-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_8095974-8252627

-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 GlimmerHMM_glimmerT_41578-T1
Valid prediction for GlimmerHMM_glimmerT_41577-T1
Valid prediction for GeneMark_model.71609_t
Valid prediction for GeneMark_model.71588_t
Valid prediction for GeneMark_model.71620_t
Valid prediction for GeneMark_model.71612_t
Valid prediction for GlimmerHMM_glimmerT_41592-T1
Valid prediction for CodingQuarry_transcript_22006-T1
Valid prediction for GeneMark_model.71604_t
Valid prediction for snap_scaffold_17-snap.1610-T1
Valid prediction for GlimmerHMM_glimmerT_41598-T1
Valid prediction for GeneMark_model.71598_t
Valid prediction for HiQ_model.g27870.t1
Valid prediction for snap_scaffold_17-snap.1629-T1
Valid prediction for snap_scaffold_17-snap.1634-T1
Valid prediction for Augustus_model.g27872.t1
Valid prediction for GeneMark_model.71596_t
Valid prediction for GlimmerHMM_glimmerT_41601-T1
Valid prediction for snap_scaffold_17-snap.1637-T1
Valid prediction for snap_scaffold_17-snap.1619-T1
Valid prediction for GlimmerHMM_glimmerT_41582-T1
Valid prediction for GeneMark_model.71618_t
Couldn't classify 98415, 98528
Couldn't classify 100553, 100611
Sorry, prediction pasa_asmbl_18612.p1 fails validation.
(AAG)	 AC	98415-98528	GT	AGG
(AAC)	 AG	98765-98816	GT	GGG
(AAC)	 AG	98929-99018	GT	CGG
(ATA)	 AG	99140-99277	GT	AGG
(GAC)	 AG	99381-99486	GT	AGG
(CTC)	 AG	99595-99698	GT	ACG
(CTA)	 AG	99795-99904	GT	AGG
(CCG)	 AG	100024-100183	GT	CGG
(GAG)	 AG	100301-100444	GT	AGG
(TCA)	 AG	100553-100611	AG	ACA
-recovered pasa_asmbl_18612.p1, terminal, 99140, 99277
-recovered pasa_asmbl_18612.p1, internal, 98765, 98816
-recovered pasa_asmbl_18612.p1, internal, 98929, 99018
-recovered pasa_asmbl_18612.p1, internal, 99140, 99277
-recovered pasa_asmbl_18612.p1, internal, 99381, 99486
-recovered pasa_asmbl_18612.p1, internal, 99595, 99698
-recovered pasa_asmbl_18612.p1, internal, 99795, 99904
-recovered pasa_asmbl_18612.p1, internal, 100024, 100183
-recovered pasa_asmbl_18612.p1, internal, 100301, 100444
Valid prediction for Augustus_model.g27873.t1
Valid prediction for CodingQuarry_transcript_22002-T1
Couldn't classify 60694, 60764
Sorry, prediction pasa_asmbl_18067.p1 fails validation.
(TGG)	 GA	60694-60764	GT	AGG
(CTC)	 AG	62050-62135	GT	GTG
(GCG)	 AG	62272-62686	GT	AGG
(GGT)	 AG	62788-62942	GT	GGG
(GGC)	 AG	63032-63143	GT	AGG
(TGG)	 AG	63375-63555	GT	AAG
(GTG)	 AG	63839-63928	AG	AGA
-recovered pasa_asmbl_18067.p1, terminal, 63839, 63928
-recovered pasa_asmbl_18067.p1, internal, 62050, 62135
-recovered pasa_asmbl_18067.p1, internal, 62272, 62686
-recovered pasa_asmbl_18067.p1, internal, 62788, 62942
-recovered pasa_asmbl_18067.p1, internal, 63032, 63143
-recovered pasa_asmbl_18067.p1, internal, 63375, 63555
Valid prediction for GeneMark_model.71615_t
Valid prediction for GeneMark_model.71586_t
Valid prediction for snap_scaffold_17-snap.1630-T1
Valid prediction for GeneMark_model.71597_t
Valid prediction for Augustus_model.g27877.t1
Couldn't classify 125174, 125420
Sorry, prediction pasa_asmbl_18084.p1 fails validation.
(CTT)	 CT	125174-125420	GT	AGG
(GAA)	 AG	125567-125665	GT	GGG
(GTC)	 AG	125878-126038	GT	AGG
(ATG)	 AG	127475-127689	GT	AGG
(CTT)	 AG	127919-128054	GT	TCG
(GGC)	 AG	128213-128341	GT	CGG
(GTG)	 AG	128528-128651	GT	TGG
(TGG)	 AG	128807-128991	GA	GAG
-recovered pasa_asmbl_18084.p1, initial, 127475, 127689
-recovered pasa_asmbl_18084.p1, terminal, 128807, 128991
-recovered pasa_asmbl_18084.p1, internal, 125567, 125665
-recovered pasa_asmbl_18084.p1, internal, 125878, 126038
-recovered pasa_asmbl_18084.p1, internal, 127475, 127689
-recovered pasa_asmbl_18084.p1, internal, 127919, 128054
-recovered pasa_asmbl_18084.p1, internal, 128213, 128341
-recovered pasa_asmbl_18084.p1, internal, 128528, 128651
Valid prediction for GlimmerHMM_glimmerT_41587-T1
Valid prediction for snap_scaffold_17-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_41597-T1
Couldn't classify 127884, 128054
Sorry, prediction pasa_asmbl_18080.p1 fails validation.
(CAT)	 AA	127884-128054	GT	TCG
(GGC)	 AG	128213-128341	GT	CGG
(GTG)	 AG	128528-128651	GT	TGG
(TGG)	 AG	128807-128991	GA	GAG
-recovered pasa_asmbl_18080.p1, terminal, 128807, 128991
-recovered pasa_asmbl_18080.p1, internal, 128213, 128341
-recovered pasa_asmbl_18080.p1, internal, 128528, 128651
Valid prediction for snap_scaffold_17-snap.1618-T1
Valid prediction for snap_scaffold_17-snap.1626-T1
Valid prediction for GlimmerHMM_glimmerT_41596-T1
Valid prediction for Augustus_model.g27867.t1
Couldn't classify 100672, 100799
Couldn't classify 101409, 101507
Sorry, prediction pasa_asmbl_18074.p2 fails validation.
(TGG)	 CC	100672-100799	GT	AGG
(TGT)	 AG	100924-100999	GT	AGG
(GAC)	 AG	101091-101312	GT	TGG
(GGC)	 AG	101409-101507	CA	ACC
-recovered pasa_asmbl_18074.p2, internal, 100924, 100999
-recovered pasa_asmbl_18074.p2, internal, 101091, 101312
Valid prediction for pasa_asmbl_18071.p1
Valid prediction for GeneMark_model.71607_t
Valid prediction for GlimmerHMM_glimmerT_41586-T1
Valid prediction for snap_scaffold_17-snap.1633-T1
Valid prediction for snap_scaffold_17-snap.1638-T1
Valid prediction for GeneMark_model.71622_t
Valid prediction for GeneMark_model.71601_t
Valid prediction for snap_scaffold_17-snap.1613-T1
Valid prediction for snap_scaffold_17-snap.1621-T1
Valid prediction for GlimmerHMM_glimmerT_41590-T1
Valid prediction for GeneMark_model.71594_t
Valid prediction for snap_scaffold_17-snap.1611-T1
Valid prediction for GlimmerHMM_glimmerT_41600-T1
Valid prediction for CodingQuarry_transcript_22004-T1
Valid prediction for snap_scaffold_17-snap.1615-T1
Valid prediction for GeneMark_model.71591_t
Valid prediction for CodingQuarry_transcript_22001-T1
Valid prediction for HiQ_model.g27876.t1
Valid prediction for snap_scaffold_17-snap.1624-T1
Valid prediction for GlimmerHMM_glimmerT_41583-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_17-snap.1614-T1
Valid prediction for HiQ_model.g27869.t1
Valid prediction for CodingQuarry_transcript_22005-T1
Valid prediction for GeneMark_model.71614_t
Valid prediction for snap_scaffold_17-snap.1623-T1
Valid prediction for snap_scaffold_17-snap.1622-T1
Valid prediction for GlimmerHMM_glimmerT_41595-T1
Valid prediction for Augustus_model.g27868.t1
Valid prediction for GlimmerHMM_glimmerT_41589-T1
Valid prediction for GeneMark_model.71602_t
Valid prediction for snap_scaffold_17-snap.1620-T1
Valid prediction for GlimmerHMM_glimmerT_41584-T1
Valid prediction for Augustus_model.g27875.t1
Valid prediction for GeneMark_model.71587_t
Valid prediction for GlimmerHMM_glimmerT_41580-T1
Valid prediction for GlimmerHMM_glimmerT_41593-T1
Valid prediction for GeneMark_model.71611_t
Valid prediction for GeneMark_model.71619_t
Valid prediction for GlimmerHMM_glimmerT_41581-T1
Valid prediction for GeneMark_model.71592_t
Couldn't classify 63661, 63753
Sorry, prediction pasa_asmbl_19121.p1 fails validation.
(CTG)	 TC	63661-63753	GT	AGG
(AAG)	 AG	64012-64174	GT	AGG
(AGT)	 AG	64277-64374	GT	TTG
(AGA)	 AG	64479-64547	GT	AGG
(AAT)	 AG	64713-64779	GT	AGG
(GAG)	 AG	64902-64961	GT	TGG
(GGT)	 AG	65105-65301	AT	AGA
-recovered pasa_asmbl_19121.p1, terminal, 65105, 65301
-recovered pasa_asmbl_19121.p1, internal, 64012, 64174
-recovered pasa_asmbl_19121.p1, internal, 64277, 64374
-recovered pasa_asmbl_19121.p1, internal, 64479, 64547
-recovered pasa_asmbl_19121.p1, internal, 64713, 64779
-recovered pasa_asmbl_19121.p1, internal, 64902, 64961
Valid prediction for snap_scaffold_17-snap.1635-T1
Valid prediction for Augustus_model.g27865.t1
Couldn't classify 85211, 85618
Sorry, prediction pasa_asmbl_19119.p3 fails validation.
(GAG)	 CA	85211-85618	GG	ACG
Valid prediction for GlimmerHMM_glimmerT_41594-T1
Valid prediction for HiQ_model.g27871.t1
Valid prediction for GeneMark_model.71589_t
Valid prediction for snap_scaffold_17-snap.1631-T1
Couldn't classify 40959, 40973
Sorry, prediction pasa_asmbl_19124.p1 fails validation.
(TGT)	 AG	40959-40973	GT	AGG
(ATG)	 AG	41170-41316	GT	AGG
(CAC)	 AG	41634-41772	GT	AGG
(CTG)	 AG	41959-42081	GT	AGG
(AGT)	 AG	42214-42242	CC	AAC
-recovered pasa_asmbl_19124.p1, initial, 41170, 41316
-recovered pasa_asmbl_19124.p1, terminal, 42214, 42242
-recovered pasa_asmbl_19124.p1, internal, 40959, 40973
-recovered pasa_asmbl_19124.p1, internal, 41170, 41316
-recovered pasa_asmbl_19124.p1, internal, 41634, 41772
-recovered pasa_asmbl_19124.p1, internal, 41959, 42081
Valid prediction for CodingQuarry_transcript_22003-T1
Valid prediction for snap_scaffold_17-snap.1636-T1
Valid prediction for Augustus_model.g27866.t1
Valid prediction for GeneMark_model.71599_t
Valid prediction for Augustus_model.g27874.t1
Valid prediction for GeneMark_model.71606_t
Valid prediction for GlimmerHMM_glimmerT_41585-T1
Valid prediction for Augustus_model.g27863.t1
Valid prediction for GeneMark_model.71610_t
Valid prediction for GlimmerHMM_glimmerT_41591-T1
Valid prediction for GeneMark_model.71590_t
Valid prediction for snap_scaffold_17-snap.1609-T1
Valid prediction for snap_scaffold_17-snap.1612-T1
Valid prediction for GeneMark_model.71605_t
Couldn't classify 39966, 40070
Sorry, prediction pasa_asmbl_19127.p1 fails validation.
(ATG)	 TT	36255-36318	GT	GGG
(ATG)	 AG	37355-37531	GT	TGG
(CTC)	 AG	39517-39620	GT	AGG
(GTT)	 AG	39813-39878	GT	AGG
(CTG)	 AG	39966-40070	AN	CCA
-recovered pasa_asmbl_19127.p1, initial, 36255, 36318
add_exon() Sorry, pasa_asmbl_19127.p1 37355-37531-initial-1 is invalid.
-recovered pasa_asmbl_19127.p1, initial, 37355, 37531
-recovered pasa_asmbl_19127.p1, internal, 37355, 37531
-recovered pasa_asmbl_19127.p1, internal, 39517, 39620
-recovered pasa_asmbl_19127.p1, internal, 39813, 39878
Valid prediction for GlimmerHMM_glimmerT_41588-T1
Valid prediction for snap_scaffold_17-snap.1628-T1
Valid prediction for GeneMark_model.71593_t
Valid prediction for GeneMark_model.71595_t
Valid prediction for Augustus_model.g27864.t1
Valid prediction for GlimmerHMM_glimmerT_41599-T1
Valid prediction for GeneMark_model.71608_t
Valid prediction for pasa_asmbl_19120.p1
Valid prediction for snap_scaffold_17-snap.1632-T1
Valid prediction for snap_scaffold_17-snap.1627-T1
Valid prediction for GeneMark_model.71617_t
Valid prediction for GeneMark_model.71600_t
Valid prediction for GeneMark_model.71621_t
Valid prediction for snap_scaffold_17-snap.1617-T1
Valid prediction for snap_scaffold_17-snap.1625-T1
Valid prediction for GeneMark_model.71603_t
Valid prediction for GlimmerHMM_glimmerT_41579-T1
Valid prediction for GeneMark_model.71613_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24844, rend_intergenic: 17523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33235, rend_intergenic: 30631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42880, rend_intergenic: 35843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50553, rend_intergenic: 45732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59494, rend_intergenic: 52107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63928, rend_intergenic: 63480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74332, rend_intergenic: 68326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102292, rend_intergenic: 100053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156654
-exon list size: 470


building trellis

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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 24844, rend_intergenic: 17523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33235, rend_intergenic: 30631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42880, rend_intergenic: 35843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50553, rend_intergenic: 45732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59494, rend_intergenic: 52107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63928, rend_intergenic: 63480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74332, rend_intergenic: 68326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102292, rend_intergenic: 100053  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