-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_8802821-8995141

-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_9-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_22613-T1
Valid prediction for snap_scaffold_9-snap.1805-T1
Couldn't classify 157486, 157538
Couldn't classify 161949, 162067
Sorry, prediction pasa_asmbl_54186.p1 fails validation.
(CCG)	 CT	157486-157538	GT	AGG
(GTC)	 AG	160364-160505	GT	AGG
(GAG)	 AG	160994-161113	GT	AGG
(GCC)	 AG	161329-161387	GT	AGG
(GTT)	 AG	161622-161731	GT	CGG
(GTG)	 AG	161949-162067	CA	AGC
-recovered pasa_asmbl_54186.p1, internal, 160364, 160505
-recovered pasa_asmbl_54186.p1, internal, 160994, 161113
-recovered pasa_asmbl_54186.p1, internal, 161329, 161387
-recovered pasa_asmbl_54186.p1, internal, 161622, 161731
Valid prediction for Augustus_model.g15058.t1
Couldn't classify 152447, 152563
Couldn't classify 154920, 155063
Sorry, prediction pasa_asmbl_54185.p1 fails validation.
(GTG)	 AG	152447-152563	GT	AGG
(GTC)	 AG	152728-152791	GT	CGG
(ACC)	 AG	152983-153144	GT	AGG
(ACT)	 AG	153504-153628	GT	GGG
(AGT)	 AG	153733-153856	GT	GGG
(ATT)	 AG	153946-154064	GT	GGG
(TTG)	 AG	154296-154406	GT	AGG
(TCA)	 AG	154920-155063	CA	TCC
-recovered pasa_asmbl_54185.p1, internal, 152447, 152563
-recovered pasa_asmbl_54185.p1, internal, 152728, 152791
-recovered pasa_asmbl_54185.p1, internal, 152983, 153144
-recovered pasa_asmbl_54185.p1, internal, 153504, 153628
-recovered pasa_asmbl_54185.p1, internal, 153733, 153856
-recovered pasa_asmbl_54185.p1, internal, 153946, 154064
-recovered pasa_asmbl_54185.p1, internal, 154296, 154406
Valid prediction for snap_scaffold_9-snap.1795-T1
Couldn't classify 122821, 123010
Sorry, prediction pasa_asmbl_54180.p1 fails validation.
(ATG)	 CC	121801-121882	GT	AGG
(AGA)	 AG	122346-122457	GT	TGG
(TCA)	 AG	122821-123010	GA	AGG
-recovered pasa_asmbl_54180.p1, initial, 121801, 121882
-recovered pasa_asmbl_54180.p1, internal, 122346, 122457
Valid prediction for Augustus_model.g15055.t1
Valid prediction for snap_scaffold_9-snap.1811-T1
Valid prediction for snap_scaffold_9-snap.1789-T1
Valid prediction for snap_scaffold_9-snap.1785-T1
Couldn't classify 163970, 164330
Sorry, prediction pasa_asmbl_54191.p1 fails validation.
(CCC)	 CC	163970-164330	GT	AGG
(ACA)	 AG	164463-164617	GT	ACG
(GAT)	 AG	164893-165022	GT	AGG
(TGT)	 AG	165179-165300	CA	AGC
-recovered pasa_asmbl_54191.p1, terminal, 165179, 165300
-recovered pasa_asmbl_54191.p1, internal, 164463, 164617
-recovered pasa_asmbl_54191.p1, internal, 164893, 165022
Valid prediction for snap_scaffold_9-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_22624-T1
Valid prediction for Augustus_model.g15052.t1
Valid prediction for Augustus_model.g15046.t1
Couldn't classify 187839, 188012
Sorry, prediction pasa_asmbl_54195.p1 fails validation.
(GGG)	 CA	187839-188012	GT	CTG
(GTG)	 AG	188606-188816	GT	AGG
(CTT)	 AG	189031-189197	GA	AAG
-recovered pasa_asmbl_54195.p1, terminal, 189031, 189197
-recovered pasa_asmbl_54195.p1, internal, 188606, 188816
Valid prediction for snap_scaffold_9-snap.1787-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22612-T1
Valid prediction for GlimmerHMM_glimmerT_22606-T1
Valid prediction for GlimmerHMM_glimmerT_22616-T1
Valid prediction for Augustus_model.g15043.t1
Couldn't classify 162125, 162255
Couldn't classify 163576, 163837
Sorry, prediction pasa_asmbl_54190.p2 fails validation.
(CAG)	 AG	162125-162255	GT	AGG
(TCG)	 AG	163576-163837	AC	CCA
-recovered pasa_asmbl_54190.p2, internal, 162125, 162255
Valid prediction for snap_scaffold_9-snap.1812-T1
Valid prediction for snap_scaffold_9-snap.1782-T1
Valid prediction for Augustus_model.g15057.t1
Valid prediction for GlimmerHMM_glimmerT_22608-T1
Valid prediction for Augustus_model.g15050.t1
Valid prediction for snap_scaffold_9-snap.1807-T1
Valid prediction for snap_scaffold_9-snap.1803-T1
Valid prediction for Augustus_model.g15059.t1
Valid prediction for Augustus_model.g15060.t1
Valid prediction for Augustus_model.g15045.t1
Valid prediction for GlimmerHMM_glimmerT_22628-T1
Valid prediction for GlimmerHMM_glimmerT_22630-T1
Valid prediction for snap_scaffold_9-snap.1797-T1
Valid prediction for snap_scaffold_9-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_22632-T1
Valid prediction for snap_scaffold_9-snap.1816-T1
Valid prediction for snap_scaffold_9-snap.1794-T1
Valid prediction for snap_scaffold_9-snap.1784-T1
Valid prediction for snap_scaffold_9-snap.1809-T1
Valid prediction for snap_scaffold_9-snap.1799-T1
Valid prediction for pasa_asmbl_54181.p1
Valid prediction for snap_scaffold_9-snap.1802-T1
Valid prediction for GlimmerHMM_glimmerT_22620-T1
Valid prediction for snap_scaffold_9-snap.1780-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 CodingQuarry_transcript_62250-T1
Valid prediction for GlimmerHMM_glimmerT_22621-T1
Valid prediction for snap_scaffold_9-snap.1814-T1
Couldn't classify 168670, 169200
Sorry, prediction pasa_asmbl_55141.p1 fails validation.
(CCT)	 GT	168670-169200	CA	AGC
Valid prediction for snap_scaffold_9-snap.1793-T1
Valid prediction for snap_scaffold_9-snap.1781-T1
Couldn't classify 46775, 46786
Sorry, prediction pasa_asmbl_55152.p1 fails validation.
(ACC)	 TC	46775-46786	GT	AGG
(ACT)	 AG	46911-47032	GT	CTG
(GTA)	 AG	48333-48497	GT	CAG
(GAC)	 AG	48762-48807	GT	AGG
(TAC)	 AG	49203-49304	GT	AGG
(TGC)	 AG	49563-49646	GT	AGG
(AGG)	 AG	49819-49984	GT	GTG
(TGG)	 AG	50187-50280	GT	AGG
(AAT)	 AG	50407-50584	TG	AAT
-recovered pasa_asmbl_55152.p1, terminal, 50407, 50584
-recovered pasa_asmbl_55152.p1, internal, 46911, 47032
-recovered pasa_asmbl_55152.p1, internal, 48333, 48497
-recovered pasa_asmbl_55152.p1, internal, 48762, 48807
-recovered pasa_asmbl_55152.p1, internal, 49203, 49304
-recovered pasa_asmbl_55152.p1, internal, 49563, 49646
-recovered pasa_asmbl_55152.p1, internal, 49819, 49984
-recovered pasa_asmbl_55152.p1, internal, 50187, 50280
Valid prediction for GlimmerHMM_glimmerT_22623-T1
Valid prediction for GlimmerHMM_glimmerT_22610-T1
Valid prediction for Augustus_model.g15053.t1
Valid prediction for snap_scaffold_9-snap.1779-T1
Valid prediction for Augustus_model.g15041.t1
Valid prediction for GlimmerHMM_glimmerT_22619-T1
Valid prediction for snap_scaffold_9-snap.1808-T1
Couldn't classify 138515, 138709
Sorry, prediction pasa_asmbl_55144.p1 fails validation.
(CAC)	 TC	138515-138709	GT	ACG
(GGT)	 AG	138834-138913	GT	AGG
(ATG)	 AG	140074-140348	GT	AGG
(TGG)	 AG	140657-140817	AA	GAA
add_exon() Sorry, pasa_asmbl_55144.p1 140074-140348-initial-1 is invalid.
-recovered pasa_asmbl_55144.p1, initial, 140074, 140348
-recovered pasa_asmbl_55144.p1, terminal, 140657, 140817
-recovered pasa_asmbl_55144.p1, internal, 138834, 138913
-recovered pasa_asmbl_55144.p1, internal, 140074, 140348
Valid prediction for pasa_asmbl_55147.p1
Valid prediction for GlimmerHMM_glimmerT_22626-T1
Couldn't classify 163969, 164280
Sorry, prediction pasa_asmbl_55143.p1 fails validation.
(ATG)	 AA	163969-164280	AG	GTA
Valid prediction for snap_scaffold_9-snap.1783-T1
Valid prediction for GlimmerHMM_glimmerT_22607-T1
Valid prediction for GlimmerHMM_glimmerT_22627-T1
Valid prediction for Augustus_model.g15054.t1
Valid prediction for snap_scaffold_9-snap.1798-T1
Valid prediction for GlimmerHMM_glimmerT_22615-T1
Valid prediction for Augustus_model.g15047.t1
Couldn't classify 169282, 169927
Sorry, prediction pasa_asmbl_55140.p1 fails validation.
(TCA)	 CT	169282-169927	GT	AGG
(GCC)	 AG	170085-170339	GT	CGG
(GTA)	 AG	170457-171658	TT	GAT
-recovered pasa_asmbl_55140.p1, terminal, 170457, 171658
-recovered pasa_asmbl_55140.p1, internal, 170085, 170339
Valid prediction for snap_scaffold_9-snap.1796-T1
Valid prediction for Augustus_model.g15049.t1
Valid prediction for GlimmerHMM_glimmerT_22614-T1
Valid prediction for GlimmerHMM_glimmerT_22625-T1
Valid prediction for snap_scaffold_9-snap.1788-T1
Valid prediction for Augustus_model.g15051.t1
Valid prediction for Augustus_model.g15048.t1
Valid prediction for snap_scaffold_9-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_22629-T1
Valid prediction for snap_scaffold_9-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_22617-T1
Valid prediction for Augustus_model.g15044.t1
Valid prediction for snap_scaffold_9-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_22631-T1
Valid prediction for snap_scaffold_9-snap.1801-T1
Couldn't classify 167743, 168180
Sorry, prediction pasa_asmbl_55142.p1 fails validation.
(ATT)	 CC	167743-168180	CC	AAC
Valid prediction for GlimmerHMM_glimmerT_22611-T1
Valid prediction for pasa_asmbl_55139.p1
Valid prediction for GlimmerHMM_glimmerT_22618-T1
Valid prediction for snap_scaffold_9-snap.1804-T1
Valid prediction for CodingQuarry_transcript_62249-T1
Valid prediction for snap_scaffold_9-snap.1813-T1
Valid prediction for snap_scaffold_9-snap.1806-T1
Valid prediction for HiQ_model.g15042.t1
Valid prediction for CodingQuarry_transcript_62248-T1
Valid prediction for GlimmerHMM_glimmerT_22609-T1
Valid prediction for GlimmerHMM_glimmerT_22605-T1
Couldn't classify 188406, 188585
Sorry, prediction pasa_asmbl_55773.p1 fails validation.
(GAC)	 CA	188406-188585	GT	AGG
(GAG)	 AG	188746-188871	TG	AAT
-recovered pasa_asmbl_55773.p1, terminal, 188746, 188871
Valid prediction for snap_scaffold_9-snap.1810-T1
Valid prediction for CodingQuarry_transcript_62251-T1
Valid prediction for HiQ_model.g15056.t1
Valid prediction for GlimmerHMM_glimmerT_22622-T1
Valid prediction for snap_scaffold_9-snap.1815-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28353, rend_intergenic: 25521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53966, rend_intergenic: 51505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64919, rend_intergenic: 54053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68296, rend_intergenic: 64977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86604, rend_intergenic: 82434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91938, rend_intergenic: 89198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92896, rend_intergenic: 91964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97504, rend_intergenic: 93244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100533, rend_intergenic: 98026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110338, rend_intergenic: 105812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115479, rend_intergenic: 113609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134622, rend_intergenic: 126015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140165, rend_intergenic: 135836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155116, rend_intergenic: 149721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171939, rend_intergenic: 159712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192321
-exon list size: 458


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 28353, rend_intergenic: 25521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53966, rend_intergenic: 51505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64919, rend_intergenic: 54053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68296, rend_intergenic: 64977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86604, rend_intergenic: 82434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91938, rend_intergenic: 89198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92896, rend_intergenic: 91964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97504, rend_intergenic: 93244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100533, rend_intergenic: 98026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110338, rend_intergenic: 105812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115479, rend_intergenic: 113609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134622, rend_intergenic: 126015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140165, rend_intergenic: 135836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155116, rend_intergenic: 149721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171939, rend_intergenic: 159712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support