AG	72580-72653	GT	AGG
(GGT)	 AG	72861-72957	GT	CAG
(AGA)	 AG	73308-73392	GT	GAG
(GTA)	 AG	73705-73789	GT	ACG
-recovered pasa_asmbl_30349.p1, internal, 72095, 72242
-recovered pasa_asmbl_30349.p1, internal, 72353, 72454
-recovered pasa_asmbl_30349.p1, internal, 72580, 72653
-recovered pasa_asmbl_30349.p1, internal, 72861, 72957
-recovered pasa_asmbl_30349.p1, internal, 73308, 73392
-recovered pasa_asmbl_30349.p1, internal, 73705, 73789
Valid prediction for snap_scaffold_22-snap.2100-T1
Valid prediction for snap_scaffold_22-snap.2069-T1
Valid prediction for Augustus_model.g33437.t1
Valid prediction for snap_scaffold_22-snap.2064-T1
Valid prediction for CodingQuarry_transcript_34268-T1
Valid prediction for snap_scaffold_22-snap.2074-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50109-T1
Valid prediction for GlimmerHMM_glimmerT_50115-T1
Valid prediction for snap_scaffold_22-snap.2107-T1
Valid prediction for Augustus_model.g33434.t1
Valid prediction for snap_scaffold_22-snap.2105-T1
Valid prediction for GlimmerHMM_glimmerT_50113-T1
Valid prediction for snap_scaffold_22-snap.2087-T1
Valid prediction for GlimmerHMM_glimmerT_50103-T1
Valid prediction for snap_scaffold_22-snap.2103-T1
Valid prediction for snap_scaffold_22-snap.2089-T1
Valid prediction for Augustus_model.g33435.t1
Valid prediction for snap_scaffold_22-snap.2101-T1
Valid prediction for snap_scaffold_22-snap.2085-T1
Valid prediction for GlimmerHMM_glimmerT_50111-T1
Valid prediction for snap_scaffold_22-snap.2066-T1
Valid prediction for GlimmerHMM_glimmerT_50100-T1
Couldn't classify 56699, 56786
Couldn't classify 57949, 58041
Sorry, prediction pasa_asmbl_30348.p1 fails validation.
(ATC)	 TG	56699-56786	GT	CAG
(CCC)	 AG	56997-57090	GT	AAG
(GTT)	 AG	57623-57725	GT	AGG
(GGT)	 AG	57949-58041	AG	AGA
-recovered pasa_asmbl_30348.p1, internal, 56997, 57090
-recovered pasa_asmbl_30348.p1, internal, 57623, 57725
Couldn't classify 240380, 240778
Sorry, prediction pasa_asmbl_29594.p3 fails validation.
(GAA)	 AT	240380-240778	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_50104-T1
Valid prediction for Augustus_model.g33436.t1
Valid prediction for GlimmerHMM_glimmerT_50107-T1
Valid prediction for snap_scaffold_22-snap.2063-T1
Valid prediction for snap_scaffold_22-snap.2086-T1
Valid prediction for snap_scaffold_22-snap.2068-T1
Valid prediction for snap_scaffold_22-snap.2092-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_50108-T1
Valid prediction for snap_scaffold_22-snap.2080-T1
Valid prediction for snap_scaffold_22-snap.2088-T1
Valid prediction for pasa_asmbl_29590.p1
Valid prediction for snap_scaffold_22-snap.2061-T1
Valid prediction for snap_scaffold_22-snap.2096-T1
Valid prediction for snap_scaffold_22-snap.2078-T1
Couldn't classify 258126, 258298
Sorry, prediction pasa_asmbl_29576.p2 fails validation.
(CAG)	 CT	258126-258298	GT	AGG
(GTG)	 AG	258556-258724	AG	AGA
-recovered pasa_asmbl_29576.p2, terminal, 258556, 258724
Valid prediction for Augustus_model.g33430.t1
Valid prediction for snap_scaffold_22-snap.2081-T1
Valid prediction for snap_scaffold_22-snap.2104-T1
Valid prediction for snap_scaffold_22-snap.2077-T1
Valid prediction for snap_scaffold_22-snap.2073-T1
Valid prediction for snap_scaffold_22-snap.2090-T1
Valid prediction for Augustus_model.g33441.t1
Couldn't classify 49630, 49737
Couldn't classify 55321, 55446
Sorry, prediction pasa_asmbl_29589.p1 fails validation.
(AGG)	 GC	49630-49737	GT	GAG
(GCC)	 AG	51079-51193	GT	AAG
(TGA)	 AG	51489-51733	GT	AGG
(GTG)	 AG	52212-52340	GT	AGG
(ACG)	 AG	53068-53130	GT	ACG
(GTA)	 AG	53606-53656	GT	AGG
(ATG)	 AG	54251-54281	GT	CCG
(GAC)	 AG	54885-55000	GT	CGG
(GTG)	 AG	55321-55446	AG	AGA
-recovered pasa_asmbl_29589.p1, initial, 54251, 54281
-recovered pasa_asmbl_29589.p1, internal, 51079, 51193
-recovered pasa_asmbl_29589.p1, internal, 51489, 51733
-recovered pasa_asmbl_29589.p1, internal, 52212, 52340
-recovered pasa_asmbl_29589.p1, internal, 53068, 53130
-recovered pasa_asmbl_29589.p1, internal, 53606, 53656
-recovered pasa_asmbl_29589.p1, internal, 54251, 54281
-recovered pasa_asmbl_29589.p1, internal, 54885, 55000
Couldn't classify 24918, 25722
Sorry, prediction pasa_asmbl_29769.p1 fails validation.
(ATG)	 GG	24532-24572	GT	ACG
(AAA)	 AG	24918-25722	AC	CCA
-recovered pasa_asmbl_29769.p1, initial, 24532, 24572
Valid prediction for snap_scaffold_22-snap.2083-T1
Valid prediction for snap_scaffold_22-snap.2059-T1
Couldn't classify 17554, 18636
Sorry, prediction pasa_asmbl_29704.p1 fails validation.
(GGT)	 GT	17554-18636	TC	AAT
Valid prediction for snap_scaffold_22-snap.2095-T1
Valid prediction for snap_scaffold_22-snap.2102-T1
Valid prediction for snap_scaffold_22-snap.2091-T1
Valid prediction for snap_scaffold_22-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_50106-T1
Valid prediction for snap_scaffold_22-snap.2070-T1
Valid prediction for CodingQuarry_transcript_34270-T1
Couldn't classify 63604, 63738
Couldn't classify 64807, 64977
Sorry, prediction pasa_asmbl_29585.p1 fails validation.
(CAC)	 AA	63604-63738	GT	AGG
(ACT)	 AG	64476-64538	GT	AGG
(GAG)	 AG	64807-64977	AA	TCA
-recovered pasa_asmbl_29585.p1, internal, 64476, 64538
Couldn't classify 30394, 30507
Couldn't classify 32554, 32613
Sorry, prediction pasa_asmbl_29717.p1 fails validation.
(GGG)	 GT	30394-30507	GT	TGG
(GCC)	 AG	31689-31814	GT	AGG
(GAA)	 AG	31930-31971	GT	AGG
(TGC)	 AG	32554-32613	GT	TGG
-recovered pasa_asmbl_29717.p1, internal, 31689, 31814
-recovered pasa_asmbl_29717.p1, internal, 31930, 31971
-recovered pasa_asmbl_29717.p1, internal, 32554, 32613
Valid prediction for snap_scaffold_22-snap.2072-T1
Valid prediction for GlimmerHMM_glimmerT_50102-T1
Valid prediction for GlimmerHMM_glimmerT_50097-T1
Valid prediction for GlimmerHMM_glimmerT_50098-T1
Valid prediction for CodingQuarry_transcript_34269-T1
Valid prediction for Augustus_model.g33440.t1
Valid prediction for snap_scaffold_22-snap.2079-T1
Valid prediction for GlimmerHMM_glimmerT_50118-T1
Valid prediction for Augustus_model.g33431.t1
Valid prediction for snap_scaffold_22-snap.2097-T1
Couldn't classify 58022, 58055
Couldn't classify 61373, 61549
Sorry, prediction pasa_asmbl_29586.p1 fails validation.
(CTC)	 CG	58022-58055	GT	GAG
(TGG)	 AG	58741-58844	GT	CGG
(ATG)	 AG	59225-59293	GT	GAG
(TTT)	 AG	59616-59659	GT	TGG
(GGA)	 AG	59808-59890	GT	TGG
(ATG)	 AG	60501-60530	GT	CAG
(TGG)	 AG	60803-60918	GT	AGG
(GGG)	 AG	61014-61127	GT	AGG
(AAG)	 AG	61373-61549	GG	ACG
-recovered pasa_asmbl_29586.p1, initial, 59225, 59293
-recovered pasa_asmbl_29586.p1, initial, 60501, 60530
-recovered pasa_asmbl_29586.p1, internal, 58741, 58844
-recovered pasa_asmbl_29586.p1, internal, 59225, 59293
-recovered pasa_asmbl_29586.p1, internal, 59616, 59659
-recovered pasa_asmbl_29586.p1, internal, 59808, 59890
-recovered pasa_asmbl_29586.p1, internal, 60501, 60530
-recovered pasa_asmbl_29586.p1, internal, 60803, 60918
-recovered pasa_asmbl_29586.p1, internal, 61014, 61127
Valid prediction for snap_scaffold_22-snap.2076-T1
Valid prediction for snap_scaffold_22-snap.2065-T1
Couldn't classify 254392, 254677
Sorry, prediction pasa_asmbl_29580.p1 fails validation.
(ATG)	 TC	253941-254179	GT	AGG
(TAA)	 AG	254392-254677	GT	AGG
-recovered pasa_asmbl_29580.p1, initial, 253941, 254179
-recovered pasa_asmbl_29580.p1, internal, 254392, 254677
Valid prediction for CodingQuarry_transcript_34271-T1
Valid prediction for Augustus_model.g33439.t1
Valid prediction for snap_scaffold_22-snap.2093-T1
Valid prediction for snap_scaffold_22-snap.2062-T1
Valid prediction for snap_scaffold_22-snap.2075-T1
Valid prediction for snap_scaffold_22-snap.2082-T1
Couldn't classify 33278, 33378
Couldn't classify 33505, 34933
Sorry, prediction pasa_asmbl_29592.p1 fails validation.
(ACG)	 AG	33278-33378	GT	AGG
(GCC)	 AG	33505-34933	GT	AGG
-recovered pasa_asmbl_29592.p1, internal, 33278, 33378
-recovered pasa_asmbl_29592.p1, internal, 33505, 34933
Valid prediction for snap_scaffold_22-snap.2071-T1
Valid prediction for GlimmerHMM_glimmerT_50117-T1
Valid prediction for GlimmerHMM_glimmerT_50116-T1
Valid prediction for GlimmerHMM_glimmerT_50114-T1
Valid prediction for Augustus_model.g33427.t1
Valid prediction for GlimmerHMM_glimmerT_50105-T1
Valid prediction for HiQ_model.g33428.t1
Valid prediction for snap_scaffold_22-snap.2106-T1
Couldn't classify 26029, 26097
Couldn't classify 27423, 27545
Sorry, prediction pasa_asmbl_29593.p1 fails validation.
(CAA)	 TA	26029-26097	GC	AGG
(GCC)	 AG	26119-26373	GT	AGG
(CTG)	 AG	26618-26737	GT	TGG
(GTG)	 AG	27423-27545	GT	AGG
-recovered pasa_asmbl_29593.p1, internal, 26119, 26373
-recovered pasa_asmbl_29593.p1, internal, 26618, 26737
-recovered pasa_asmbl_29593.p1, internal, 27423, 27545
Valid prediction for snap_scaffold_22-snap.2067-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24420, rend_intergenic: 10318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31790, rend_intergenic: 24986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43865, rend_intergenic: 32876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56814, rend_intergenic: 47353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85876, rend_intergenic: 56948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128563, rend_intergenic: 88194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157898, rend_intergenic: 129560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160462, rend_intergenic: 157986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167069, rend_intergenic: 162613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181388, rend_intergenic: 180678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201201, rend_intergenic: 188804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228525, rend_intergenic: 201227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233760, rend_intergenic: 229003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242811, rend_intergenic: 235003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248565, rend_intergenic: 245451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259944, rend_intergenic: 250768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 262408
-exon list size: 475


building trellis

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89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 24420, rend_intergenic: 10318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31790, rend_intergenic: 24986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43865, rend_intergenic: 32876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56814, rend_intergenic: 47353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85876, rend_intergenic: 56948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128563, rend_intergenic: 88194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157898, rend_intergenic: 129560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160462, rend_intergenic: 157986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167069, rend_intergenic: 162613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181388, rend_intergenic: 180678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201201, rend_intergenic: 188804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228525, rend_intergenic: 201227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233760, rend_intergenic: 229003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242811, rend_intergenic: 235003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248565, rend_intergenic: 245451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259944, rend_intergenic: 250768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support