-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_9123201-9357563

-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.g16765.t1
Valid prediction for snap_scaffold_10-snap.1785-T1
Valid prediction for snap_scaffold_10-snap.1807-T1
Valid prediction for GlimmerHMM_glimmerT_25179-T1
Valid prediction for GlimmerHMM_glimmerT_25184-T1
Valid prediction for snap_scaffold_10-snap.1814-T1
Valid prediction for snap_scaffold_10-snap.1783-T1
Valid prediction for snap_scaffold_10-snap.1811-T1
Valid prediction for Augustus_model.g16771.t1
Valid prediction for snap_scaffold_10-snap.1816-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 211866, 211994
Sorry, prediction pasa_asmbl_3369.p1 fails validation.
(AGG)	 AC	211866-211994	GT	GGG
(GAG)	 AG	212471-212596	GT	GGG
(GAC)	 AG	212703-212857	GT	AGG
(TGC)	 AG	213153-213288	GT	AGG
(GAC)	 AG	214417-214485	TC	AGT
add_exon() Sorry, pasa_asmbl_3369.p1 212703-212857-terminal-2 is invalid.
-recovered pasa_asmbl_3369.p1, terminal, 212703, 212857
-recovered pasa_asmbl_3369.p1, terminal, 214417, 214485
-recovered pasa_asmbl_3369.p1, internal, 212471, 212596
-recovered pasa_asmbl_3369.p1, internal, 212703, 212857
-recovered pasa_asmbl_3369.p1, internal, 213153, 213288
Valid prediction for snap_scaffold_10-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_25192-T1
Valid prediction for snap_scaffold_10-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_25187-T1
Valid prediction for snap_scaffold_10-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_25188-T1
Valid prediction for snap_scaffold_10-snap.1793-T1
Valid prediction for snap_scaffold_10-snap.1791-T1
Valid prediction for snap_scaffold_10-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_25191-T1
Valid prediction for snap_scaffold_10-snap.1798-T1
Valid prediction for Augustus_model.g16767.t1
Valid prediction for snap_scaffold_10-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_25185-T1
Valid prediction for snap_scaffold_10-snap.1796-T1
Valid prediction for snap_scaffold_10-snap.1774-T1
Valid prediction for snap_scaffold_10-snap.1775-T1
Valid prediction for CodingQuarry_transcript_5522-T1
Valid prediction for snap_scaffold_10-snap.1815-T1
Valid prediction for Augustus_model.g16774.t1
Valid prediction for Augustus_model.g16772.t1
Valid prediction for snap_scaffold_10-snap.1781-T1
Valid prediction for snap_scaffold_10-snap.1804-T1
Valid prediction for snap_scaffold_10-snap.1803-T1
Valid prediction for snap_scaffold_10-snap.1797-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_10-snap.1782-T1
Valid prediction for Augustus_model.g16766.t1
Valid prediction for snap_scaffold_10-snap.1776-T1
Valid prediction for GlimmerHMM_glimmerT_25181-T1
Valid prediction for snap_scaffold_10-snap.1805-T1
Valid prediction for snap_scaffold_10-snap.1810-T1
Valid prediction for snap_scaffold_10-snap.1806-T1
Valid prediction for GlimmerHMM_glimmerT_25186-T1
Valid prediction for GlimmerHMM_glimmerT_25177-T1
Valid prediction for pasa_asmbl_4684.p1
Valid prediction for GlimmerHMM_glimmerT_25178-T1
Valid prediction for snap_scaffold_10-snap.1777-T1
Valid prediction for snap_scaffold_10-snap.1813-T1
Valid prediction for Augustus_model.g16773.t1
Valid prediction for CodingQuarry_transcript_5523-T1
Valid prediction for snap_scaffold_10-snap.1784-T1
Valid prediction for snap_scaffold_10-snap.1779-T1
Valid prediction for CodingQuarry_transcript_5524-T1
Valid prediction for snap_scaffold_10-snap.1812-T1
Valid prediction for Augustus_model.g16768.t1
Valid prediction for Augustus_model.g16769.t1
Valid prediction for Augustus_model.g16763.t1
Couldn't classify 4201, 5289
Couldn't classify 6771, 6821
Sorry, prediction pasa_asmbl_4688.p1 fails validation.
(CCT)	 CG	4201-5289	GT	CTG
(TAT)	 AG	5481-5592	GT	TGG
(AAC)	 AG	6491-6672	GT	AGG
(CCC)	 AG	6771-6821	AG	AGA
-recovered pasa_asmbl_4688.p1, internal, 5481, 5592
-recovered pasa_asmbl_4688.p1, internal, 6491, 6672
Valid prediction for snap_scaffold_10-snap.1789-T1
Valid prediction for GlimmerHMM_glimmerT_25190-T1
Valid prediction for snap_scaffold_10-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_25189-T1
Valid prediction for Augustus_model.g16775.t1
Valid prediction for CodingQuarry_transcript_5525-T1
Valid prediction for snap_scaffold_10-snap.1792-T1
Valid prediction for snap_scaffold_10-snap.1780-T1
Valid prediction for snap_scaffold_10-snap.1795-T1
Valid prediction for snap_scaffold_10-snap.1800-T1
Valid prediction for Augustus_model.g16770.t1
Valid prediction for snap_scaffold_10-snap.1787-T1
Valid prediction for snap_scaffold_10-snap.1808-T1
Couldn't classify 133700, 133749
Couldn't classify 135423, 135630
Sorry, prediction pasa_asmbl_4683.p1 fails validation.
(TGC)	 TC	133700-133749	GT	AGG
(TAC)	 AG	134706-135061	GT	GGG
(TCA)	 AG	135148-135256	GT	CGG
(GTA)	 AG	135423-135630	AT	ACA
-recovered pasa_asmbl_4683.p1, internal, 134706, 135061
-recovered pasa_asmbl_4683.p1, internal, 135148, 135256
Valid prediction for GlimmerHMM_glimmerT_25182-T1
Valid prediction for GlimmerHMM_glimmerT_25193-T1
Couldn't classify 135810, 136017
Sorry, prediction pasa_asmbl_4682.p1 fails validation.
(CAG)	 GT	135810-136017	GT	CAG
(GCA)	 AG	136925-137092	GT	GGG
(GTT)	 AG	137378-137557	GT	AGG
(GTG)	 AG	137680-137826	GT	AAG
(CTC)	 AG	137970-138175	CT	AGC
-recovered pasa_asmbl_4682.p1, terminal, 137970, 138175
-recovered pasa_asmbl_4682.p1, internal, 136925, 137092
-recovered pasa_asmbl_4682.p1, internal, 137378, 137557
-recovered pasa_asmbl_4682.p1, internal, 137680, 137826
Valid prediction for GlimmerHMM_glimmerT_25180-T1
Valid prediction for snap_scaffold_10-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_25183-T1
Valid prediction for snap_scaffold_10-snap.1802-T1
Valid prediction for Augustus_model.g16764.t1
Couldn't classify 1818, 1850
Couldn't classify 2779, 2827
Sorry, prediction pasa_asmbl_4689.p1 fails validation.
(GTC)	 CT	1818-1850	GT	AGG
(ATC)	 AG	2138-2275	GT	AGG
(TGC)	 AG	2372-2565	GT	AGG
(CAA)	 AG	2779-2827	GA	AGG
-recovered pasa_asmbl_4689.p1, internal, 2138, 2275
-recovered pasa_asmbl_4689.p1, internal, 2372, 2565
Valid prediction for snap_scaffold_10-snap.1809-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34599, rend_intergenic: 21267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51592, rend_intergenic: 35051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60899, rend_intergenic: 55914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66075, rend_intergenic: 62315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79225, rend_intergenic: 73487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89621, rend_intergenic: 82540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105740, rend_intergenic: 99670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152478, rend_intergenic: 138400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170076, rend_intergenic: 153852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173416, rend_intergenic: 170322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202219, rend_intergenic: 173704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205923, rend_intergenic: 202892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214485, rend_intergenic: 207795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232963, rend_intergenic: 220042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234363
-exon list size: 402


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 34599, rend_intergenic: 21267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51592, rend_intergenic: 35051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60899, rend_intergenic: 55914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66075, rend_intergenic: 62315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79225, rend_intergenic: 73487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89621, rend_intergenic: 82540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105740, rend_intergenic: 99670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152478, rend_intergenic: 138400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170076, rend_intergenic: 153852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173416, rend_intergenic: 170322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202219, rend_intergenic: 173704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205923, rend_intergenic: 202892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214485, rend_intergenic: 207795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232963, rend_intergenic: 220042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support