-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_12992401-13245865

-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_1-snap.2239-T1
Valid prediction for snap_scaffold_1-snap.2222-T1
Valid prediction for snap_scaffold_1-snap.2234-T1
Valid prediction for snap_scaffold_1-snap.2230-T1
Valid prediction for snap_scaffold_1-snap.2228-T1
Valid prediction for Augustus_model.g1312.t1
Couldn't classify 190256, 190407
Sorry, prediction pasa_asmbl_2301.p1 fails validation.
(CAA)	 GA	190256-190407	GT	AGG
(GAC)	 AG	190733-190810	GT	TGG
(TGG)	 AG	191187-191311	GT	AGG
(GCC)	 AG	191432-191526	AG	AGA
-recovered pasa_asmbl_2301.p1, terminal, 191432, 191526
-recovered pasa_asmbl_2301.p1, internal, 190733, 190810
-recovered pasa_asmbl_2301.p1, internal, 191187, 191311
Valid prediction for GlimmerHMM_glimmerT_1727-T1
Valid prediction for snap_scaffold_1-snap.2231-T1
Valid prediction for snap_scaffold_1-snap.2237-T1
Valid prediction for GlimmerHMM_glimmerT_1712-T1
Valid prediction for GlimmerHMM_glimmerT_1705-T1
Valid prediction for CodingQuarry_transcript_2881-T1
Valid prediction for GlimmerHMM_glimmerT_1724-T1
Valid prediction for GlimmerHMM_glimmerT_1732-T1
Valid prediction for HiQ_model.g1302.t1
Valid prediction for snap_scaffold_1-snap.2242-T1
Valid prediction for snap_scaffold_1-snap.2244-T1
Valid prediction for GlimmerHMM_glimmerT_1716-T1
Valid prediction for Augustus_model.g1301.t1
Valid prediction for GlimmerHMM_glimmerT_1713-T1
Valid prediction for snap_scaffold_1-snap.2229-T1
Valid prediction for snap_scaffold_1-snap.2221-T1
Valid prediction for snap_scaffold_1-snap.2258-T1
Valid prediction for snap_scaffold_1-snap.2252-T1
Valid prediction for GlimmerHMM_glimmerT_1710-T1
Valid prediction for snap_scaffold_1-snap.2261-T1
Valid prediction for Augustus_model.g1304.t1
Valid prediction for snap_scaffold_1-snap.2224-T1
Valid prediction for snap_scaffold_1-snap.2250-T1
Valid prediction for snap_scaffold_1-snap.2248-T1
Valid prediction for GlimmerHMM_glimmerT_1709-T1
Valid prediction for GlimmerHMM_glimmerT_1717-T1
Valid prediction for GlimmerHMM_glimmerT_1706-T1
Valid prediction for GlimmerHMM_glimmerT_1730-T1
Valid prediction for snap_scaffold_1-snap.2263-T1
Valid prediction for snap_scaffold_1-snap.2260-T1
Valid prediction for snap_scaffold_1-snap.2246-T1
Valid prediction for snap_scaffold_1-snap.2255-T1
Valid prediction for Augustus_model.g1303.t1
Valid prediction for Augustus_model.g1313.t1
Valid prediction for snap_scaffold_1-snap.2236-T1
Valid prediction for snap_scaffold_1-snap.2262-T1
Valid prediction for snap_scaffold_1-snap.2253-T1
Valid prediction for Augustus_model.g1297.t1
Couldn't classify 47828, 48271
Sorry, prediction pasa_asmbl_2299.p1 fails validation.
(AGA)	 CC	47828-48271	GT	ATG
(GTG)	 AG	48461-48646	GT	AGG
(CTG)	 AG	49016-49173	GT	AGG
(GGA)	 AG	49361-49557	GT	GAG
(GTA)	 AG	50044-50122	GT	AGG
(GTA)	 AG	50211-50301	AG	AGA
add_exon() Sorry, pasa_asmbl_2299.p1 49016-49173-terminal-2 is invalid.
-recovered pasa_asmbl_2299.p1, terminal, 49016, 49173
-recovered pasa_asmbl_2299.p1, terminal, 50211, 50301
-recovered pasa_asmbl_2299.p1, internal, 48461, 48646
-recovered pasa_asmbl_2299.p1, internal, 49016, 49173
-recovered pasa_asmbl_2299.p1, internal, 49361, 49557
-recovered pasa_asmbl_2299.p1, internal, 50044, 50122
Valid prediction for snap_scaffold_1-snap.2249-T1
Valid prediction for Augustus_model.g1300.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_1-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_1731-T1
Valid prediction for snap_scaffold_1-snap.2226-T1
Valid prediction for snap_scaffold_1-snap.2238-T1
Couldn't classify 140604, 140718
Sorry, prediction pasa_asmbl_795.p1 fails validation.
(ATC)	 AC	140604-140718	GT	AGG
(ATC)	 AG	140822-140937	GT	AGG
(TGG)	 AG	141046-141189	CC	AAC
-recovered pasa_asmbl_795.p1, terminal, 141046, 141189
-recovered pasa_asmbl_795.p1, internal, 140822, 140937
Valid prediction for snap_scaffold_1-snap.2241-T1
Couldn't classify 108561, 108745
Couldn't classify 109623, 109700
Sorry, prediction pasa_asmbl_801.p1 fails validation.
(ATT)	 TT	108561-108745	GT	AAG
(GAT)	 AG	109078-109288	GT	AGG
(GTG)	 AG	109403-109513	GT	AGG
(GAC)	 AG	109623-109700	AC	ACA
-recovered pasa_asmbl_801.p1, internal, 109078, 109288
-recovered pasa_asmbl_801.p1, internal, 109403, 109513
Valid prediction for snap_scaffold_1-snap.2220-T1
Valid prediction for snap_scaffold_1-snap.2245-T1
Valid prediction for GlimmerHMM_glimmerT_1714-T1
Valid prediction for GlimmerHMM_glimmerT_1722-T1
Valid prediction for Augustus_model.g1308.t1
Valid prediction for snap_scaffold_1-snap.2240-T1
Valid prediction for GlimmerHMM_glimmerT_1704-T1
Valid prediction for snap_scaffold_1-snap.2259-T1
Valid prediction for snap_scaffold_1-snap.2227-T1
Valid prediction for GlimmerHMM_glimmerT_1708-T1
Valid prediction for pasa_asmbl_787.p1
Valid prediction for GlimmerHMM_glimmerT_1707-T1
Valid prediction for GlimmerHMM_glimmerT_1720-T1
Valid prediction for GlimmerHMM_glimmerT_1715-T1
Valid prediction for Augustus_model.g1307.t1
Valid prediction for Augustus_model.g1309.t1
Valid prediction for GlimmerHMM_glimmerT_1729-T1
Valid prediction for snap_scaffold_1-snap.2254-T1
Valid prediction for GlimmerHMM_glimmerT_1726-T1
Valid prediction for snap_scaffold_1-snap.2233-T1
Valid prediction for pasa_asmbl_788.p1
Valid prediction for GlimmerHMM_glimmerT_1721-T1
Valid prediction for Augustus_model.g1299.t1
Valid prediction for snap_scaffold_1-snap.2257-T1
Valid prediction for CodingQuarry_transcript_2877-T1
Valid prediction for snap_scaffold_1-snap.2256-T1
Valid prediction for Augustus_model.g1298.t1
Valid prediction for snap_scaffold_1-snap.2232-T1
Valid prediction for GlimmerHMM_glimmerT_1728-T1
Valid prediction for Augustus_model.g1311.t1
Valid prediction for Augustus_model.g1306.t1
Couldn't classify 150864, 151066
Sorry, prediction pasa_asmbl_790.p1 fails validation.
(GTC)	 AG	150864-151066	GT	AGG
(CAC)	 AG	151205-151517	GT	AGG
(GTG)	 AG	151647-152063	GT	AGG
(GTG)	 AG	152184-152918	AG	AGA
-recovered pasa_asmbl_790.p1, terminal, 152184, 152918
-recovered pasa_asmbl_790.p1, internal, 150864, 151066
-recovered pasa_asmbl_790.p1, internal, 151205, 151517
-recovered pasa_asmbl_790.p1, internal, 151647, 152063
Valid prediction for GlimmerHMM_glimmerT_1711-T1
Valid prediction for pasa_asmbl_797.p1
Valid prediction for snap_scaffold_1-snap.2223-T1
Valid prediction for GlimmerHMM_glimmerT_1723-T1
Valid prediction for GlimmerHMM_glimmerT_1725-T1
Valid prediction for Augustus_model.g1296.t1
Valid prediction for GlimmerHMM_glimmerT_1703-T1
Valid prediction for HiQ_model.g1310.t1
Valid prediction for GlimmerHMM_glimmerT_1719-T1
Couldn't classify 160191, 160343
Couldn't classify 160649, 160810
Sorry, prediction pasa_asmbl_1266.p1 fails validation.
(GCC)	 CA	160191-160343	GC	AGG
(ACC)	 AG	160649-160810	AG	TGA
Valid prediction for snap_scaffold_1-snap.2235-T1
Valid prediction for snap_scaffold_1-snap.2251-T1
Valid prediction for CodingQuarry_transcript_2879-T1
Valid prediction for snap_scaffold_1-snap.2243-T1
Valid prediction for Augustus_model.g1305.t1
Valid prediction for snap_scaffold_1-snap.2247-T1
Valid prediction for snap_scaffold_1-snap.2225-T1
Valid prediction for CodingQuarry_transcript_2880-T1
Valid prediction for GlimmerHMM_glimmerT_1718-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10519, rend_intergenic: 2716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17799, rend_intergenic: 17297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37272, rend_intergenic: 24951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76034, rend_intergenic: 67472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83765, rend_intergenic: 80655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94044, rend_intergenic: 89514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96320, rend_intergenic: 94083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106820, rend_intergenic: 96976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115374, rend_intergenic: 115298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133253, rend_intergenic: 115378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139083, rend_intergenic: 134827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145114, rend_intergenic: 141018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164291, rend_intergenic: 145159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187643, rend_intergenic: 164715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204875, rend_intergenic: 200317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211660, rend_intergenic: 205217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218760, rend_intergenic: 212202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218991, rend_intergenic: 218875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240472, rend_intergenic: 219212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247988, rend_intergenic: 240483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253465
-exon list size: 454


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10519, rend_intergenic: 2716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17799, rend_intergenic: 17297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37272, rend_intergenic: 24951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76034, rend_intergenic: 67472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83765, rend_intergenic: 80655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94044, rend_intergenic: 89514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96320, rend_intergenic: 94083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106820, rend_intergenic: 96976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115374, rend_intergenic: 115298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133253, rend_intergenic: 115378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139083, rend_intergenic: 134827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145114, rend_intergenic: 141018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164291, rend_intergenic: 145159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187643, rend_intergenic: 164715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204875, rend_intergenic: 200317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211660, rend_intergenic: 205217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218760, rend_intergenic: 212202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218991, rend_intergenic: 218875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240472, rend_intergenic: 219212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247988, rend_intergenic: 240483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support