-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_7370262-7610499

-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: +)Couldn't classify 149628, 149765
Sorry, prediction pasa_asmbl_42836.p2 fails validation.
(ATG)	 AG	145066-145112	GT	AGG
(GCA)	 AG	147504-147711	GT	AGG
(ACG)	 AG	149628-149765	TA	GGT
-recovered pasa_asmbl_42836.p2, initial, 145066, 145112
-recovered pasa_asmbl_42836.p2, internal, 145066, 145112
-recovered pasa_asmbl_42836.p2, internal, 147504, 147711
Valid prediction for snap_scaffold_4-snap.1594-T1
Valid prediction for GlimmerHMM_glimmerT_9845-T1
Valid prediction for snap_scaffold_4-snap.1605-T1
Valid prediction for Augustus_model.g6457.t1
Valid prediction for snap_scaffold_4-snap.1585-T1
Valid prediction for snap_scaffold_4-snap.1598-T1
Valid prediction for snap_scaffold_4-snap.1581-T1
Valid prediction for GeneMark_model.16024_t
Valid prediction for CodingQuarry_transcript_48952-T1
Valid prediction for snap_scaffold_4-snap.1588-T1
Valid prediction for GlimmerHMM_glimmerT_9856-T1
Valid prediction for snap_scaffold_4-snap.1571-T1
Valid prediction for GeneMark_model.16041_t
Valid prediction for GeneMark_model.16012_t
Valid prediction for snap_scaffold_4-snap.1600-T1
Valid prediction for GlimmerHMM_glimmerT_9863-T1
Valid prediction for snap_scaffold_4-snap.1580-T1
Valid prediction for GeneMark_model.16022_t
Valid prediction for Augustus_model.g6463.t1
Valid prediction for snap_scaffold_4-snap.1608-T1
Valid prediction for HiQ_model.g6450.t1
Valid prediction for GeneMark_model.16031_t
Valid prediction for GeneMark_model.16026_t
Valid prediction for snap_scaffold_4-snap.1582-T1
Valid prediction for snap_scaffold_4-snap.1569-T1
Valid prediction for GeneMark_model.16032_t
Couldn't classify 113003, 113875
Sorry, prediction pasa_asmbl_42834.p1 fails validation.
(GCC)	 TG	113003-113875	TG	GAT
Valid prediction for Augustus_model.g6461.t1
Valid prediction for pasa_asmbl_42831.p1
Valid prediction for CodingQuarry_transcript_48948-T1
Couldn't classify 174434, 174556
Sorry, prediction pasa_asmbl_42839.p1 fails validation.
(ATG)	 AA	171421-171447	GT	AGG
(CAA)	 AG	171714-171837	GT	AAG
(GTG)	 AG	172235-172328	GT	GGG
(GTA)	 AG	172753-172813	GT	CGG
(ATA)	 AG	173577-173663	GT	ACG
(GAG)	 AG	174434-174556	TA	CGT
-recovered pasa_asmbl_42839.p1, initial, 171421, 171447
add_exon() Sorry, pasa_asmbl_42839.p1 171714-171837-terminal-3 is invalid.
-recovered pasa_asmbl_42839.p1, terminal, 171714, 171837
-recovered pasa_asmbl_42839.p1, internal, 171714, 171837
-recovered pasa_asmbl_42839.p1, internal, 172235, 172328
-recovered pasa_asmbl_42839.p1, internal, 172753, 172813
-recovered pasa_asmbl_42839.p1, internal, 173577, 173663
Valid prediction for GlimmerHMM_glimmerT_9853-T1
Valid prediction for GeneMark_model.16009_t
Valid prediction for snap_scaffold_4-snap.1590-T1
Valid prediction for GeneMark_model.16039_t
Valid prediction for GlimmerHMM_glimmerT_9859-T1
Valid prediction for GeneMark_model.16038_t
Valid prediction for GlimmerHMM_glimmerT_9850-T1
Valid prediction for pasa_asmbl_42832.p1
Valid prediction for GeneMark_model.16016_t
Valid prediction for snap_scaffold_4-snap.1602-T1
Valid prediction for GeneMark_model.16044_t
Valid prediction for snap_scaffold_4-snap.1589-T1
Valid prediction for GeneMark_model.16036_t
Valid prediction for GeneMark_model.16019_t
Valid prediction for GeneMark_model.16014_t
Valid prediction for snap_scaffold_4-snap.1577-T1
Valid prediction for Augustus_model.g6459.t1
Valid prediction for snap_scaffold_4-snap.1597-T1
Valid prediction for Augustus_model.g6455.t1
Valid prediction for GlimmerHMM_glimmerT_9860-T1
Valid prediction for Augustus_model.g6460.t1
Valid prediction for snap_scaffold_4-snap.1573-T1
Valid prediction for GlimmerHMM_glimmerT_9849-T1
Couldn't classify 150532, 150697
Couldn't classify 152816, 152946
Sorry, prediction pasa_asmbl_42837.p1 fails validation.
(CCC)	 CC	150532-150697	GT	AAG
(GCT)	 AG	152816-152946	GC	TGG
-recovered pasa_asmbl_42837.p1, internal, 152816, 152946
Valid prediction for CodingQuarry_transcript_48950-T1
Valid prediction for HiQ_model.g6453.t1
Valid prediction for GeneMark_model.16028_t
Valid prediction for GlimmerHMM_glimmerT_9865-T1
Valid prediction for GeneMark_model.16030_t

-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 GeneMark_model.16025_t
Valid prediction for GeneMark_model.16043_t
Valid prediction for CodingQuarry_transcript_48949-T1
Valid prediction for GeneMark_model.16042_t
Couldn't classify 212013, 213608
Sorry, prediction pasa_asmbl_41458.p1 fails validation.
(CTC)	 TC	212013-213608	CT	GCC
Valid prediction for GlimmerHMM_glimmerT_9857-T1
Valid prediction for GlimmerHMM_glimmerT_9855-T1
Valid prediction for GlimmerHMM_glimmerT_9846-T1
Valid prediction for snap_scaffold_4-snap.1591-T1
Valid prediction for GeneMark_model.16029_t
Valid prediction for snap_scaffold_4-snap.1601-T1
Valid prediction for Augustus_model.g6462.t1
Valid prediction for snap_scaffold_4-snap.1595-T1
Valid prediction for snap_scaffold_4-snap.1611-T1
Valid prediction for snap_scaffold_4-snap.1575-T1
Valid prediction for snap_scaffold_4-snap.1584-T1
Valid prediction for GeneMark_model.16045_t
Valid prediction for snap_scaffold_4-snap.1570-T1
Valid prediction for GlimmerHMM_glimmerT_9864-T1
Valid prediction for snap_scaffold_4-snap.1578-T1
Valid prediction for Augustus_model.g6456.t1
Valid prediction for GeneMark_model.16035_t
Valid prediction for GeneMark_model.16018_t
Valid prediction for snap_scaffold_4-snap.1593-T1
Valid prediction for GeneMark_model.16020_t
Couldn't classify 213651, 214139
Sorry, prediction pasa_asmbl_41456.p1 fails validation.
(GAG)	 CT	213651-214139	AA	GAA
Valid prediction for GeneMark_model.16034_t
Valid prediction for Augustus_model.g6464.t1
Valid prediction for Augustus_model.g6454.t1
Valid prediction for GlimmerHMM_glimmerT_9848-T1
Valid prediction for snap_scaffold_4-snap.1610-T1
Valid prediction for GlimmerHMM_glimmerT_9861-T1
Valid prediction for snap_scaffold_4-snap.1606-T1
Valid prediction for GeneMark_model.16021_t
Valid prediction for Augustus_model.g6452.t1
Valid prediction for GlimmerHMM_glimmerT_9851-T1
Couldn't classify 227555, 227689
Couldn't classify 230204, 230248
Sorry, prediction pasa_asmbl_41454.p1 fails validation.
(GTA)	 GG	227555-227689	GT	AGG
(ATG)	 AG	227883-227975	GT	AGG
(CGC)	 AG	229306-229452	GT	GCG
(GTG)	 AG	229880-230074	GT	AGG
(TGG)	 AG	230204-230248	CA	GAC
-recovered pasa_asmbl_41454.p1, initial, 227883, 227975
-recovered pasa_asmbl_41454.p1, internal, 227883, 227975
-recovered pasa_asmbl_41454.p1, internal, 229306, 229452
-recovered pasa_asmbl_41454.p1, internal, 229880, 230074
Valid prediction for GeneMark_model.16037_t
Valid prediction for snap_scaffold_4-snap.1586-T1
Valid prediction for snap_scaffold_4-snap.1574-T1
Valid prediction for GlimmerHMM_glimmerT_9858-T1
Valid prediction for snap_scaffold_4-snap.1607-T1
Valid prediction for snap_scaffold_4-snap.1576-T1
Couldn't classify 59667, 59975
Sorry, prediction pasa_asmbl_41461.p1 fails validation.
(GTT)	 AT	59667-59975	CA	GAC
Valid prediction for GeneMark_model.16023_t
Valid prediction for Augustus_model.g6465.t1
Valid prediction for GlimmerHMM_glimmerT_9854-T1
Valid prediction for snap_scaffold_4-snap.1603-T1
Valid prediction for GeneMark_model.16033_t
Valid prediction for GeneMark_model.16040_t
Valid prediction for GeneMark_model.16015_t
Valid prediction for GeneMark_model.16011_t
Valid prediction for GeneMark_model.16017_t
Valid prediction for snap_scaffold_4-snap.1609-T1
Valid prediction for snap_scaffold_4-snap.1587-T1
Valid prediction for snap_scaffold_4-snap.1579-T1
Valid prediction for GlimmerHMM_glimmerT_9862-T1
Valid prediction for Augustus_model.g6451.t1
Valid prediction for GeneMark_model.16027_t
Valid prediction for snap_scaffold_4-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_9847-T1
Valid prediction for snap_scaffold_4-snap.1583-T1
Valid prediction for Augustus_model.g6458.t1
Valid prediction for snap_scaffold_4-snap.1599-T1
Valid prediction for snap_scaffold_4-snap.1604-T1
Valid prediction for GeneMark_model.16013_t
Valid prediction for snap_scaffold_4-snap.1572-T1
Valid prediction for GeneMark_model.16010_t
Valid prediction for snap_scaffold_4-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_9852-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14943, rend_intergenic: 11599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128411, rend_intergenic: 124606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163433, rend_intergenic: 157653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187079, rend_intergenic: 183334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200722, rend_intergenic: 197259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214241, rend_intergenic: 212066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240238
-exon list size: 554


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 14943, rend_intergenic: 11599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128411, rend_intergenic: 124606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163433, rend_intergenic: 157653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187079, rend_intergenic: 183334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200722, rend_intergenic: 197259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214241, rend_intergenic: 212066  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