-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_11522931-11711084

-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.g22275.t1
Valid prediction for HiQ_model.g22271.t1
Valid prediction for snap_scaffold_13-snap.2174-T1
Valid prediction for snap_scaffold_13-snap.2157-T1
Couldn't classify 86034, 86234
Couldn't classify 90040, 90136
Sorry, prediction pasa_asmbl_11281.p1 fails validation.
(GCG)	 AG	86034-86234	GT	TGG
(ATT)	 AG	88775-88870	GT	ACG
(GAG)	 AG	89181-89521	GT	CGG
(CTC)	 AG	89846-89953	GT	AGG
(TCA)	 AG	90040-90136	AC	GGA
-recovered pasa_asmbl_11281.p1, internal, 86034, 86234
-recovered pasa_asmbl_11281.p1, internal, 88775, 88870
-recovered pasa_asmbl_11281.p1, internal, 89181, 89521
-recovered pasa_asmbl_11281.p1, internal, 89846, 89953
Valid prediction for GlimmerHMM_glimmerT_33163-T1
Valid prediction for snap_scaffold_13-snap.2160-T1
Valid prediction for snap_scaffold_13-snap.2155-T1
Valid prediction for CodingQuarry_transcript_13225-T1
Valid prediction for GeneMark_model.56552_t
Valid prediction for pasa_asmbl_11274.p1
Valid prediction for snap_scaffold_13-snap.2162-T1
Valid prediction for GeneMark_model.56556_t
Valid prediction for Augustus_model.g22280.t1
Valid prediction for GeneMark_model.56577_t
Couldn't classify 90833, 90875
Sorry, prediction pasa_asmbl_11284.p1 fails validation.
(GGC)	 TA	90833-90875	GT	AGG
(GTG)	 AG	91069-91168	GT	AGG
(TGA)	 AG	91390-91574	GT	AGG
(AGA)	 AG	91711-91804	GT	AGG
(GTA)	 AG	91901-91970	GT	AGG
(GCC)	 AG	92059-92151	GT	AGG
(TCG)	 AG	92241-92320	GT	CCG
(GCC)	 AG	92445-92586	GT	TAG
(GCC)	 AG	93194-93342	GT	AAG
(GTC)	 AG	94250-94336	GT	GAG
(GAA)	 AG	94488-94640	GT	AGG
(AGA)	 AG	94962-95076	GT	ATG
(GAT)	 AG	96266-96369	GT	TCG
(GTA)	 AG	97105-97249	CC	GAC
add_exon() Sorry, pasa_asmbl_11284.p1 91711-91804-terminal-3 is invalid.
-recovered pasa_asmbl_11284.p1, terminal, 91711, 91804
-recovered pasa_asmbl_11284.p1, terminal, 97105, 97249
-recovered pasa_asmbl_11284.p1, internal, 91069, 91168
-recovered pasa_asmbl_11284.p1, internal, 91390, 91574
-recovered pasa_asmbl_11284.p1, internal, 91711, 91804
-recovered pasa_asmbl_11284.p1, internal, 91901, 91970
-recovered pasa_asmbl_11284.p1, internal, 92059, 92151
-recovered pasa_asmbl_11284.p1, internal, 92241, 92320
-recovered pasa_asmbl_11284.p1, internal, 92445, 92586
-recovered pasa_asmbl_11284.p1, internal, 93194, 93342
-recovered pasa_asmbl_11284.p1, internal, 94250, 94336
-recovered pasa_asmbl_11284.p1, internal, 94488, 94640
-recovered pasa_asmbl_11284.p1, internal, 94962, 95076
-recovered pasa_asmbl_11284.p1, internal, 96266, 96369
Valid prediction for GeneMark_model.56557_t
Valid prediction for GeneMark_model.56545_t
Valid prediction for Augustus_model.g22277.t1
Valid prediction for snap_scaffold_13-snap.2149-T1
Valid prediction for GeneMark_model.56560_t
Valid prediction for GeneMark_model.56548_t
Valid prediction for CodingQuarry_transcript_13223-T1
Valid prediction for GeneMark_model.56580_t
Valid prediction for GeneMark_model.56546_t
Valid prediction for pasa_asmbl_11265.p2
Valid prediction for GlimmerHMM_glimmerT_33151-T1
Valid prediction for CodingQuarry_transcript_13220-T1
Valid prediction for Augustus_model.g22287.t1
Valid prediction for Augustus_model.g22284.t1
Valid prediction for HiQ_model.g22274.t1
Valid prediction for snap_scaffold_13-snap.2163-T1
Valid prediction for Augustus_model.g22283.t1
Valid prediction for HiQ_model.g22272.t1
Valid prediction for CodingQuarry_transcript_13226-T1
Valid prediction for GlimmerHMM_glimmerT_33155-T1
Valid prediction for GeneMark_model.56550_t
Valid prediction for GeneMark_model.56582_t
Valid prediction for snap_scaffold_13-snap.2152-T1
Valid prediction for snap_scaffold_13-snap.2178-T1
Valid prediction for GeneMark_model.56566_t
Valid prediction for snap_scaffold_13-snap.2158-T1
Valid prediction for snap_scaffold_13-snap.2167-T1
Valid prediction for GeneMark_model.56554_t
Valid prediction for snap_scaffold_13-snap.2172-T1
Couldn't classify 15408, 15578
Couldn't classify 17389, 17445
Couldn't classify 17631, 17785
Sorry, prediction pasa_asmbl_11256.p1 fails validation.
(TTC)	 GT	15408-15578	GT	GGG
(TCT)	 AG	16429-16491	GT	AGG
(TCC)	 AG	16574-16679	GT	GGG
(ATG)	 AG	16823-16925	GT	AGG
(CTC)	 AG	17037-17182	GT	AGG
(ATG)	 AG	17389-17445	AT	ATA
(GCA)	 AC	17631-17785	GT	AGG
(GAA)	 AG	18089-18235	GT	AGG
(GTC)	 AG	18475-18546	GT	AGG
(TTC)	 AG	18676-18684	AG	GAA
-recovered pasa_asmbl_11256.p1, initial, 16823, 16925
-recovered pasa_asmbl_11256.p1, terminal, 18676, 18684
-recovered pasa_asmbl_11256.p1, internal, 16429, 16491
-recovered pasa_asmbl_11256.p1, internal, 16574, 16679
-recovered pasa_asmbl_11256.p1, internal, 16823, 16925
-recovered pasa_asmbl_11256.p1, internal, 17037, 17182
-recovered pasa_asmbl_11256.p1, internal, 18089, 18235
-recovered pasa_asmbl_11256.p1, internal, 18475, 18546
Valid prediction for GlimmerHMM_glimmerT_33150-T1
Valid prediction for pasa_asmbl_11273.p1
Valid prediction for GlimmerHMM_glimmerT_33160-T1
Valid prediction for snap_scaffold_13-snap.2148-T1
Valid prediction for GlimmerHMM_glimmerT_33153-T1
Valid prediction for GeneMark_model.56567_t
Valid prediction for GlimmerHMM_glimmerT_33154-T1
Valid prediction for GeneMark_model.56575_t
Valid prediction for GlimmerHMM_glimmerT_33159-T1
Valid prediction for GlimmerHMM_glimmerT_33148-T1
Valid prediction for snap_scaffold_13-snap.2146-T1
Valid prediction for GlimmerHMM_glimmerT_33147-T1
Valid prediction for CodingQuarry_transcript_13216-T1
Valid prediction for GlimmerHMM_glimmerT_33161-T1
Valid prediction for CodingQuarry_transcript_13218-T1
Valid prediction for GeneMark_model.56574_t
Valid prediction for CodingQuarry_transcript_13217-T1
Valid prediction for pasa_asmbl_11260.p1
Valid prediction for snap_scaffold_13-snap.2173-T1
Valid prediction for CodingQuarry_transcript_13222-T1
Valid prediction for GeneMark_model.56571_t
Valid prediction for snap_scaffold_13-snap.2156-T1
Valid prediction for GeneMark_model.56562_t
Valid prediction for GeneMark_model.56564_t
Valid prediction for snap_scaffold_13-snap.2170-T1
Valid prediction for snap_scaffold_13-snap.2175-T1
Valid prediction for GeneMark_model.56558_t
Valid prediction for CodingQuarry_transcript_13221-T1
Valid prediction for HiQ_model.g22279.t1
Valid prediction for HiQ_model.g22276.t1
Couldn't classify 90155, 90166
Couldn't classify 90290, 90622
Sorry, prediction pasa_asmbl_11282.p1 fails validation.
(GAA)	 CA	90155-90166	GT	GGG
(GTA)	 AG	90290-90622	AC	TGA

-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_13-snap.2159-T1
Valid prediction for snap_scaffold_13-snap.2161-T1
Valid prediction for HiQ_model.g22278.t1
Valid prediction for GlimmerHMM_glimmerT_33158-T1
Valid prediction for snap_scaffold_13-snap.2151-T1
Valid prediction for GlimmerHMM_glimmerT_33164-T1
Valid prediction for snap_scaffold_13-snap.2176-T1
Valid prediction for snap_scaffold_13-snap.2154-T1
Valid prediction for GeneMark_model.56555_t
Valid prediction for GeneMark_model.56568_t
Valid prediction for GlimmerHMM_glimmerT_33146-T1
Valid prediction for GlimmerHMM_glimmerT_33165-T1
Valid prediction for Augustus_model.g22270.t1
Valid prediction for GlimmerHMM_glimmerT_33162-T1
Valid prediction for GeneMark_model.56576_t
Valid prediction for Augustus_model.g22285.t1
Valid prediction for Augustus_model.g22281.t1
Valid prediction for GeneMark_model.56572_t
Couldn't classify 78575, 80565
Sorry, prediction pasa_asmbl_10064.p1 fails validation.
(ATG)	 AA	76472-76629	GT	AGG
(GAA)	 AG	77017-77142	GT	CTG
(CCA)	 AG	78238-78425	GT	AAG
(GAG)	 AG	78575-80565	GG	CAG
-recovered pasa_asmbl_10064.p1, initial, 76472, 76629
-recovered pasa_asmbl_10064.p1, internal, 77017, 77142
-recovered pasa_asmbl_10064.p1, internal, 78238, 78425
Valid prediction for GeneMark_model.56570_t
Valid prediction for snap_scaffold_13-snap.2165-T1
Valid prediction for snap_scaffold_13-snap.2177-T1
Valid prediction for snap_scaffold_13-snap.2150-T1
Valid prediction for GeneMark_model.56578_t
Valid prediction for GeneMark_model.56565_t
Valid prediction for GeneMark_model.56569_t
Valid prediction for snap_scaffold_13-snap.2168-T1
Valid prediction for snap_scaffold_13-snap.2147-T1
Valid prediction for snap_scaffold_13-snap.2169-T1
Valid prediction for snap_scaffold_13-snap.2166-T1
Valid prediction for Augustus_model.g22288.t1
Valid prediction for GeneMark_model.56553_t
Valid prediction for GlimmerHMM_glimmerT_33152-T1
Valid prediction for GeneMark_model.56544_t
Valid prediction for snap_scaffold_13-snap.2179-T1
Valid prediction for Augustus_model.g22282.t1
Valid prediction for CodingQuarry_transcript_13219-T1
Valid prediction for GeneMark_model.56573_t
Valid prediction for Augustus_model.g22273.t1
Couldn't classify 86707, 87087
Sorry, prediction pasa_asmbl_10063.p1 fails validation.
(TCT)	 TC	86707-87087	CT	AGC
Valid prediction for GeneMark_model.56547_t
Valid prediction for GeneMark_model.56551_t
Valid prediction for GlimmerHMM_glimmerT_33149-T1
Valid prediction for Augustus_model.g22289.t1
Valid prediction for GlimmerHMM_glimmerT_33157-T1
Valid prediction for GeneMark_model.56561_t
Valid prediction for snap_scaffold_13-snap.2171-T1
Valid prediction for GeneMark_model.56581_t
Valid prediction for GeneMark_model.56549_t
Valid prediction for GlimmerHMM_glimmerT_33156-T1
Valid prediction for Augustus_model.g22286.t1
Valid prediction for snap_scaffold_13-snap.2164-T1
Valid prediction for pasa_asmbl_10285.p2
Valid prediction for GeneMark_model.56579_t
Valid prediction for snap_scaffold_13-snap.2153-T1
Valid prediction for GeneMark_model.56559_t
Valid prediction for GlimmerHMM_glimmerT_33145-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9209, rend_intergenic: 5640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44118, rend_intergenic: 35700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79526, rend_intergenic: 70281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97568, rend_intergenic: 93680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105816, rend_intergenic: 103976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163643, rend_intergenic: 161635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169198, rend_intergenic: 166912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188154
-exon list size: 446


building trellis

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34.2    
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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 9209, rend_intergenic: 5640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44118, rend_intergenic: 35700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79526, rend_intergenic: 70281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97568, rend_intergenic: 93680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105816, rend_intergenic: 103976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163643, rend_intergenic: 161635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169198, rend_intergenic: 166912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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