-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_7332114-7501299

-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_28-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_59100-T1
Couldn't classify 85048, 85176
Couldn't classify 85978, 86295
Sorry, prediction pasa_asmbl_37675.p1 fails validation.
(GCT)	 AG	85048-85176	GT	AGG
(TTC)	 AG	85978-86295	AT	GCA
-recovered pasa_asmbl_37675.p1, internal, 85048, 85176
Valid prediction for GlimmerHMM_glimmerT_59101-T1
Valid prediction for Augustus_model.g39169.t1
Valid prediction for snap_scaffold_28-snap.1673-T1
Valid prediction for snap_scaffold_28-snap.1658-T1
Valid prediction for HiQ_model.g39181.t1
Couldn't classify 139059, 139547
Couldn't classify 142998, 143056
Sorry, prediction pasa_asmbl_37682.p1 fails validation.
(TCC)	 GC	139059-139547	GT	AGG
(GCC)	 AG	141001-141055	GT	AGG
(CGC)	 AG	142998-143056	AG	ACA
-recovered pasa_asmbl_37682.p1, internal, 141001, 141055
Valid prediction for CodingQuarry_transcript_43712-T1
Valid prediction for pasa_asmbl_37680.p1
Valid prediction for snap_scaffold_28-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_59122-T1
Valid prediction for pasa_asmbl_37677.p1
Valid prediction for snap_scaffold_28-snap.1681-T1
Valid prediction for snap_scaffold_28-snap.1674-T1
Valid prediction for HiQ_model.g39171.t1
Valid prediction for GlimmerHMM_glimmerT_59106-T1
Valid prediction for snap_scaffold_28-snap.1668-T1
Couldn't classify 19949, 19991
Couldn't classify 20549, 20605
Sorry, prediction pasa_asmbl_37820.p2 fails validation.
(GGC)	 AC	19949-19991	GT	CCG
(GCC)	 AG	20097-20233	GT	AGG
(GAA)	 AG	20327-20437	GT	ACG
(GAA)	 AG	20549-20605	AG	AAA
-recovered pasa_asmbl_37820.p2, internal, 20097, 20233
-recovered pasa_asmbl_37820.p2, internal, 20327, 20437
Valid prediction for GlimmerHMM_glimmerT_59118-T1
Couldn't classify 124169, 124326
Couldn't classify 128026, 128042
Sorry, prediction pasa_asmbl_37856.p2 fails validation.
(CTG)	 AG	124169-124326	GT	AGG
(GTC)	 AG	126230-126308	GT	TGG
(CTC)	 AG	127348-127420	GT	AGG
(GCA)	 AG	128026-128042	AG	GGA
-recovered pasa_asmbl_37856.p2, internal, 124169, 124326
-recovered pasa_asmbl_37856.p2, internal, 126230, 126308
-recovered pasa_asmbl_37856.p2, internal, 127348, 127420
Valid prediction for HiQ_model.g39182.t1
Valid prediction for snap_scaffold_28-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_59111-T1
Valid prediction for GlimmerHMM_glimmerT_59115-T1
Valid prediction for CodingQuarry_transcript_43707-T1
Couldn't classify 76015, 76079
Couldn't classify 77076, 77362
Sorry, prediction pasa_asmbl_37819.p1 fails validation.
(CGT)	 AC	76015-76079	GT	AGG
(CCT)	 AG	76534-76709	GT	CGG
(TGG)	 AG	77076-77362	AC	ACA
-recovered pasa_asmbl_37819.p1, internal, 76534, 76709
Couldn't classify 69306, 69402
Couldn't classify 74152, 74344
Sorry, prediction pasa_asmbl_37830.p1 fails validation.
(GCC)	 CA	69306-69402	GT	CGG
(AGG)	 AG	71266-71370	GT	TGG
(GTG)	 AG	71683-71747	GT	AGG
(GAT)	 AG	73754-73998	GT	AAG
(CTT)	 AG	74152-74344	AG	TGA
-recovered pasa_asmbl_37830.p1, internal, 71266, 71370
-recovered pasa_asmbl_37830.p1, internal, 71683, 71747
-recovered pasa_asmbl_37830.p1, internal, 73754, 73998
Valid prediction for pasa_asmbl_37685.p1
Valid prediction for pasa_asmbl_37683.p1
Valid prediction for Augustus_model.g39176.t1
Valid prediction for GlimmerHMM_glimmerT_59102-T1
Valid prediction for pasa_asmbl_37670.p1
Valid prediction for snap_scaffold_28-snap.1675-T1
Valid prediction for Augustus_model.g39178.t1
Valid prediction for Augustus_model.g39184.t1
Valid prediction for HiQ_model.g39173.t1
Valid prediction for snap_scaffold_28-snap.1655-T1
Valid prediction for HiQ_model.g39170.t1
Valid prediction for snap_scaffold_28-snap.1670-T1
Valid prediction for snap_scaffold_28-snap.1683-T1
Valid prediction for GlimmerHMM_glimmerT_59108-T1
Valid prediction for Augustus_model.g39185.t1
Valid prediction for Augustus_model.g39187.t1
Valid prediction for pasa_asmbl_37666.p1
Couldn't classify 81503, 81800
Couldn't classify 84588, 84729
Sorry, prediction pasa_asmbl_37829.p1 fails validation.
(CAA)	 CA	81503-81800	GT	AGG
(TTG)	 AG	82601-82749	GT	AGG
(GTG)	 AG	83119-83235	GT	GGG
(AAC)	 AG	83342-83458	GT	AGG
(GTG)	 AG	83809-83957	GT	AGG
(GGG)	 AG	84184-84333	GT	AGG
(ACA)	 AG	84588-84729	CT	CCC
-recovered pasa_asmbl_37829.p1, internal, 82601, 82749
-recovered pasa_asmbl_37829.p1, internal, 83119, 83235
-recovered pasa_asmbl_37829.p1, internal, 83342, 83458
-recovered pasa_asmbl_37829.p1, internal, 83809, 83957
-recovered pasa_asmbl_37829.p1, internal, 84184, 84333
Valid prediction for HiQ_model.g39189.t1
Valid prediction for snap_scaffold_28-snap.1660-T1
Valid prediction for snap_scaffold_28-snap.1648-T1
Couldn't classify 64504, 64703
Couldn't classify 67825, 68030
Sorry, prediction pasa_asmbl_37673.p1 fails validation.
(GAG)	 AG	64504-64703	GT	AGG
(GTA)	 AG	65545-65666	GT	AGG
(ACC)	 AG	67311-67544	GT	CGG
(GCT)	 AG	67825-68030	GC	AGG
-recovered pasa_asmbl_37673.p1, terminal, 65545, 65666
-recovered pasa_asmbl_37673.p1, internal, 64504, 64703
-recovered pasa_asmbl_37673.p1, internal, 65545, 65666
-recovered pasa_asmbl_37673.p1, internal, 67311, 67544
-recovered pasa_asmbl_37673.p1, internal, 67825, 68030
Valid prediction for CodingQuarry_transcript_43708-T1
Valid prediction for GlimmerHMM_glimmerT_59116-T1
Valid prediction for GlimmerHMM_glimmerT_59119-T1
Valid prediction for GlimmerHMM_glimmerT_59120-T1
Valid prediction for Augustus_model.g39177.t1
Valid prediction for CodingQuarry_transcript_43713-T1
Valid prediction for GlimmerHMM_glimmerT_59112-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_28-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_59113-T1
Valid prediction for snap_scaffold_28-snap.1649-T1
Valid prediction for Augustus_model.g39186.t1
Valid prediction for snap_scaffold_28-snap.1662-T1
Valid prediction for snap_scaffold_28-snap.1677-T1
Valid prediction for snap_scaffold_28-snap.1672-T1
Valid prediction for Augustus_model.g39172.t1
Valid prediction for Augustus_model.g39175.t1
Valid prediction for snap_scaffold_28-snap.1676-T1
Valid prediction for pasa_asmbl_38396.p1
Valid prediction for snap_scaffold_28-snap.1669-T1
Valid prediction for snap_scaffold_28-snap.1659-T1
Valid prediction for Augustus_model.g39179.t1
Valid prediction for HiQ_model.g39174.t1
Valid prediction for GlimmerHMM_glimmerT_59110-T1
Valid prediction for pasa_asmbl_38397.p1
Valid prediction for GlimmerHMM_glimmerT_59104-T1
Valid prediction for snap_scaffold_28-snap.1651-T1
Valid prediction for GlimmerHMM_glimmerT_59105-T1
Valid prediction for snap_scaffold_28-snap.1653-T1
Valid prediction for HiQ_model.g39180.t1
Valid prediction for snap_scaffold_28-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_59121-T1
Valid prediction for snap_scaffold_28-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_59109-T1
Valid prediction for snap_scaffold_28-snap.1678-T1
Valid prediction for GlimmerHMM_glimmerT_59114-T1
Valid prediction for snap_scaffold_28-snap.1671-T1
Valid prediction for pasa_asmbl_38399.p1
Valid prediction for GlimmerHMM_glimmerT_59117-T1
Valid prediction for snap_scaffold_28-snap.1684-T1
Valid prediction for snap_scaffold_28-snap.1679-T1
Valid prediction for snap_scaffold_28-snap.1661-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g39183.t1
Valid prediction for snap_scaffold_28-snap.1663-T1
Valid prediction for CodingQuarry_transcript_43710-T1
Valid prediction for CodingQuarry_transcript_43711-T1
Valid prediction for GlimmerHMM_glimmerT_59107-T1
Valid prediction for snap_scaffold_28-snap.1650-T1
Valid prediction for snap_scaffold_28-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_59103-T1
Valid prediction for Augustus_model.g39188.t1
Valid prediction for CodingQuarry_transcript_43709-T1
Valid prediction for snap_scaffold_28-snap.1664-T1
Valid prediction for snap_scaffold_28-snap.1682-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 73369, 73502
Sorry, prediction pasa_asmbl_38401.p1 fails validation.
(TGT)	 TC	73369-73502	GT	AGG
(ACA)	 AG	74816-75000	GT	TGG
(GCA)	 AG	75372-75494	GT	AGG
(AGC)	 AG	75786-75938	GT	CGG
(GTA)	 AG	76625-76732	GT	AGG
(GCG)	 AG	76824-76916	GT	AGG
(GGA)	 AG	77090-77215	GT	AGG
(GTG)	 AG	77329-77477	GA	AAG
-recovered pasa_asmbl_38401.p1, terminal, 77329, 77477
-recovered pasa_asmbl_38401.p1, internal, 74816, 75000
-recovered pasa_asmbl_38401.p1, internal, 75372, 75494
-recovered pasa_asmbl_38401.p1, internal, 75786, 75938
-recovered pasa_asmbl_38401.p1, internal, 76625, 76732
-recovered pasa_asmbl_38401.p1, internal, 76824, 76916
-recovered pasa_asmbl_38401.p1, internal, 77090, 77215
Valid prediction for snap_scaffold_28-snap.1657-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23317, rend_intergenic: 4584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30876, rend_intergenic: 24759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57469, rend_intergenic: 43907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64167, rend_intergenic: 61208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69701, rend_intergenic: 64252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78291, rend_intergenic: 73078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78523, rend_intergenic: 78352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132403, rend_intergenic: 110908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143103, rend_intergenic: 134407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149217, rend_intergenic: 143179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156626, rend_intergenic: 151809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166908, rend_intergenic: 157036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 78082, rend_intergenic: 78079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169186
-exon list size: 437


building trellis

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27.6    
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28.9    
29.2    
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29.6    
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30.1    
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31.0    
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31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
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33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
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35.5    
35.8    
36.0    
36.2    
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36.7    
36.9    
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37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
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39.6    
39.9    
40.1    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.1    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.6    
44.9    
45.1    
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45.6    
45.8    
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97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 23317, rend_intergenic: 4584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30876, rend_intergenic: 24759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57469, rend_intergenic: 43907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64167, rend_intergenic: 61208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69701, rend_intergenic: 64252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78291, rend_intergenic: 73078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78523, rend_intergenic: 78352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132403, rend_intergenic: 110908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143103, rend_intergenic: 134407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149217, rend_intergenic: 143179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156626, rend_intergenic: 151809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166908, rend_intergenic: 157036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 78082, rend_intergenic: 78079  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