-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_6669301-6886287

-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_12115-T1
Valid prediction for GlimmerHMM_glimmerT_12122-T1
Valid prediction for snap_scaffold_5-snap.1350-T1
Valid prediction for CodingQuarry_transcript_52103-T1
Valid prediction for CodingQuarry_transcript_52104-T1
Valid prediction for GlimmerHMM_glimmerT_12112-T1
Valid prediction for CodingQuarry_transcript_52107-T1
Valid prediction for HiQ_model.g7954.t1
Valid prediction for snap_scaffold_5-snap.1347-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1329-T1
Valid prediction for GlimmerHMM_glimmerT_12108-T1
Valid prediction for pasa_asmbl_45446.p1
Valid prediction for HiQ_model.g7962.t1
Valid prediction for pasa_asmbl_45450.p1
Valid prediction for HiQ_model.g7952.t1
Valid prediction for snap_scaffold_5-snap.1341-T1
Valid prediction for CodingQuarry_transcript_52101-T1
Valid prediction for GlimmerHMM_glimmerT_12128-T1
Valid prediction for snap_scaffold_5-snap.1339-T1
Valid prediction for snap_scaffold_5-snap.1327-T1
Couldn't classify 63582, 63668
Sorry, prediction pasa_asmbl_45447.p1 fails validation.
(GTT)	 CT	63582-63668	GT	AGG
(ATA)	 AG	63876-63966	GT	CGG
(CTA)	 AG	64082-64173	GT	AGG
(ATA)	 AG	64474-64641	GT	AGG
(GCG)	 AG	64795-64920	GG	GAG
-recovered pasa_asmbl_45447.p1, terminal, 64795, 64920
-recovered pasa_asmbl_45447.p1, internal, 63876, 63966
-recovered pasa_asmbl_45447.p1, internal, 64082, 64173
-recovered pasa_asmbl_45447.p1, internal, 64474, 64641
Valid prediction for HiQ_model.g7955.t1
Valid prediction for snap_scaffold_5-snap.1334-T1
Valid prediction for snap_scaffold_5-snap.1332-T1
Valid prediction for snap_scaffold_5-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_12127-T1
Valid prediction for snap_scaffold_5-snap.1333-T1
Valid prediction for pasa_asmbl_45443.p1
Valid prediction for snap_scaffold_5-snap.1318-T1
Valid prediction for snap_scaffold_5-snap.1344-T1
Valid prediction for snap_scaffold_5-snap.1349-T1
Valid prediction for snap_scaffold_5-snap.1346-T1
Valid prediction for snap_scaffold_5-snap.1324-T1
Valid prediction for snap_scaffold_5-snap.1322-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_12113-T1
Valid prediction for GlimmerHMM_glimmerT_12121-T1
Valid prediction for snap_scaffold_5-snap.1351-T1
Valid prediction for snap_scaffold_5-snap.1317-T1
Valid prediction for snap_scaffold_5-snap.1343-T1
Couldn't classify 173318, 173463
Sorry, prediction pasa_asmbl_44132.p1 fails validation.
(GAG)	 GT	173318-173463	GT	AAG
(CAT)	 AG	175399-175567	GT	AGG
(CGT)	 AG	175757-175874	GT	AGG
(GGC)	 AG	176292-176485	GT	AGG
(ATA)	 AG	176668-176799	GT	AGG
(GAG)	 AG	177107-177286	CA	GAC
-recovered pasa_asmbl_44132.p1, terminal, 177107, 177286
-recovered pasa_asmbl_44132.p1, internal, 175399, 175567
-recovered pasa_asmbl_44132.p1, internal, 175757, 175874
-recovered pasa_asmbl_44132.p1, internal, 176292, 176485
-recovered pasa_asmbl_44132.p1, internal, 176668, 176799
Valid prediction for snap_scaffold_5-snap.1340-T1
Valid prediction for GlimmerHMM_glimmerT_12125-T1
Valid prediction for Augustus_model.g7959.t1
Valid prediction for GlimmerHMM_glimmerT_12109-T1
Valid prediction for snap_scaffold_5-snap.1335-T1
Valid prediction for snap_scaffold_5-snap.1323-T1
Valid prediction for GlimmerHMM_glimmerT_12111-T1
Valid prediction for GlimmerHMM_glimmerT_12129-T1
Valid prediction for snap_scaffold_5-snap.1336-T1
Couldn't classify 29822, 29990
Sorry, prediction CodingQuarry_transcript_52108-T1 fails validation.
(ATG)	 TC	24541-24732	GT	AGG
(GTC)	 AG	24949-25173	GT	AGG
(ATG)	 AG	25801-25896	GT	CGG
(CTG)	 AG	27736-27853	GT	TGG
(ATG)	 AG	28647-28703	GT	GAG
(TCG)	 AG	29632-29707	GT	CCG
(ACC)	 TG	29822-29990	GT	AGG
(GAG)	 AG	30141-30572	CC	AGC
-recovered CodingQuarry_transcript_52108-T1, initial, 24541, 24732
-recovered CodingQuarry_transcript_52108-T1, initial, 25801, 25896
add_exon() Sorry, CodingQuarry_transcript_52108-T1 28647-28703-initial-1 is invalid.
-recovered CodingQuarry_transcript_52108-T1, initial, 28647, 28703
add_exon() Sorry, CodingQuarry_transcript_52108-T1 28647-28703-terminal-1 is invalid.
-recovered CodingQuarry_transcript_52108-T1, terminal, 28647, 28703
-recovered CodingQuarry_transcript_52108-T1, terminal, 30141, 30572
-recovered CodingQuarry_transcript_52108-T1, internal, 24949, 25173
-recovered CodingQuarry_transcript_52108-T1, internal, 25801, 25896
-recovered CodingQuarry_transcript_52108-T1, internal, 27736, 27853
-recovered CodingQuarry_transcript_52108-T1, internal, 28647, 28703
-recovered CodingQuarry_transcript_52108-T1, internal, 29632, 29707
Valid prediction for Augustus_model.g7949.t1
Valid prediction for snap_scaffold_5-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_12107-T1
Valid prediction for Augustus_model.g7964.t1
Valid prediction for snap_scaffold_5-snap.1338-T1
Valid prediction for Augustus_model.g7957.t1
Valid prediction for CodingQuarry_transcript_52109-T1
Valid prediction for GlimmerHMM_glimmerT_12116-T1
Valid prediction for Augustus_model.g7966.t1
Valid prediction for GlimmerHMM_glimmerT_12120-T1
Valid prediction for snap_scaffold_5-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_12123-T1
Valid prediction for Augustus_model.g7951.t1
Valid prediction for GlimmerHMM_glimmerT_12114-T1
Valid prediction for snap_scaffold_5-snap.1315-T1
Valid prediction for snap_scaffold_5-snap.1328-T1
Valid prediction for snap_scaffold_5-snap.1326-T1
Valid prediction for GlimmerHMM_glimmerT_12118-T1
Valid prediction for Augustus_model.g7965.t1
Valid prediction for GlimmerHMM_glimmerT_12110-T1
Valid prediction for snap_scaffold_5-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_12119-T1
Valid prediction for Augustus_model.g7963.t1
Couldn't classify 12524, 12652
Couldn't classify 13588, 13629
Sorry, prediction pasa_asmbl_45041.p1 fails validation.
(CTG)	 TG	12524-12652	GT	TGG
(TTC)	 AG	12752-12844	GT	AGG
(TTG)	 AG	13119-13198	GT	AGG
(AAC)	 AG	13394-13424	GT	AGG
(GCC)	 AG	13588-13629	AC	AGA
-recovered pasa_asmbl_45041.p1, internal, 12752, 12844
-recovered pasa_asmbl_45041.p1, internal, 13119, 13198
-recovered pasa_asmbl_45041.p1, internal, 13394, 13424
Valid prediction for HiQ_model.g7958.t1
Valid prediction for Augustus_model.g7961.t1
Valid prediction for pasa_asmbl_44155.p1
Valid prediction for HiQ_model.g7956.t1
Valid prediction for HiQ_model.g7960.t1
Valid prediction for Augustus_model.g7953.t1
Valid prediction for snap_scaffold_5-snap.1348-T1
Valid prediction for snap_scaffold_5-snap.1320-T1
Valid prediction for CodingQuarry_transcript_52106-T1
Valid prediction for pasa_asmbl_44142.p1
Valid prediction for GlimmerHMM_glimmerT_12124-T1
Valid prediction for pasa_asmbl_44135.p1
Couldn't classify 79306, 79416
Sorry, prediction pasa_asmbl_44147.p1 fails validation.
(ATG)	 GA	78457-78504	GT	AGG
(GTA)	 AG	78632-78722	GT	TGG
(ACC)	 AG	78829-78959	GT	CGG
(GAG)	 AG	79041-79157	GT	AGG
(GAG)	 AG	79306-79416	GG	GGG
-recovered pasa_asmbl_44147.p1, initial, 78457, 78504
-recovered pasa_asmbl_44147.p1, internal, 78632, 78722
-recovered pasa_asmbl_44147.p1, internal, 78829, 78959
-recovered pasa_asmbl_44147.p1, internal, 79041, 79157
Valid prediction for snap_scaffold_5-snap.1319-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1342-T1
Valid prediction for snap_scaffold_5-snap.1352-T1
Couldn't classify 135636, 135755
Couldn't classify 136310, 136379
Sorry, prediction pasa_asmbl_44141.p1 fails validation.
(CAC)	 GG	135636-135755	GT	AGG
(GGA)	 AG	135870-136030	GT	AGG
(CCT)	 AG	136310-136379	AG	ACA
-recovered pasa_asmbl_44141.p1, internal, 135870, 136030
Valid prediction for GlimmerHMM_glimmerT_12126-T1
Valid prediction for CodingQuarry_transcript_52105-T1
Valid prediction for snap_scaffold_5-snap.1330-T1
Valid prediction for snap_scaffold_5-snap.1325-T1
Valid prediction for GlimmerHMM_glimmerT_12117-T1
Couldn't classify 81129, 81174
Couldn't classify 81964, 82072
Sorry, prediction pasa_asmbl_44146.p1 fails validation.
(AGA)	 TC	81129-81174	GT	TGG
(TCA)	 AG	81419-81557	GT	AGG
(TCC)	 AG	81741-81839	GT	AGG
(GTC)	 AG	81964-82072	CC	AGC
add_exon() Sorry, pasa_asmbl_44146.p1 81419-81557-terminal-3 is invalid.
-recovered pasa_asmbl_44146.p1, terminal, 81419, 81557
-recovered pasa_asmbl_44146.p1, internal, 81419, 81557
-recovered pasa_asmbl_44146.p1, internal, 81741, 81839
Valid prediction for snap_scaffold_5-snap.1316-T1
Valid prediction for CodingQuarry_transcript_52102-T1
Couldn't classify 48742, 48794
Couldn't classify 52889, 52942
Sorry, prediction pasa_asmbl_44150.p1 fails validation.
(AGA)	 GA	48742-48794	GT	AGG
(AAG)	 AG	48905-48981	GT	ACG
(CAG)	 AG	49148-49185	GT	AGG
(GTG)	 AG	50072-50146	GT	AGG
(AGA)	 AG	50377-50439	GT	AGG
(CTC)	 AG	50603-50671	GT	AGG
(GCT)	 AG	50844-50885	GT	TTG
(TTT)	 AG	51037-51189	GT	TGG
(CAA)	 AG	51372-51581	GT	ATG
(CTG)	 AG	51846-52004	GT	CCG
(TCT)	 AG	52288-52743	GT	TGG
(GTC)	 AG	52889-52942	AG	GCA
-recovered pasa_asmbl_44150.p1, internal, 48905, 48981
-recovered pasa_asmbl_44150.p1, internal, 49148, 49185
-recovered pasa_asmbl_44150.p1, internal, 50072, 50146
-recovered pasa_asmbl_44150.p1, internal, 50377, 50439
-recovered pasa_asmbl_44150.p1, internal, 50603, 50671
-recovered pasa_asmbl_44150.p1, internal, 50844, 50885
-recovered pasa_asmbl_44150.p1, internal, 51037, 51189
-recovered pasa_asmbl_44150.p1, internal, 51372, 51581
-recovered pasa_asmbl_44150.p1, internal, 51846, 52004
-recovered pasa_asmbl_44150.p1, internal, 52288, 52743
Valid prediction for Augustus_model.g7950.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21357, rend_intergenic: 15869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38816, rend_intergenic: 38116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57850, rend_intergenic: 52969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69536, rend_intergenic: 68800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70845, rend_intergenic: 69725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105008, rend_intergenic: 82887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112835, rend_intergenic: 110473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128864, rend_intergenic: 121362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141944, rend_intergenic: 134250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150298, rend_intergenic: 149686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154421, rend_intergenic: 150644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169083, rend_intergenic: 163824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187157, rend_intergenic: 186416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194358, rend_intergenic: 189191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213399, rend_intergenic: 201776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216987
-exon list size: 452


building trellis

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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 21357, rend_intergenic: 15869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38816, rend_intergenic: 38116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57850, rend_intergenic: 52969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69536, rend_intergenic: 68800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70845, rend_intergenic: 69725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105008, rend_intergenic: 82887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112835, rend_intergenic: 110473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128864, rend_intergenic: 121362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141944, rend_intergenic: 134250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150298, rend_intergenic: 149686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154421, rend_intergenic: 150644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169083, rend_intergenic: 163824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187157, rend_intergenic: 186416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194358, rend_intergenic: 189191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213399, rend_intergenic: 201776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10760
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10555
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support