-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_7638511-7797758

-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 Augustus_model.g795.t1
Valid prediction for snap_scaffold_1-snap.1365-T1
Valid prediction for GlimmerHMM_glimmerT_1120-T1
Valid prediction for pasa_asmbl_1911.p2
Valid prediction for GlimmerHMM_glimmerT_1126-T1
Valid prediction for Augustus_model.g811.t1
Valid prediction for HiQ_model.g798.t1
Valid prediction for pasa_asmbl_1914.p1
Valid prediction for GeneMark_model.1383_t
Valid prediction for GlimmerHMM_glimmerT_1107-T1
Valid prediction for GeneMark_model.1380_t
Valid prediction for snap_scaffold_1-snap.1399-T1
Valid prediction for HiQ_model.g802.t1
Valid prediction for snap_scaffold_1-snap.1385-T1
Valid prediction for GlimmerHMM_glimmerT_1104-T1
Valid prediction for snap_scaffold_1-snap.1395-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.1392-T1
Valid prediction for Augustus_model.g818.t1
Valid prediction for snap_scaffold_1-snap.1398-T1
Valid prediction for GlimmerHMM_glimmerT_1116-T1
Valid prediction for pasa_asmbl_1910.p1
Valid prediction for GeneMark_model.1414_t
Valid prediction for GeneMark_model.1411_t
Valid prediction for GeneMark_model.1413_t
Valid prediction for GlimmerHMM_glimmerT_1114-T1
Valid prediction for GeneMark_model.1377_t
Valid prediction for GeneMark_model.1382_t
Valid prediction for Augustus_model.g810.t1
Valid prediction for GeneMark_model.1385_t
Valid prediction for GeneMark_model.1399_t
Couldn't classify 39857, 40345
Sorry, prediction pasa_asmbl_1905.p1 fails validation.
(ATG)	 AT	39857-40345	AA	AAA
Valid prediction for GeneMark_model.1416_t
Valid prediction for GeneMark_model.1378_t
Valid prediction for GlimmerHMM_glimmerT_1098-T1
Valid prediction for Augustus_model.g812.t1
Valid prediction for snap_scaffold_1-snap.1384-T1
Valid prediction for GeneMark_model.1391_t
Valid prediction for GeneMark_model.1392_t
Valid prediction for GlimmerHMM_glimmerT_1111-T1
Valid prediction for Augustus_model.g816.t1
Valid prediction for GeneMark_model.1389_t
Valid prediction for snap_scaffold_1-snap.1382-T1
Valid prediction for GeneMark_model.1394_t
Valid prediction for GeneMark_model.1420_t
Valid prediction for GeneMark_model.1402_t
Valid prediction for GlimmerHMM_glimmerT_1094-T1
Valid prediction for Augustus_model.g805.t1
Valid prediction for snap_scaffold_1-snap.1364-T1
Valid prediction for GlimmerHMM_glimmerT_1125-T1
Valid prediction for snap_scaffold_1-snap.1362-T1
Valid prediction for GlimmerHMM_glimmerT_1101-T1
Valid prediction for snap_scaffold_1-snap.1361-T1
Valid prediction for GeneMark_model.1403_t
Couldn't classify 154984, 155209
Sorry, prediction pasa_asmbl_1915.p1 fails validation.
(TTA)	 AA	154984-155209	GT	GGG
(GCT)	 AG	156707-156834	GG	GAG
-recovered pasa_asmbl_1915.p1, terminal, 156707, 156834
Valid prediction for GlimmerHMM_glimmerT_1103-T1
Valid prediction for GeneMark_model.1417_t
Valid prediction for snap_scaffold_1-snap.1393-T1
Valid prediction for GeneMark_model.1407_t
Valid prediction for GeneMark_model.1405_t
Valid prediction for GlimmerHMM_glimmerT_1130-T1
Valid prediction for GeneMark_model.1387_t
Valid prediction for Augustus_model.g800.t1
Valid prediction for snap_scaffold_1-snap.1373-T1
Valid prediction for snap_scaffold_1-snap.1369-T1
Valid prediction for GeneMark_model.1404_t
Valid prediction for snap_scaffold_1-snap.1371-T1
Valid prediction for GeneMark_model.1418_t
Valid prediction for CodingQuarry_transcript_2695-T1
Valid prediction for snap_scaffold_1-snap.1383-T1
Valid prediction for pasa_asmbl_1904.p1
Couldn't classify 68839, 68912
Sorry, prediction CodingQuarry_transcript_2694-T1 fails validation.
(ATG)	 CC	65162-65202	GT	GGG
(GTT)	 AG	66812-66905	GT	AGG
(GCA)	 AG	67328-67420	GT	CGG
(CCC)	 AG	67741-67788	GT	AGG
(GAC)	 AG	67990-68145	GT	AGG
(GGT)	 AG	68483-68632	GT	AGG
(GGA)	 AG	68839-68912	GG	ATG
(GGT)	 AG	69140-69209	GG	GAG
-recovered CodingQuarry_transcript_2694-T1, initial, 65162, 65202
-recovered CodingQuarry_transcript_2694-T1, terminal, 69140, 69209
-recovered CodingQuarry_transcript_2694-T1, internal, 66812, 66905
-recovered CodingQuarry_transcript_2694-T1, internal, 67328, 67420
-recovered CodingQuarry_transcript_2694-T1, internal, 67741, 67788
-recovered CodingQuarry_transcript_2694-T1, internal, 67990, 68145
-recovered CodingQuarry_transcript_2694-T1, internal, 68483, 68632
Valid prediction for GlimmerHMM_glimmerT_1115-T1
Valid prediction for GeneMark_model.1397_t
Valid prediction for snap_scaffold_1-snap.1378-T1
Valid prediction for snap_scaffold_1-snap.1376-T1
Valid prediction for snap_scaffold_1-snap.1390-T1
Valid prediction for HiQ_model.g819.t1
Valid prediction for GlimmerHMM_glimmerT_1124-T1
Valid prediction for snap_scaffold_1-snap.1368-T1
Valid prediction for GlimmerHMM_glimmerT_1129-T1
Valid prediction for GlimmerHMM_glimmerT_1118-T1
Valid prediction for GlimmerHMM_glimmerT_1123-T1
Valid prediction for HiQ_model.g821.t1
Valid prediction for GlimmerHMM_glimmerT_1128-T1
Valid prediction for GlimmerHMM_glimmerT_1095-T1
Valid prediction for GlimmerHMM_glimmerT_1105-T1
Valid prediction for GlimmerHMM_glimmerT_1122-T1
Valid prediction for CodingQuarry_transcript_2693-T1
Valid prediction for Augustus_model.g801.t1
Valid prediction for snap_scaffold_1-snap.1394-T1
Couldn't classify 127843, 127993
Sorry, prediction pasa_asmbl_1912.p1 fails validation.
(GAA)	 AC	127843-127993	GT	AGG
(GTG)	 AG	128331-128413	GT	AGG
(GAA)	 AG	128674-128882	GT	AAG
(AGT)	 AG	129055-129238	GT	AGG
(GTC)	 AG	129340-129432	GT	AGG
(AGA)	 AG	130022-130175	GT	AGG
(AGT)	 AG	130658-130839	GC	AGG
(GGT)	 AG	130990-131071	GT	CAG
(ATC)	 AG	131547-131647	GT	CGG
(TTT)	 AG	132128-132133	GT	CAG
(TTT)	 AG	132866-133021	GT	GGG
(GTG)	 AG	133283-133395	GT	TTG
(TGC)	 AG	133776-133863	GT	AGG
(ATT)	 AG	134023-134174	GT	GAG
(TGT)	 AG	134512-134567	GT	AGG
(AAC)	 AG	134731-134780	GT	AGG
(GGT)	 AG	134896-135000	GT	AGG
(GTT)	 AG	135151-135251	GT	CAG
(GAC)	 AG	135411-135479	GT	AGG
(TCG)	 AG	135635-135881	GC	GAG
add_exon() Sorry, pasa_asmbl_1912.p1 134023-134174-terminal-2 is invalid.
-recovered pasa_asmbl_1912.p1, terminal, 134023, 134174
-recovered pasa_asmbl_1912.p1, terminal, 135635, 135881
-recovered pasa_asmbl_1912.p1, internal, 128331, 128413
-recovered pasa_asmbl_1912.p1, internal, 128674, 128882
-recovered pasa_asmbl_1912.p1, internal, 129055, 129238
-recovered pasa_asmbl_1912.p1, internal, 129340, 129432
-recovered pasa_asmbl_1912.p1, internal, 130022, 130175
-recovered pasa_asmbl_1912.p1, internal, 130658, 130839
-recovered pasa_asmbl_1912.p1, internal, 130990, 131071
-recovered pasa_asmbl_1912.p1, internal, 131547, 131647
-recovered pasa_asmbl_1912.p1, internal, 132128, 132133
-recovered pasa_asmbl_1912.p1, internal, 132866, 133021
-recovered pasa_asmbl_1912.p1, internal, 133283, 133395
-recovered pasa_asmbl_1912.p1, internal, 133776, 133863
-recovered pasa_asmbl_1912.p1, internal, 134023, 134174
-recovered pasa_asmbl_1912.p1, internal, 134512, 134567
-recovered pasa_asmbl_1912.p1, internal, 134731, 134780
-recovered pasa_asmbl_1912.p1, internal, 134896, 135000
-recovered pasa_asmbl_1912.p1, internal, 135151, 135251
-recovered pasa_asmbl_1912.p1, internal, 135411, 135479
-recovered pasa_asmbl_1912.p1, internal, 135635, 135881
Valid prediction for Augustus_model.g820.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_1121-T1
Valid prediction for snap_scaffold_1-snap.1389-T1
Valid prediction for GeneMark_model.1406_t
Valid prediction for GeneMark_model.1401_t
Valid prediction for GlimmerHMM_glimmerT_1096-T1
Valid prediction for GeneMark_model.1386_t
Valid prediction for snap_scaffold_1-snap.1379-T1
Valid prediction for snap_scaffold_1-snap.1377-T1
Valid prediction for GeneMark_model.1415_t
Valid prediction for Augustus_model.g806.t1
Valid prediction for GeneMark_model.1381_t
Valid prediction for GeneMark_model.1412_t
Valid prediction for GlimmerHMM_glimmerT_1119-T1
Valid prediction for Augustus_model.g817.t1
Valid prediction for snap_scaffold_1-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_1110-T1
Couldn't classify 121189, 121246
Sorry, prediction pasa_asmbl_1280.p1 fails validation.
(CCA)	 CT	121189-121246	GT	AAG
(TTT)	 AG	121680-121738	GT	AGG
(TTA)	 AG	121877-121980	GT	AGG
(ATT)	 AG	122168-122249	GT	AGG
(GTC)	 AG	122359-122426	GT	GAG
(ATA)	 AG	122735-122886	GT	GGG
(GAG)	 AG	123142-123218	GT	TGG
(AAA)	 AG	123357-123500	GA	GAG
-recovered pasa_asmbl_1280.p1, terminal, 123357, 123500
-recovered pasa_asmbl_1280.p1, internal, 121680, 121738
-recovered pasa_asmbl_1280.p1, internal, 121877, 121980
-recovered pasa_asmbl_1280.p1, internal, 122168, 122249
-recovered pasa_asmbl_1280.p1, internal, 122359, 122426
-recovered pasa_asmbl_1280.p1, internal, 122735, 122886
-recovered pasa_asmbl_1280.p1, internal, 123142, 123218
Valid prediction for snap_scaffold_1-snap.1396-T1
Valid prediction for GlimmerHMM_glimmerT_1113-T1
Valid prediction for Augustus_model.g814.t1
Valid prediction for snap_scaffold_1-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_1102-T1
Valid prediction for Augustus_model.g803.t1
Valid prediction for GeneMark_model.1390_t
Valid prediction for snap_scaffold_1-snap.1387-T1
Valid prediction for Augustus_model.g808.t1
Valid prediction for snap_scaffold_1-snap.1372-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g813.t1
Valid prediction for GeneMark_model.1388_t
Valid prediction for snap_scaffold_1-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_1106-T1
Valid prediction for GlimmerHMM_glimmerT_1099-T1
Valid prediction for GlimmerHMM_glimmerT_1117-T1
Valid prediction for Augustus_model.g797.t1
Valid prediction for snap_scaffold_1-snap.1386-T1
Valid prediction for HiQ_model.g799.t1
Valid prediction for snap_scaffold_1-snap.1367-T1
Valid prediction for snap_scaffold_1-snap.1363-T1
Valid prediction for Augustus_model.g796.t1
Valid prediction for snap_scaffold_1-snap.1381-T1
Valid prediction for GlimmerHMM_glimmerT_1097-T1
Valid prediction for Augustus_model.g804.t1
Valid prediction for Augustus_model.g815.t1
Valid prediction for GeneMark_model.1408_t
Valid prediction for snap_scaffold_1-snap.1366-T1
Valid prediction for snap_scaffold_1-snap.1400-T1
Valid prediction for GlimmerHMM_glimmerT_1109-T1
Valid prediction for GeneMark_model.1419_t
Valid prediction for GlimmerHMM_glimmerT_1108-T1
Valid prediction for GlimmerHMM_glimmerT_1127-T1
Valid prediction for snap_scaffold_1-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_1112-T1
Valid prediction for GeneMark_model.1393_t
Valid prediction for GeneMark_model.1409_t
Valid prediction for GeneMark_model.1379_t
Valid prediction for snap_scaffold_1-snap.1375-T1
Valid prediction for GeneMark_model.1400_t
Valid prediction for Augustus_model.g809.t1
Valid prediction for GeneMark_model.1376_t
Valid prediction for snap_scaffold_1-snap.1397-T1
Valid prediction for snap_scaffold_1-snap.1380-T1
Valid prediction for snap_scaffold_1-snap.1360-T1
Valid prediction for snap_scaffold_1-snap.1359-T1
Valid prediction for GeneMark_model.1410_t
Valid prediction for GeneMark_model.1384_t
Valid prediction for Augustus_model.g807.t1
Valid prediction for GeneMark_model.1396_t
Valid prediction for GlimmerHMM_glimmerT_1100-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21152, rend_intergenic: 10218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28396, rend_intergenic: 22914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39978, rend_intergenic: 38564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47631, rend_intergenic: 46299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51751, rend_intergenic: 49543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53156, rend_intergenic: 52166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54766, rend_intergenic: 53834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60427, rend_intergenic: 56692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69336, rend_intergenic: 66778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147564, rend_intergenic: 139564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155285, rend_intergenic: 154226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159248
-exon list size: 487


building trellis

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94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 21152, rend_intergenic: 10218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28396, rend_intergenic: 22914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39978, rend_intergenic: 38564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47631, rend_intergenic: 46299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51751, rend_intergenic: 49543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53156, rend_intergenic: 52166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54766, rend_intergenic: 53834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60427, rend_intergenic: 56692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69336, rend_intergenic: 66778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147564, rend_intergenic: 139564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155285, rend_intergenic: 154226  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