-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_10548564-10735533

-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 pasa_asmbl_24719.p1
Valid prediction for GlimmerHMM_glimmerT_4472-T1
Valid prediction for snap_scaffold_2-snap.2070-T1
Valid prediction for Augustus_model.g2983.t1
Valid prediction for CodingQuarry_transcript_28661-T1
Valid prediction for snap_scaffold_2-snap.2062-T1
Valid prediction for CodingQuarry_transcript_28660-T1
Valid prediction for GlimmerHMM_glimmerT_4468-T1
Valid prediction for snap_scaffold_2-snap.2092-T1
Valid prediction for Augustus_model.g2986.t1
Valid prediction for snap_scaffold_2-snap.2104-T1
Valid prediction for GlimmerHMM_glimmerT_4479-T1
Valid prediction for CodingQuarry_transcript_28666-T1
Valid prediction for Augustus_model.g2994.t1
Valid prediction for snap_scaffold_2-snap.2085-T1
Valid prediction for GlimmerHMM_glimmerT_4447-T1
Valid prediction for snap_scaffold_2-snap.2106-T1
Valid prediction for snap_scaffold_2-snap.2100-T1
Valid prediction for snap_scaffold_2-snap.2072-T1
Valid prediction for HiQ_model.g2978.t1
Valid prediction for GlimmerHMM_glimmerT_4478-T1
Valid prediction for snap_scaffold_2-snap.2069-T1
Valid prediction for GlimmerHMM_glimmerT_4465-T1
Valid prediction for snap_scaffold_2-snap.2076-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g2999.t1
Valid prediction for HiQ_model.g2993.t1
Valid prediction for GlimmerHMM_glimmerT_4470-T1
Valid prediction for snap_scaffold_2-snap.2074-T1
Valid prediction for pasa_asmbl_24723.p1
Couldn't classify 49471, 49590
Sorry, prediction pasa_asmbl_24706.p1 fails validation.
(GTC)	 CT	49471-49590	GT	GGG
(GTT)	 AG	50034-50350	GT	CTG
(AAC)	 AG	50615-50702	GT	AGG
(AGA)	 AG	51096-51165	GT	AGG
(GTC)	 AG	51334-51412	GT	AGG
(ACG)	 AG	52554-52593	GC	GAG
-recovered pasa_asmbl_24706.p1, terminal, 52554, 52593
-recovered pasa_asmbl_24706.p1, internal, 50034, 50350
-recovered pasa_asmbl_24706.p1, internal, 50615, 50702
-recovered pasa_asmbl_24706.p1, internal, 51096, 51165
-recovered pasa_asmbl_24706.p1, internal, 51334, 51412
-recovered pasa_asmbl_24706.p1, internal, 52554, 52593
Valid prediction for GlimmerHMM_glimmerT_4469-T1
Valid prediction for snap_scaffold_2-snap.2094-T1
Valid prediction for pasa_asmbl_24730.p1
Couldn't classify 172330, 172930
Sorry, prediction pasa_asmbl_24724.p1 fails validation.
(ATG)	 CC	170364-170376	GT	TGG
(ACA)	 AG	170923-171090	GT	TGG
(ATG)	 AG	171168-171268	GT	AGG
(CTC)	 AG	171632-171715	GT	TGG
(ATT)	 AG	171872-171945	GT	GGG
(TCT)	 AG	172330-172930	CA	AGC
-recovered pasa_asmbl_24724.p1, initial, 170364, 170376
-recovered pasa_asmbl_24724.p1, initial, 171168, 171268
-recovered pasa_asmbl_24724.p1, internal, 170923, 171090
-recovered pasa_asmbl_24724.p1, internal, 171168, 171268
-recovered pasa_asmbl_24724.p1, internal, 171632, 171715
-recovered pasa_asmbl_24724.p1, internal, 171872, 171945
Valid prediction for GlimmerHMM_glimmerT_4449-T1
Valid prediction for Augustus_model.g2977.t1
Valid prediction for GlimmerHMM_glimmerT_4453-T1
Valid prediction for GlimmerHMM_glimmerT_4445-T1
Valid prediction for pasa_asmbl_24705.p1
Valid prediction for HiQ_model.g2998.t1
Valid prediction for Augustus_model.g2976.t1
Valid prediction for snap_scaffold_2-snap.2071-T1
Valid prediction for GlimmerHMM_glimmerT_4455-T1
Valid prediction for CodingQuarry_transcript_28669-T1
Valid prediction for snap_scaffold_2-snap.2096-T1
Valid prediction for HiQ_model.g2997.t1
Valid prediction for snap_scaffold_2-snap.2103-T1
Valid prediction for Augustus_model.g2996.t1
Valid prediction for GlimmerHMM_glimmerT_4474-T1
Valid prediction for GlimmerHMM_glimmerT_4471-T1
Valid prediction for GlimmerHMM_glimmerT_4475-T1
Valid prediction for GlimmerHMM_glimmerT_4461-T1
Valid prediction for GlimmerHMM_glimmerT_4454-T1
Valid prediction for snap_scaffold_2-snap.2087-T1
Valid prediction for GlimmerHMM_glimmerT_4477-T1
Valid prediction for Augustus_model.g2991.t1
Valid prediction for snap_scaffold_2-snap.2078-T1
Valid prediction for HiQ_model.g2992.t1
Valid prediction for pasa_asmbl_24715.p1
Valid prediction for snap_scaffold_2-snap.2093-T1
Valid prediction for Augustus_model.g2995.t1
Valid prediction for GlimmerHMM_glimmerT_4463-T1
Valid prediction for snap_scaffold_2-snap.2105-T1
Couldn't classify 107114, 107188
Sorry, prediction pasa_asmbl_24712.p1 fails validation.
(ATG)	 GG	105332-105468	GT	AGG
(GAA)	 AG	105591-105826	GT	ATG
(ACC)	 AG	106074-106257	GT	AGG
(GTT)	 AG	106468-106521	GT	AGG
(AAC)	 AG	106606-106711	GT	AGG
(AAT)	 AG	106946-107026	GT	AGG
(GCC)	 AG	107114-107188	AA	GGA
-recovered pasa_asmbl_24712.p1, initial, 105332, 105468
-recovered pasa_asmbl_24712.p1, internal, 105591, 105826
-recovered pasa_asmbl_24712.p1, internal, 106074, 106257
-recovered pasa_asmbl_24712.p1, internal, 106468, 106521
-recovered pasa_asmbl_24712.p1, internal, 106606, 106711
-recovered pasa_asmbl_24712.p1, internal, 106946, 107026
Valid prediction for CodingQuarry_transcript_28668-T1
Valid prediction for snap_scaffold_2-snap.2080-T1
Valid prediction for CodingQuarry_transcript_28671-T1
Valid prediction for snap_scaffold_2-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_4451-T1
Valid prediction for snap_scaffold_2-snap.2067-T1
Valid prediction for Augustus_model.g2988.t1
Valid prediction for snap_scaffold_2-snap.2066-T1
Couldn't classify 133022, 133022
Sorry, prediction CodingQuarry_transcript_28667-T1 fails validation.
(AGT)	 AA	133022-133022	GT	AAG
(TGC)	 AG	134681-134878	GT	CAG
(CAC)	 AG	135217-135335	GT	AGG
(CTT)	 AG	136834-136929	GT	AGG
(GTG)	 AG	137315-137377	GT	AGG
(GAC)	 AG	139715-139873	GT	AGG
(CTG)	 AG	140099-140260	CC	GAC
-recovered CodingQuarry_transcript_28667-T1, terminal, 140099, 140260
-recovered CodingQuarry_transcript_28667-T1, internal, 134681, 134878
-recovered CodingQuarry_transcript_28667-T1, internal, 135217, 135335
-recovered CodingQuarry_transcript_28667-T1, internal, 136834, 136929
-recovered CodingQuarry_transcript_28667-T1, internal, 137315, 137377
-recovered CodingQuarry_transcript_28667-T1, internal, 139715, 139873
Valid prediction for snap_scaffold_2-snap.2101-T1
Valid prediction for snap_scaffold_2-snap.2089-T1
Valid prediction for Augustus_model.g2979.t1
Valid prediction for snap_scaffold_2-snap.2098-T1
Valid prediction for snap_scaffold_2-snap.2073-T1
Valid prediction for snap_scaffold_2-snap.2083-T1
Valid prediction for GlimmerHMM_glimmerT_4456-T1
Valid prediction for GlimmerHMM_glimmerT_4452-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 GlimmerHMM_glimmerT_4480-T1
Valid prediction for snap_scaffold_2-snap.2091-T1
Valid prediction for snap_scaffold_2-snap.2079-T1
Valid prediction for snap_scaffold_2-snap.2063-T1
Valid prediction for Augustus_model.g2990.t1
Valid prediction for GlimmerHMM_glimmerT_4450-T1
Valid prediction for HiQ_model.g2985.t1
Couldn't classify 126120, 126422
Sorry, prediction pasa_asmbl_23424.p3 fails validation.
(TGG)	 GC	126120-126422	CT	TGC
Valid prediction for pasa_asmbl_23434.p1
Valid prediction for snap_scaffold_2-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_4466-T1
Valid prediction for GlimmerHMM_glimmerT_4457-T1
Valid prediction for snap_scaffold_2-snap.2088-T1
Valid prediction for snap_scaffold_2-snap.2090-T1
Valid prediction for Augustus_model.g2982.t1
Valid prediction for Augustus_model.g2981.t1
Valid prediction for snap_scaffold_2-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_4462-T1
Valid prediction for Augustus_model.g2975.t1
Valid prediction for GlimmerHMM_glimmerT_4473-T1
Valid prediction for snap_scaffold_2-snap.2095-T1
Valid prediction for snap_scaffold_2-snap.2086-T1
Valid prediction for GlimmerHMM_glimmerT_4467-T1
Valid prediction for CodingQuarry_transcript_28665-T1
Valid prediction for GlimmerHMM_glimmerT_4459-T1
Valid prediction for pasa_asmbl_23426.p1
Valid prediction for snap_scaffold_2-snap.2065-T1
Valid prediction for GlimmerHMM_glimmerT_4460-T1
Valid prediction for Augustus_model.g2980.t1
Valid prediction for GlimmerHMM_glimmerT_4458-T1
Valid prediction for pasa_asmbl_23439.p1
Valid prediction for snap_scaffold_2-snap.2099-T1
Valid prediction for HiQ_model.g2989.t1
Valid prediction for Augustus_model.g2987.t1
Valid prediction for snap_scaffold_2-snap.2084-T1
Valid prediction for snap_scaffold_2-snap.2077-T1
Valid prediction for snap_scaffold_2-snap.2081-T1
Valid prediction for GlimmerHMM_glimmerT_4476-T1
Valid prediction for snap_scaffold_2-snap.2064-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for pasa_asmbl_23436.p1
Valid prediction for GlimmerHMM_glimmerT_4464-T1
Valid prediction for snap_scaffold_2-snap.2061-T1
Valid prediction for snap_scaffold_2-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_4446-T1
Valid prediction for GlimmerHMM_glimmerT_4448-T1
Couldn't classify 127054, 127077
Couldn't classify 128166, 128243
Sorry, prediction pasa_asmbl_23423.p1 fails validation.
(CAG)	 AA	127054-127077	GT	AGG
(AGG)	 AG	127349-127513	GT	CTG
(GGC)	 AG	127687-127878	GT	AGG
(ACA)	 AG	128166-128243	TT	AGT
-recovered pasa_asmbl_23423.p1, internal, 127349, 127513
-recovered pasa_asmbl_23423.p1, internal, 127687, 127878
Valid prediction for Augustus_model.g2974.t1
Valid prediction for Augustus_model.g2984.t1
Valid prediction for snap_scaffold_2-snap.2068-T1
Valid prediction for CodingQuarry_transcript_28663-T1
Valid prediction for CodingQuarry_transcript_28664-T1
Valid prediction for snap_scaffold_2-snap.2075-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12459, rend_intergenic: 3550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33242, rend_intergenic: 29188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60193, rend_intergenic: 58056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63832, rend_intergenic: 60393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71413, rend_intergenic: 66731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73569, rend_intergenic: 71873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78171, rend_intergenic: 73893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83845, rend_intergenic: 80872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90579, rend_intergenic: 86609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140260, rend_intergenic: 135853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154338, rend_intergenic: 149372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160450, rend_intergenic: 154733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186970
-exon list size: 446


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 12459, rend_intergenic: 3550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33242, rend_intergenic: 29188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60193, rend_intergenic: 58056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63832, rend_intergenic: 60393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71413, rend_intergenic: 66731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73569, rend_intergenic: 71873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78171, rend_intergenic: 73893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83845, rend_intergenic: 80872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90579, rend_intergenic: 86609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140260, rend_intergenic: 135853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154338, rend_intergenic: 149372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160450, rend_intergenic: 154733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support