-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_7863858-8071848

-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 GlimmerHMM_glimmerT_49835-T1
Valid prediction for snap_scaffold_22-snap.1578-T1
Valid prediction for GlimmerHMM_glimmerT_49815-T1
Valid prediction for GlimmerHMM_glimmerT_49831-T1
Valid prediction for snap_scaffold_22-snap.1611-T1
Valid prediction for Augustus_model.g33248.t1
Valid prediction for GlimmerHMM_glimmerT_49813-T1
Valid prediction for snap_scaffold_22-snap.1610-T1
Valid prediction for snap_scaffold_22-snap.1603-T1
Valid prediction for snap_scaffold_22-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_49827-T1
Valid prediction for Augustus_model.g33253.t1
Valid prediction for Augustus_model.g33251.t1
Valid prediction for GlimmerHMM_glimmerT_49814-T1
Valid prediction for GlimmerHMM_glimmerT_49838-T1
Valid prediction for snap_scaffold_22-snap.1579-T1
Valid prediction for GlimmerHMM_glimmerT_49837-T1
Valid prediction for pasa_asmbl_30228.p1
Valid prediction for GlimmerHMM_glimmerT_49834-T1
Valid prediction for GlimmerHMM_glimmerT_49818-T1
Valid prediction for snap_scaffold_22-snap.1594-T1
Valid prediction for Augustus_model.g33250.t1
Valid prediction for snap_scaffold_22-snap.1607-T1
Couldn't classify 75579, 75620
Couldn't classify 77007, 77305
Sorry, prediction pasa_asmbl_30238.p1 fails validation.
(GAT)	 AG	75579-75620	GT	AAG
(GAG)	 AG	75994-76099	GT	CAG
(GCA)	 AG	77007-77305	TN	TGT
-recovered pasa_asmbl_30238.p1, internal, 75579, 75620
-recovered pasa_asmbl_30238.p1, internal, 75994, 76099
Valid prediction for snap_scaffold_22-snap.1598-T1
Valid prediction for snap_scaffold_22-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_49830-T1
Couldn't classify 12262, 12351
Sorry, prediction pasa_asmbl_30443.p1 fails validation.
(GTC)	 TG	12262-12351	GT	AGG
(GCA)	 AG	12538-12762	GT	AGG
(TCT)	 AG	12918-12984	GT	AAG
(ACG)	 AG	13094-13240	GT	AGG
(GTG)	 AG	13329-13388	GT	AGG
(CTG)	 AG	13613-13789	GT	CGG
(GTG)	 AG	14287-14425	GT	AGG
(ATC)	 AG	14530-14585	GT	AGG
(AGA)	 AG	14764-15465	GT	AAG
(TAC)	 AG	15642-15775	GT	AGG
(ATT)	 AG	16070-16241	GT	CAG
(CCA)	 AG	16403-16683	AA	GAA
-recovered pasa_asmbl_30443.p1, terminal, 16403, 16683
-recovered pasa_asmbl_30443.p1, internal, 12538, 12762
-recovered pasa_asmbl_30443.p1, internal, 12918, 12984
-recovered pasa_asmbl_30443.p1, internal, 13094, 13240
-recovered pasa_asmbl_30443.p1, internal, 13329, 13388
-recovered pasa_asmbl_30443.p1, internal, 13613, 13789
-recovered pasa_asmbl_30443.p1, internal, 14287, 14425
-recovered pasa_asmbl_30443.p1, internal, 14530, 14585
-recovered pasa_asmbl_30443.p1, internal, 14764, 15465
-recovered pasa_asmbl_30443.p1, internal, 15642, 15775
-recovered pasa_asmbl_30443.p1, internal, 16070, 16241
Couldn't classify 54983, 54987
Sorry, prediction CodingQuarry_transcript_34229-T1 fails validation.
(ATG)	 AT	50926-50930	GT	GAG
(TCG)	 AG	52368-52633	GT	AGG
(ACA)	 AG	53000-53072	GT	AGG
(CTC)	 AG	53207-53254	GT	AGG
(GAT)	 AG	53352-53515	GT	CAG
(TGA)	 AG	53935-54048	GT	AGG
(ATT)	 GC	54983-54987	AA	GAA
-recovered CodingQuarry_transcript_34229-T1, initial, 50926, 50930
add_exon() Sorry, CodingQuarry_transcript_34229-T1 52368-52633-terminal-2 is invalid.
-recovered CodingQuarry_transcript_34229-T1, terminal, 52368, 52633
-recovered CodingQuarry_transcript_34229-T1, internal, 52368, 52633
-recovered CodingQuarry_transcript_34229-T1, internal, 53000, 53072
-recovered CodingQuarry_transcript_34229-T1, internal, 53207, 53254
-recovered CodingQuarry_transcript_34229-T1, internal, 53352, 53515
-recovered CodingQuarry_transcript_34229-T1, internal, 53935, 54048
Valid prediction for snap_scaffold_22-snap.1570-T1
Couldn't classify 141285, 141358
Couldn't classify 142484, 142593
Sorry, prediction pasa_asmbl_30432.p1 fails validation.
(GAT)	 GG	141285-141358	GT	AGG
(GAG)	 AG	141766-142016	GT	AGG
(AAA)	 AG	142148-142342	GT	AGG
(GTA)	 AG	142484-142593	AC	TCA
add_exon() Sorry, pasa_asmbl_30432.p1 141766-142016-terminal-2 is invalid.
-recovered pasa_asmbl_30432.p1, terminal, 141766, 142016
-recovered pasa_asmbl_30432.p1, internal, 141766, 142016
-recovered pasa_asmbl_30432.p1, internal, 142148, 142342
Couldn't classify 106510, 106554
Sorry, prediction pasa_asmbl_30245.p1 fails validation.
(ATG)	 AC	104891-104959	GT	AGG
(GAC)	 AG	105199-105243	GT	AGG
(GGG)	 AG	105394-105447	GT	AGG
(AGC)	 AG	105645-105704	GT	AGG
(AAC)	 AG	105894-105959	GT	AGG
(GTG)	 AG	106510-106554	AC	CAA
-recovered pasa_asmbl_30245.p1, initial, 104891, 104959
-recovered pasa_asmbl_30245.p1, internal, 105199, 105243
-recovered pasa_asmbl_30245.p1, internal, 105394, 105447
-recovered pasa_asmbl_30245.p1, internal, 105645, 105704
-recovered pasa_asmbl_30245.p1, internal, 105894, 105959
Valid prediction for snap_scaffold_22-snap.1584-T1
Valid prediction for Augustus_model.g33254.t1
Couldn't classify 110693, 110839
Sorry, prediction pasa_asmbl_30247.p1 fails validation.
(ATG)	 TC	109578-109961	GT	AGG
(GTG)	 AG	110130-110417	GT	AGG
(GGT)	 AG	110693-110839	GA	AGG
-recovered pasa_asmbl_30247.p1, initial, 109578, 109961
-recovered pasa_asmbl_30247.p1, internal, 110130, 110417
Couldn't classify 107769, 107826
Couldn't classify 107977, 108089
Sorry, prediction CodingQuarry_transcript_34232-T1 fails validation.
(ATG)	 GG	107205-107249	GT	AGG
(GAC)	 AG	107769-107826	AC	CAA
(AGG)	 GC	107977-108089	CT	AAC
-recovered CodingQuarry_transcript_34232-T1, initial, 107205, 107249
Valid prediction for Augustus_model.g33244.t1
Valid prediction for HiQ_model.g33238.t1
Valid prediction for GlimmerHMM_glimmerT_49843-T1
Couldn't classify 139646, 140050
Sorry, prediction pasa_asmbl_30252.p1 fails validation.
(CAC)	 AA	139646-140050	CT	TAC
Valid prediction for Augustus_model.g33252.t1
Valid prediction for snap_scaffold_22-snap.1583-T1
Valid prediction for snap_scaffold_22-snap.1596-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.1589-T1
Valid prediction for GlimmerHMM_glimmerT_49825-T1
Valid prediction for snap_scaffold_22-snap.1568-T1
Valid prediction for GlimmerHMM_glimmerT_49829-T1
Valid prediction for snap_scaffold_22-snap.1590-T1
Couldn't classify 81734, 81913
Sorry, prediction pasa_asmbl_30240.p1 fails validation.
(TGT)	 CC	81734-81913	GT	CAG
(GTG)	 AG	82077-82124	GT	AGG
(ATG)	 AG	82337-82372	GT	AGG
(CCC)	 AG	82502-82553	GT	CAG
(TGG)	 AG	82848-83203	AG	GAA
-recovered pasa_asmbl_30240.p1, initial, 82337, 82372
-recovered pasa_asmbl_30240.p1, terminal, 82848, 83203
-recovered pasa_asmbl_30240.p1, internal, 82077, 82124
-recovered pasa_asmbl_30240.p1, internal, 82337, 82372
-recovered pasa_asmbl_30240.p1, internal, 82502, 82553
Couldn't classify 148914, 149081
Couldn't classify 152584, 152681
Sorry, prediction pasa_asmbl_30253.p1 fails validation.
(TTC)	 CC	148914-149081	GT	CGG
(GTT)	 AG	151751-151930	GT	AGG
(GCA)	 AG	152099-152279	GT	AGG
(AGC)	 AG	152584-152681	CT	CCC
-recovered pasa_asmbl_30253.p1, internal, 151751, 151930
-recovered pasa_asmbl_30253.p1, internal, 152099, 152279
Valid prediction for GlimmerHMM_glimmerT_49819-T1
Valid prediction for snap_scaffold_22-snap.1572-T1
Valid prediction for CodingQuarry_transcript_34230-T1
Valid prediction for snap_scaffold_22-snap.1595-T1
Valid prediction for Augustus_model.g33246.t1
Valid prediction for GlimmerHMM_glimmerT_49840-T1
Valid prediction for HiQ_model.g33236.t1
Valid prediction for GlimmerHMM_glimmerT_49842-T1
Couldn't classify 10365, 10817
Sorry, prediction pasa_asmbl_30226.p1 fails validation.
(ATG)	 AG	10365-10817	CA	ACC
Valid prediction for snap_scaffold_22-snap.1588-T1
Valid prediction for snap_scaffold_22-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_49823-T1
Valid prediction for GlimmerHMM_glimmerT_49836-T1
Valid prediction for snap_scaffold_22-snap.1573-T1
Couldn't classify 9696, 10085
Sorry, prediction pasa_asmbl_30225.p1 fails validation.
(ATG)	 AA	8785-8965	GT	AGG
(ACC)	 AG	9371-9504	GT	GAG
(GGT)	 AG	9696-10085	TT	GCT
-recovered pasa_asmbl_30225.p1, initial, 8785, 8965
-recovered pasa_asmbl_30225.p1, internal, 9371, 9504
Valid prediction for GlimmerHMM_glimmerT_49816-T1
Couldn't classify 11304, 11747
Sorry, prediction pasa_asmbl_30227.p2 fails validation.
(GCA)	 GG	11304-11747	GA	TGG
Valid prediction for CodingQuarry_transcript_34222-T1
Valid prediction for Augustus_model.g33243.t1
Valid prediction for snap_scaffold_22-snap.1587-T1
Valid prediction for GlimmerHMM_glimmerT_49833-T1
Valid prediction for HiQ_model.g33249.t1
Valid prediction for GlimmerHMM_glimmerT_49826-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_22-snap.1609-T1
Valid prediction for CodingQuarry_transcript_34226-T1
Valid prediction for GlimmerHMM_glimmerT_49844-T1
Valid prediction for Augustus_model.g33239.t1
Valid prediction for snap_scaffold_22-snap.1571-T1
Valid prediction for GlimmerHMM_glimmerT_49821-T1
Valid prediction for snap_scaffold_22-snap.1577-T1
Valid prediction for GlimmerHMM_glimmerT_49841-T1
Valid prediction for Augustus_model.g33247.t1
Valid prediction for pasa_asmbl_29434.p2
Valid prediction for GlimmerHMM_glimmerT_49820-T1
Valid prediction for snap_scaffold_22-snap.1582-T1
Valid prediction for pasa_asmbl_29438.p1
Valid prediction for GlimmerHMM_glimmerT_49822-T1
Valid prediction for CodingQuarry_transcript_34231-T1
Valid prediction for snap_scaffold_22-snap.1608-T1
Valid prediction for snap_scaffold_22-snap.1576-T1
Valid prediction for pasa_asmbl_29445.p1
Valid prediction for pasa_asmbl_29443.p1
Valid prediction for GlimmerHMM_glimmerT_49832-T1
Valid prediction for snap_scaffold_22-snap.1567-T1
Valid prediction for CodingQuarry_transcript_34224-T1
Valid prediction for snap_scaffold_22-snap.1604-T1
Valid prediction for snap_scaffold_22-snap.1599-T1
Valid prediction for snap_scaffold_22-snap.1580-T1
Valid prediction for snap_scaffold_22-snap.1591-T1
Valid prediction for HiQ_model.g33245.t1
Valid prediction for snap_scaffold_22-snap.1597-T1
Valid prediction for snap_scaffold_22-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_49817-T1
Valid prediction for snap_scaffold_22-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_49824-T1
Valid prediction for snap_scaffold_22-snap.1574-T1
Valid prediction for snap_scaffold_22-snap.1569-T1
Valid prediction for snap_scaffold_22-snap.1606-T1
Valid prediction for snap_scaffold_22-snap.1585-T1
Valid prediction for CodingQuarry_transcript_34223-T1
Valid prediction for HiQ_model.g33237.t1
Valid prediction for pasa_asmbl_29716.p1
Valid prediction for snap_scaffold_22-snap.1600-T1
Valid prediction for snap_scaffold_22-snap.1575-T1
Valid prediction for Augustus_model.g33242.t1
Valid prediction for snap_scaffold_22-snap.1612-T1
Valid prediction for CodingQuarry_transcript_34228-T1
Valid prediction for Augustus_model.g33241.t1
Valid prediction for CodingQuarry_transcript_34225-T1
Valid prediction for snap_scaffold_22-snap.1605-T1
Valid prediction for GlimmerHMM_glimmerT_49828-T1
Valid prediction for CodingQuarry_transcript_34221-T1
Valid prediction for CodingQuarry_transcript_34227-T1
Valid prediction for GlimmerHMM_glimmerT_49839-T1
Valid prediction for HiQ_model.g33240.t1
Valid prediction for pasa_asmbl_29429.p2
Valid prediction for snap_scaffold_22-snap.1593-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7231, rend_intergenic: 5845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45018, rend_intergenic: 42830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55400, rend_intergenic: 50952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60427, rend_intergenic: 56199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64441, rend_intergenic: 62101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83203, rend_intergenic: 71845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107171, rend_intergenic: 105187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110890, rend_intergenic: 108265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144365, rend_intergenic: 130749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153956, rend_intergenic: 144711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176104, rend_intergenic: 168903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194246, rend_intergenic: 188475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200474, rend_intergenic: 198771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206075, rend_intergenic: 202427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207991
-exon list size: 473


building trellis

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86.9    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 7231, rend_intergenic: 5845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45018, rend_intergenic: 42830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55400, rend_intergenic: 50952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60427, rend_intergenic: 56199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64441, rend_intergenic: 62101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83203, rend_intergenic: 71845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107171, rend_intergenic: 105187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110890, rend_intergenic: 108265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144365, rend_intergenic: 130749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153956, rend_intergenic: 144711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176104, rend_intergenic: 168903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194246, rend_intergenic: 188475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200474, rend_intergenic: 198771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206075, rend_intergenic: 202427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support