-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_9880782-10075496

-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_6-snap.2167-T1
Valid prediction for GlimmerHMM_glimmerT_15331-T1
Valid prediction for snap_scaffold_6-snap.2141-T1
Valid prediction for Augustus_model.g10183.t1
Valid prediction for snap_scaffold_6-snap.2135-T1
Couldn't classify 80535, 80774
Sorry, prediction pasa_asmbl_47258.p1 fails validation.
(CTG)	 AC	80535-80774	GT	AGG
(TCT)	 AG	80990-81082	GT	AGG
(GGG)	 AG	81472-81611	GT	AGG
(TGT)	 AG	81865-82009	GT	CGG
(GTG)	 AG	82504-82839	GT	AGG
(CAA)	 AG	83014-83098	GT	AGG
(GTG)	 AG	83542-83657	GT	AGG
(CCT)	 AG	83792-83959	GT	ATG
(GGT)	 AG	84083-84175	GT	TGG
(GAG)	 AG	84292-84408	GA	GAG
-recovered pasa_asmbl_47258.p1, terminal, 84292, 84408
-recovered pasa_asmbl_47258.p1, internal, 80990, 81082
-recovered pasa_asmbl_47258.p1, internal, 81472, 81611
-recovered pasa_asmbl_47258.p1, internal, 81865, 82009
-recovered pasa_asmbl_47258.p1, internal, 82504, 82839
-recovered pasa_asmbl_47258.p1, internal, 83014, 83098
-recovered pasa_asmbl_47258.p1, internal, 83542, 83657
-recovered pasa_asmbl_47258.p1, internal, 83792, 83959
-recovered pasa_asmbl_47258.p1, internal, 84083, 84175
Valid prediction for snap_scaffold_6-snap.2129-T1
Valid prediction for snap_scaffold_6-snap.2133-T1
Valid prediction for snap_scaffold_6-snap.2137-T1
Valid prediction for GlimmerHMM_glimmerT_15321-T1
Valid prediction for GlimmerHMM_glimmerT_15329-T1
Valid prediction for GlimmerHMM_glimmerT_15333-T1
Valid prediction for snap_scaffold_6-snap.2148-T1
Valid prediction for snap_scaffold_6-snap.2178-T1
Valid prediction for GlimmerHMM_glimmerT_15334-T1
Valid prediction for GlimmerHMM_glimmerT_15326-T1
Valid prediction for Augustus_model.g10189.t1
Valid prediction for GlimmerHMM_glimmerT_15341-T1
Valid prediction for GlimmerHMM_glimmerT_15342-T1
Valid prediction for snap_scaffold_6-snap.2150-T1
Valid prediction for GlimmerHMM_glimmerT_15340-T1
Valid prediction for Augustus_model.g10191.t1
Valid prediction for Augustus_model.g10201.t1
Valid prediction for snap_scaffold_6-snap.2153-T1
Valid prediction for Augustus_model.g10194.t1
Valid prediction for CodingQuarry_transcript_55180-T1
Valid prediction for snap_scaffold_6-snap.2172-T1
Valid prediction for snap_scaffold_6-snap.2143-T1
Valid prediction for GlimmerHMM_glimmerT_15320-T1
Valid prediction for snap_scaffold_6-snap.2131-T1
Valid prediction for snap_scaffold_6-snap.2166-T1
Valid prediction for snap_scaffold_6-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_15332-T1
Valid prediction for snap_scaffold_6-snap.2163-T1
Couldn't classify 24316, 25764
Sorry, prediction pasa_asmbl_47246.p1 fails validation.
(CAA)	 TT	24316-25764	AG	GAA
Valid prediction for Augustus_model.g10198.t1
Valid prediction for snap_scaffold_6-snap.2130-T1
Valid prediction for Augustus_model.g10202.t1
Valid prediction for snap_scaffold_6-snap.2147-T1
Valid prediction for Augustus_model.g10207.t1
Valid prediction for GlimmerHMM_glimmerT_15319-T1
Valid prediction for Augustus_model.g10197.t1
Couldn't classify 80146, 80261
Sorry, prediction pasa_asmbl_47255.p1 fails validation.
(ATG)	 GG	74000-74130	GT	CGG
(GAC)	 AG	74505-74710	GT	GGG
(ATG)	 AG	75242-75268	GT	AGG
(AGA)	 AG	75464-75751	GT	AGG
(CTC)	 AG	77415-77495	GT	TTG
(GTG)	 AG	78407-78517	GT	AGG
(GCT)	 AG	78748-78867	GT	AGG
(GCA)	 AG	79150-79243	GT	CGG
(GTG)	 AG	79671-79729	GT	GGG
(CTC)	 AG	80146-80261	CC	TCC
-recovered pasa_asmbl_47255.p1, initial, 74000, 74130
add_exon() Sorry, pasa_asmbl_47255.p1 75242-75268-initial-1 is invalid.
-recovered pasa_asmbl_47255.p1, initial, 75242, 75268
-recovered pasa_asmbl_47255.p1, terminal, 75242, 75268
-recovered pasa_asmbl_47255.p1, internal, 74505, 74710
-recovered pasa_asmbl_47255.p1, internal, 75242, 75268
-recovered pasa_asmbl_47255.p1, internal, 75464, 75751
-recovered pasa_asmbl_47255.p1, internal, 77415, 77495
-recovered pasa_asmbl_47255.p1, internal, 78407, 78517
-recovered pasa_asmbl_47255.p1, internal, 78748, 78867
-recovered pasa_asmbl_47255.p1, internal, 79150, 79243
-recovered pasa_asmbl_47255.p1, internal, 79671, 79729
Valid prediction for Augustus_model.g10192.t1
Valid prediction for snap_scaffold_6-snap.2139-T1
Valid prediction for pasa_asmbl_47249.p1
Valid prediction for GlimmerHMM_glimmerT_15323-T1
Valid prediction for snap_scaffold_6-snap.2165-T1
Valid prediction for snap_scaffold_6-snap.2152-T1
Valid prediction for GlimmerHMM_glimmerT_15336-T1
Valid prediction for snap_scaffold_6-snap.2169-T1
Valid prediction for CodingQuarry_transcript_55178-T1
Valid prediction for CodingQuarry_transcript_55179-T1
Valid prediction for CodingQuarry_transcript_55181-T1
Valid prediction for Augustus_model.g10193.t1
Valid prediction for snap_scaffold_6-snap.2155-T1
Valid prediction for HiQ_model.g10184.t1
Valid prediction for snap_scaffold_6-snap.2161-T1
Valid prediction for snap_scaffold_6-snap.2158-T1
Valid prediction for HiQ_model.g10186.t1
Valid prediction for Augustus_model.g10200.t1
Valid prediction for GlimmerHMM_glimmerT_15330-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_6-snap.2179-T1
Valid prediction for pasa_asmbl_48651.p1
Valid prediction for snap_scaffold_6-snap.2132-T1
Valid prediction for Augustus_model.g10195.t1
Valid prediction for snap_scaffold_6-snap.2140-T1
Valid prediction for snap_scaffold_6-snap.2156-T1
Couldn't classify 140594, 140772
Sorry, prediction pasa_asmbl_48641.p1 fails validation.
(GCC)	 AC	140594-140772	GT	AAG
(AAT)	 AG	141075-141192	GT	AGG
(TAT)	 AG	141830-141903	GT	ACG
(TCT)	 AG	141999-142056	GT	CGG
(CGG)	 AG	142161-142233	GT	AGG
(ATC)	 AG	142331-142476	AG	GAA
-recovered pasa_asmbl_48641.p1, terminal, 142331, 142476
-recovered pasa_asmbl_48641.p1, internal, 141075, 141192
-recovered pasa_asmbl_48641.p1, internal, 141830, 141903
-recovered pasa_asmbl_48641.p1, internal, 141999, 142056
-recovered pasa_asmbl_48641.p1, internal, 142161, 142233
Valid prediction for snap_scaffold_6-snap.2160-T1
Valid prediction for Augustus_model.g10185.t1
Valid prediction for GlimmerHMM_glimmerT_15335-T1
Valid prediction for snap_scaffold_6-snap.2162-T1
Valid prediction for snap_scaffold_6-snap.2159-T1
Valid prediction for snap_scaffold_6-snap.2164-T1
Valid prediction for Augustus_model.g10208.t1
Valid prediction for Augustus_model.g10204.t1
Valid prediction for Augustus_model.g10196.t1
Valid prediction for snap_scaffold_6-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_15337-T1
Valid prediction for CodingQuarry_transcript_55183-T1
Valid prediction for GlimmerHMM_glimmerT_15324-T1
Valid prediction for snap_scaffold_6-snap.2146-T1
Valid prediction for snap_scaffold_6-snap.2149-T1
Valid prediction for snap_scaffold_6-snap.2177-T1
Valid prediction for CodingQuarry_transcript_55185-T1
Couldn't classify 157959, 159458
Sorry, prediction pasa_asmbl_48640.p1 fails validation.
(AGG)	 CA	157959-159458	GA	GAG
Valid prediction for snap_scaffold_6-snap.2175-T1
Valid prediction for snap_scaffold_6-snap.2174-T1
Valid prediction for GlimmerHMM_glimmerT_15328-T1
Valid prediction for GlimmerHMM_glimmerT_15322-T1
Valid prediction for Augustus_model.g10190.t1
Valid prediction for GlimmerHMM_glimmerT_15338-T1
Valid prediction for Augustus_model.g10187.t1
Valid prediction for Augustus_model.g10209.t1
Valid prediction for Augustus_model.g10203.t1
Valid prediction for snap_scaffold_6-snap.2176-T1
Valid prediction for snap_scaffold_6-snap.2138-T1
Valid prediction for snap_scaffold_6-snap.2170-T1
Valid prediction for snap_scaffold_6-snap.2157-T1
Valid prediction for GlimmerHMM_glimmerT_15339-T1
Valid prediction for snap_scaffold_6-snap.2136-T1
Valid prediction for HiQ_model.g10206.t1
Valid prediction for HiQ_model.g10188.t1
Couldn't classify 32628, 32682
Sorry, prediction pasa_asmbl_48652.p2 fails validation.
(GTG)	 TA	32628-32682	GT	AGG
(TGA)	 AG	34143-34287	GT	GGG
(GTG)	 AG	34513-34618	TG	GAT
-recovered pasa_asmbl_48652.p2, terminal, 34513, 34618
-recovered pasa_asmbl_48652.p2, internal, 34143, 34287
Valid prediction for snap_scaffold_6-snap.2168-T1
Valid prediction for snap_scaffold_6-snap.2151-T1
Valid prediction for GlimmerHMM_glimmerT_15327-T1
Valid prediction for GlimmerHMM_glimmerT_15345-T1
Valid prediction for snap_scaffold_6-snap.2142-T1
Valid prediction for GlimmerHMM_glimmerT_15347-T1
Valid prediction for HiQ_model.g10199.t1
Valid prediction for snap_scaffold_6-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_15344-T1
Couldn't classify 86350, 86661
Sorry, prediction pasa_asmbl_48649.p3 fails validation.
(GAA)	 CA	86350-86661	CT	GAC
Valid prediction for GlimmerHMM_glimmerT_15325-T1
Valid prediction for CodingQuarry_transcript_55186-T1
Valid prediction for Augustus_model.g10205.t1
Valid prediction for GlimmerHMM_glimmerT_15346-T1
Valid prediction for snap_scaffold_6-snap.2171-T1
Valid prediction for snap_scaffold_6-snap.2144-T1
Valid prediction for snap_scaffold_6-snap.2134-T1
Valid prediction for GlimmerHMM_glimmerT_15343-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49702, rend_intergenic: 43704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64636, rend_intergenic: 63926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71365, rend_intergenic: 68291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74134, rend_intergenic: 71501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75694, rend_intergenic: 74374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84408, rend_intergenic: 75944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99989, rend_intergenic: 89723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108363, rend_intergenic: 103190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115901, rend_intergenic: 108627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126166, rend_intergenic: 117755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134598, rend_intergenic: 128902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141884, rend_intergenic: 138594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144181, rend_intergenic: 142222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151754, rend_intergenic: 149183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157169, rend_intergenic: 152573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194715
-exon list size: 440


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 49702, rend_intergenic: 43704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64636, rend_intergenic: 63926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71365, rend_intergenic: 68291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74134, rend_intergenic: 71501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75694, rend_intergenic: 74374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84408, rend_intergenic: 75944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99989, rend_intergenic: 89723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108363, rend_intergenic: 103190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115901, rend_intergenic: 108627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126166, rend_intergenic: 117755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134598, rend_intergenic: 128902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141884, rend_intergenic: 138594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144181, rend_intergenic: 142222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151754, rend_intergenic: 149183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157169, rend_intergenic: 152573  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