-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_6278201-6489189

-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_10-snap.1304-T1
Valid prediction for GlimmerHMM_glimmerT_24879-T1
Valid prediction for GlimmerHMM_glimmerT_24882-T1
Valid prediction for HiQ_model.g16554.t1
Valid prediction for snap_scaffold_10-snap.1339-T1
Valid prediction for snap_scaffold_10-snap.1309-T1
Valid prediction for snap_scaffold_10-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_24874-T1
Valid prediction for snap_scaffold_10-snap.1302-T1
Valid prediction for Augustus_model.g16558.t1
Valid prediction for Augustus_model.g16551.t1
Valid prediction for snap_scaffold_10-snap.1345-T1
Valid prediction for snap_scaffold_10-snap.1344-T1
Valid prediction for Augustus_model.g16564.t1
Valid prediction for snap_scaffold_10-snap.1329-T1
Valid prediction for snap_scaffold_10-snap.1346-T1
Valid prediction for GlimmerHMM_glimmerT_24885-T1
Valid prediction for snap_scaffold_10-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_24864-T1
Valid prediction for GlimmerHMM_glimmerT_24865-T1
Couldn't classify 127301, 127354
Sorry, prediction pasa_asmbl_3240.p1 fails validation.
(GGT)	 CA	127301-127354	GT	AGG
(GAG)	 AG	127506-127661	GT	AGG
(GTG)	 AG	127780-127945	GT	TGG
(ATG)	 AG	128078-128167	GT	AGG
(ACT)	 AG	128318-128418	GT	AGG
(ACG)	 AG	128494-128549	GT	AAG
(TTA)	 AG	128658-128755	GT	TGG
(ATG)	 AG	128931-129079	GT	AGG
(AAC)	 AG	129252-129342	GT	CTG
(TTG)	 AG	129503-129840	GT	ATG
(ACC)	 AG	130077-130292	GT	ACG
(TTT)	 AG	130377-130439	GT	AGG
(GAA)	 AG	130540-130617	CA	AGC
add_exon() Sorry, pasa_asmbl_3240.p1 128078-128167-initial-1 is invalid.
-recovered pasa_asmbl_3240.p1, initial, 128078, 128167
add_exon() Sorry, pasa_asmbl_3240.p1 128931-129079-initial-1 is invalid.
-recovered pasa_asmbl_3240.p1, initial, 128931, 129079
add_exon() Sorry, pasa_asmbl_3240.p1 128078-128167-terminal-1 is invalid.
-recovered pasa_asmbl_3240.p1, terminal, 128078, 128167
-recovered pasa_asmbl_3240.p1, terminal, 130540, 130617
-recovered pasa_asmbl_3240.p1, internal, 127506, 127661
-recovered pasa_asmbl_3240.p1, internal, 127780, 127945
-recovered pasa_asmbl_3240.p1, internal, 128078, 128167
-recovered pasa_asmbl_3240.p1, internal, 128318, 128418
-recovered pasa_asmbl_3240.p1, internal, 128494, 128549
-recovered pasa_asmbl_3240.p1, internal, 128658, 128755
-recovered pasa_asmbl_3240.p1, internal, 128931, 129079
-recovered pasa_asmbl_3240.p1, internal, 129252, 129342
-recovered pasa_asmbl_3240.p1, internal, 129503, 129840
-recovered pasa_asmbl_3240.p1, internal, 130077, 130292
-recovered pasa_asmbl_3240.p1, internal, 130377, 130439
Valid prediction for GlimmerHMM_glimmerT_24869-T1
Valid prediction for snap_scaffold_10-snap.1334-T1
Valid prediction for Augustus_model.g16557.t1
Valid prediction for snap_scaffold_10-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_24871-T1
Valid prediction for snap_scaffold_10-snap.1335-T1
Valid prediction for Augustus_model.g16562.t1
Valid prediction for snap_scaffold_10-snap.1325-T1
Valid prediction for snap_scaffold_10-snap.1341-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_24873-T1
Valid prediction for snap_scaffold_10-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_24862-T1
Valid prediction for Augustus_model.g16559.t1
Couldn't classify 47481, 47607
Sorry, prediction pasa_asmbl_3236.p1 fails validation.
(CCA)	 CT	47481-47607	GT	AGG
(GGA)	 AG	50574-50781	GT	TGG
(TAA)	 AG	52240-52372	GT	TGG
(GGT)	 AG	52733-52806	GT	AGG
(GTT)	 AG	52911-53032	GT	AGG
(GTA)	 AG	53114-54260	GT	AGG
(CTT)	 AG	54691-54931	CA	GAC
-recovered pasa_asmbl_3236.p1, terminal, 54691, 54931
-recovered pasa_asmbl_3236.p1, internal, 50574, 50781
-recovered pasa_asmbl_3236.p1, internal, 52240, 52372
-recovered pasa_asmbl_3236.p1, internal, 52733, 52806
-recovered pasa_asmbl_3236.p1, internal, 52911, 53032
-recovered pasa_asmbl_3236.p1, internal, 53114, 54260
Valid prediction for snap_scaffold_10-snap.1308-T1
Valid prediction for snap_scaffold_10-snap.1312-T1
Valid prediction for snap_scaffold_10-snap.1313-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 snap_scaffold_10-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_24877-T1
Valid prediction for HiQ_model.g16560.t1
Couldn't classify 39331, 39511
Sorry, prediction pasa_asmbl_4460.p1 fails validation.
(CCT)	 CC	39331-39511	GT	AGG
(CCT)	 AG	39746-39872	GT	GAG
(GGG)	 AG	40997-41163	GT	AGG
(GTG)	 AG	41448-41629	AG	GAA
-recovered pasa_asmbl_4460.p1, terminal, 41448, 41629
-recovered pasa_asmbl_4460.p1, internal, 39746, 39872
-recovered pasa_asmbl_4460.p1, internal, 40997, 41163
Valid prediction for snap_scaffold_10-snap.1331-T1
Valid prediction for snap_scaffold_10-snap.1340-T1
Valid prediction for GlimmerHMM_glimmerT_24870-T1
Valid prediction for Augustus_model.g16561.t1
Valid prediction for snap_scaffold_10-snap.1324-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.1322-T1
Valid prediction for GlimmerHMM_glimmerT_24883-T1
Valid prediction for HiQ_model.g16566.t1
Valid prediction for snap_scaffold_10-snap.1326-T1
Valid prediction for GlimmerHMM_glimmerT_24880-T1
Valid prediction for snap_scaffold_10-snap.1330-T1
Couldn't classify 13416, 13611
Sorry, prediction pasa_asmbl_4469.p1 fails validation.
(TGT)	 AT	13416-13611	GT	TGG
(ACA)	 AG	15122-15313	GT	GGG
(CCT)	 AG	17308-17469	GT	GGG
(GTG)	 AG	17601-17759	GT	GGG
(GTC)	 AG	19748-19848	GT	AGG
(GTG)	 AG	20062-20205	GT	AGG
(ATT)	 AG	20315-20474	GT	TGG
(ACA)	 AG	21439-21476	GT	AGG
(GTG)	 AG	21583-21714	GT	AGG
(GTG)	 AG	22534-22710	GT	AGG
(TTG)	 AG	22818-23114	AG	AGA
-recovered pasa_asmbl_4469.p1, terminal, 22818, 23114
-recovered pasa_asmbl_4469.p1, internal, 15122, 15313
-recovered pasa_asmbl_4469.p1, internal, 17308, 17469
-recovered pasa_asmbl_4469.p1, internal, 17601, 17759
-recovered pasa_asmbl_4469.p1, internal, 19748, 19848
-recovered pasa_asmbl_4469.p1, internal, 20062, 20205
-recovered pasa_asmbl_4469.p1, internal, 20315, 20474
-recovered pasa_asmbl_4469.p1, internal, 21439, 21476
-recovered pasa_asmbl_4469.p1, internal, 21583, 21714
-recovered pasa_asmbl_4469.p1, internal, 22534, 22710
Valid prediction for HiQ_model.g16563.t1
Valid prediction for snap_scaffold_10-snap.1315-T1
Valid prediction for snap_scaffold_10-snap.1306-T1
Valid prediction for snap_scaffold_10-snap.1310-T1
Valid prediction for pasa_asmbl_4455.p1
Valid prediction for GlimmerHMM_glimmerT_24886-T1
Valid prediction for Augustus_model.g16555.t1
Valid prediction for GlimmerHMM_glimmerT_24875-T1
Valid prediction for GlimmerHMM_glimmerT_24872-T1
Valid prediction for Augustus_model.g16556.t1
Valid prediction for GlimmerHMM_glimmerT_24878-T1
Valid prediction for GlimmerHMM_glimmerT_24863-T1
Valid prediction for snap_scaffold_10-snap.1318-T1
Valid prediction for snap_scaffold_10-snap.1319-T1
Valid prediction for CodingQuarry_transcript_5442-T1
Valid prediction for snap_scaffold_10-snap.1342-T1
Valid prediction for GlimmerHMM_glimmerT_24868-T1
Valid prediction for snap_scaffold_10-snap.1328-T1
Valid prediction for Augustus_model.g16553.t1
Valid prediction for snap_scaffold_10-snap.1333-T1
Valid prediction for pasa_asmbl_4452.p1
Valid prediction for snap_scaffold_10-snap.1332-T1
Valid prediction for GlimmerHMM_glimmerT_24867-T1
Valid prediction for GlimmerHMM_glimmerT_24884-T1
Couldn't classify 68854, 68916
Sorry, prediction pasa_asmbl_5105.p1 fails validation.
(ATG)	 AG	67656-67710	GT	TGG
(GTC)	 AG	67795-67991	GT	TGG
(GAG)	 AG	68854-68916	AG	AGA
-recovered pasa_asmbl_5105.p1, initial, 67656, 67710
-recovered pasa_asmbl_5105.p1, internal, 67656, 67710
-recovered pasa_asmbl_5105.p1, internal, 67795, 67991
Valid prediction for snap_scaffold_10-snap.1311-T1
Valid prediction for GlimmerHMM_glimmerT_24866-T1
Valid prediction for GlimmerHMM_glimmerT_24881-T1
Couldn't classify 38291, 38386
Couldn't classify 38992, 39249
Sorry, prediction pasa_asmbl_4461.p1 fails validation.
(GTC)	 GT	38291-38386	GT	CAG
(GGT)	 AG	38992-39249	CC	CGC
Valid prediction for CodingQuarry_transcript_5443-T1
Valid prediction for Augustus_model.g16552.t1
Valid prediction for snap_scaffold_10-snap.1314-T1
Valid prediction for Augustus_model.g16565.t1
Valid prediction for snap_scaffold_10-snap.1327-T1
Valid prediction for GlimmerHMM_glimmerT_24876-T1
Valid prediction for snap_scaffold_10-snap.1317-T1
Valid prediction for snap_scaffold_10-snap.1323-T1
Valid prediction for snap_scaffold_10-snap.1343-T1
Valid prediction for pasa_asmbl_4456.p1
Valid prediction for snap_scaffold_10-snap.1320-T1
Valid prediction for pasa_asmbl_4453.p1
Valid prediction for HiQ_model.g16567.t1
Valid prediction for snap_scaffold_10-snap.1303-T1
Valid prediction for snap_scaffold_10-snap.1338-T1
Valid prediction for CodingQuarry_transcript_5441-T1
Valid prediction for snap_scaffold_10-snap.1316-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7851, rend_intergenic: 4291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12873, rend_intergenic: 9985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36874, rend_intergenic: 33517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48386, rend_intergenic: 45120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102321, rend_intergenic: 96877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107886, rend_intergenic: 106398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115135, rend_intergenic: 108656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130398, rend_intergenic: 117708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148567, rend_intergenic: 138362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159022, rend_intergenic: 155527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170929, rend_intergenic: 168831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173916, rend_intergenic: 171412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206176, rend_intergenic: 181645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210989
-exon list size: 442


building trellis

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26.8    
27.0    
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27.9    
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28.8    
29.1    
29.3    
29.5    
29.7    
30.0    
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30.6    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
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35.4    
35.6    
35.8    
36.0    
36.3    
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36.7    
36.9    
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37.6    
37.8    
38.1    
38.3    
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38.7    
39.0    
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39.6    
39.9    
40.1    
40.3    
40.5    
40.8    
41.0    
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41.7    
41.9    
42.1    
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42.6    
42.8    
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43.9    
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44.6    
44.8    
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45.5    
45.7    
45.9    
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46.8    
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92.6    
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97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 7851, rend_intergenic: 4291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12873, rend_intergenic: 9985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36874, rend_intergenic: 33517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48386, rend_intergenic: 45120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102321, rend_intergenic: 96877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107886, rend_intergenic: 106398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115135, rend_intergenic: 108656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130398, rend_intergenic: 117708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148567, rend_intergenic: 138362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159022, rend_intergenic: 155527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170929, rend_intergenic: 168831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173916, rend_intergenic: 171412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206176, rend_intergenic: 181645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support