-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_4913697-5153649

-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 CodingQuarry_transcript_48972-T1
Valid prediction for pasa_asmbl_41320.p1
Valid prediction for HiQ_model.g6008.t1
Valid prediction for HiQ_model.g6003.t1
Valid prediction for HiQ_model.g6019.t1
Valid prediction for snap_scaffold_4-snap.1141-T1
Valid prediction for GlimmerHMM_glimmerT_9339-T1
Valid prediction for snap_scaffold_4-snap.1119-T1
Valid prediction for GlimmerHMM_glimmerT_9323-T1
Valid prediction for GlimmerHMM_glimmerT_9343-T1
Valid prediction for snap_scaffold_4-snap.1144-T1
Valid prediction for snap_scaffold_4-snap.1140-T1
Couldn't classify 174928, 175040
Sorry, prediction pasa_asmbl_41335.p1 fails validation.
(ATG)	 AA	170424-170463	GT	AGG
(ATA)	 AG	170776-170881	GT	GGG
(TTA)	 AG	171014-171039	GT	AAG
(GTG)	 AG	171160-171255	GT	ATG
(GCA)	 AG	172179-172259	GT	GGG
(ATC)	 AG	172479-172562	GT	AGG
(ACA)	 AG	172838-172962	GT	AGG
(TTT)	 AG	173190-173253	GT	AGG
(ACA)	 AG	173353-173466	GT	AGG
(AGG)	 AG	174065-174133	GT	AGG
(TGA)	 AG	174928-175040	GT	AGG
-recovered pasa_asmbl_41335.p1, initial, 170424, 170463
-recovered pasa_asmbl_41335.p1, internal, 170776, 170881
-recovered pasa_asmbl_41335.p1, internal, 171014, 171039
-recovered pasa_asmbl_41335.p1, internal, 171160, 171255
-recovered pasa_asmbl_41335.p1, internal, 172179, 172259
-recovered pasa_asmbl_41335.p1, internal, 172479, 172562
-recovered pasa_asmbl_41335.p1, internal, 172838, 172962
-recovered pasa_asmbl_41335.p1, internal, 173190, 173253
-recovered pasa_asmbl_41335.p1, internal, 173353, 173466
-recovered pasa_asmbl_41335.p1, internal, 174065, 174133
-recovered pasa_asmbl_41335.p1, internal, 174928, 175040
Couldn't classify 153366, 154011
Sorry, prediction pasa_asmbl_41331.p1 fails validation.
(TAC)	 CA	153366-154011	GT	GGG
(GAG)	 AG	154749-155023	GA	GAG
-recovered pasa_asmbl_41331.p1, terminal, 154749, 155023
Valid prediction for snap_scaffold_4-snap.1153-T1
Valid prediction for GlimmerHMM_glimmerT_9354-T1
Valid prediction for Augustus_model.g6020.t1
Couldn't classify 165378, 165522
Sorry, prediction pasa_asmbl_41333.p1 fails validation.
(CAG)	 AG	165378-165522	GT	GGG
(GCT)	 AG	166016-166713	GA	AAG
-recovered pasa_asmbl_41333.p1, terminal, 166016, 166713
-recovered pasa_asmbl_41333.p1, internal, 165378, 165522
Valid prediction for GlimmerHMM_glimmerT_9355-T1
Valid prediction for pasa_asmbl_41325.p1
Valid prediction for Augustus_model.g6022.t1
Valid prediction for snap_scaffold_4-snap.1125-T1
Valid prediction for snap_scaffold_4-snap.1126-T1
Couldn't classify 5352, 5418
Sorry, prediction pasa_asmbl_42261.p1 fails validation.
(ATG)	 AC	2134-2184	GT	AGG
(AAT)	 AG	2408-2512	GT	CGG
(GCT)	 AG	2614-2654	GT	CGG
(TCC)	 AG	2784-2864	GT	TGG
(GCC)	 AG	2980-3052	GT	AGG
(GTT)	 AG	3129-3206	GT	AGG
(GCG)	 AG	3321-3415	GT	AGG
(AGC)	 AG	3559-3671	GT	AGG
(CCC)	 AG	3804-3933	GT	AGG
(AGC)	 AG	4154-4259	GT	AGG
(GTT)	 AG	4549-4632	GT	AGG
(CTC)	 AG	4750-4851	GT	AGG
(GCT)	 AG	5051-5205	GC	AGG
(GTT)	 AG	5352-5418	GA	TGG
-recovered pasa_asmbl_42261.p1, initial, 2134, 2184
-recovered pasa_asmbl_42261.p1, internal, 2408, 2512
-recovered pasa_asmbl_42261.p1, internal, 2614, 2654
-recovered pasa_asmbl_42261.p1, internal, 2784, 2864
-recovered pasa_asmbl_42261.p1, internal, 2980, 3052
-recovered pasa_asmbl_42261.p1, internal, 3129, 3206
-recovered pasa_asmbl_42261.p1, internal, 3321, 3415
-recovered pasa_asmbl_42261.p1, internal, 3559, 3671
-recovered pasa_asmbl_42261.p1, internal, 3804, 3933
-recovered pasa_asmbl_42261.p1, internal, 4154, 4259
-recovered pasa_asmbl_42261.p1, internal, 4549, 4632
-recovered pasa_asmbl_42261.p1, internal, 4750, 4851
-recovered pasa_asmbl_42261.p1, internal, 5051, 5205
Valid prediction for CodingQuarry_transcript_48970-T1
Valid prediction for snap_scaffold_4-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_9331-T1
Valid prediction for Augustus_model.g6011.t1
Valid prediction for Augustus_model.g6028.t1
Valid prediction for snap_scaffold_4-snap.1134-T1
Valid prediction for snap_scaffold_4-snap.1130-T1
Valid prediction for snap_scaffold_4-snap.1142-T1
Valid prediction for snap_scaffold_4-snap.1129-T1
Valid prediction for snap_scaffold_4-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_9324-T1
Valid prediction for pasa_asmbl_41322.p1
Valid prediction for snap_scaffold_4-snap.1136-T1
Valid prediction for snap_scaffold_4-snap.1143-T1
Valid prediction for pasa_asmbl_41332.p1
Valid prediction for CodingQuarry_transcript_48976-T1
Valid prediction for GlimmerHMM_glimmerT_9322-T1
Valid prediction for Augustus_model.g6021.t1
Valid prediction for snap_scaffold_4-snap.1147-T1
Valid prediction for GlimmerHMM_glimmerT_9342-T1
Valid prediction for snap_scaffold_4-snap.1138-T1
Valid prediction for GlimmerHMM_glimmerT_9328-T1
Valid prediction for GlimmerHMM_glimmerT_9349-T1
Valid prediction for snap_scaffold_4-snap.1145-T1
Couldn't classify 5473, 5510
Sorry, prediction pasa_asmbl_41318.p2 fails validation.
(TTT)	 CC	5473-5510	GT	AGG
(GTA)	 AG	5719-5826	GT	GTG
(TGC)	 AG	6004-6190	GT	AGG
(GAG)	 AG	7150-7182	GC	AGG
-recovered pasa_asmbl_41318.p2, terminal, 7150, 7182
-recovered pasa_asmbl_41318.p2, internal, 5719, 5826
-recovered pasa_asmbl_41318.p2, internal, 6004, 6190
-recovered pasa_asmbl_41318.p2, internal, 7150, 7182
Valid prediction for snap_scaffold_4-snap.1127-T1
Valid prediction for snap_scaffold_4-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_9345-T1
Valid prediction for GlimmerHMM_glimmerT_9334-T1
Valid prediction for GlimmerHMM_glimmerT_9335-T1
Valid prediction for snap_scaffold_4-snap.1135-T1
Valid prediction for HiQ_model.g6004.t1
Valid prediction for GlimmerHMM_glimmerT_9338-T1
Valid prediction for Augustus_model.g6016.t1
Valid prediction for Augustus_model.g6025.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 CodingQuarry_transcript_48973-T1
Valid prediction for snap_scaffold_4-snap.1128-T1
Valid prediction for Augustus_model.g6023.t1
Valid prediction for snap_scaffold_4-snap.1152-T1
Valid prediction for Augustus_model.g6015.t1
Valid prediction for GlimmerHMM_glimmerT_9348-T1
Valid prediction for Augustus_model.g6018.t1
Valid prediction for GlimmerHMM_glimmerT_9341-T1
Valid prediction for GlimmerHMM_glimmerT_9337-T1
Valid prediction for GlimmerHMM_glimmerT_9344-T1
Valid prediction for Augustus_model.g6026.t1
Valid prediction for snap_scaffold_4-snap.1122-T1
Valid prediction for snap_scaffold_4-snap.1132-T1
Valid prediction for CodingQuarry_transcript_48977-T1
Valid prediction for snap_scaffold_4-snap.1121-T1
Valid prediction for HiQ_model.g6006.t1
Valid prediction for HiQ_model.g6005.t1
Valid prediction for CodingQuarry_transcript_48975-T1
Valid prediction for GlimmerHMM_glimmerT_9353-T1
Valid prediction for snap_scaffold_4-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_9350-T1
Valid prediction for GlimmerHMM_glimmerT_9351-T1
Valid prediction for CodingQuarry_transcript_48971-T1
Valid prediction for pasa_asmbl_42553.p1
Valid prediction for GlimmerHMM_glimmerT_9352-T1
Valid prediction for Augustus_model.g6014.t1
Valid prediction for HiQ_model.g6024.t1
Valid prediction for Augustus_model.g6012.t1
Valid prediction for GlimmerHMM_glimmerT_9329-T1
Valid prediction for GlimmerHMM_glimmerT_9347-T1
Valid prediction for Augustus_model.g6009.t1
Valid prediction for GlimmerHMM_glimmerT_9332-T1
Couldn't classify 195212, 195248
Couldn't classify 198491, 198761
Sorry, prediction pasa_asmbl_42548.p1 fails validation.
(CCT)	 AT	195212-195248	GT	CTG
(TGT)	 AG	197160-197215	GT	AGG
(ATG)	 AG	197568-197599	GT	GAG
(GTT)	 AG	197852-197965	GT	AGG
(GTT)	 AG	198491-198761	GT	AGG
-recovered pasa_asmbl_42548.p1, initial, 197568, 197599
-recovered pasa_asmbl_42548.p1, internal, 197160, 197215
-recovered pasa_asmbl_42548.p1, internal, 197568, 197599
-recovered pasa_asmbl_42548.p1, internal, 197852, 197965
-recovered pasa_asmbl_42548.p1, internal, 198491, 198761
Valid prediction for CodingQuarry_transcript_48978-T1
Valid prediction for snap_scaffold_4-snap.1124-T1
Valid prediction for GlimmerHMM_glimmerT_9325-T1
Valid prediction for Augustus_model.g6017.t1
Valid prediction for snap_scaffold_4-snap.1148-T1
Valid prediction for Augustus_model.g6007.t1
Valid prediction for Augustus_model.g6027.t1
Valid prediction for snap_scaffold_4-snap.1137-T1
Valid prediction for Augustus_model.g6010.t1
Couldn't classify 203326, 203403
Sorry, prediction pasa_asmbl_42547.p1 fails validation.
(TCT)	 CT	203326-203403	GT	AGG
(GTT)	 AG	205236-205320	GT	AGG
(ACT)	 AG	206698-206871	GT	AGG
(GTC)	 AG	207234-207311	GT	AGG
(ATG)	 AG	207469-207606	GT	AAG
(AAA)	 AG	207713-207818	GT	AGG
(GGT)	 AG	207925-208096	GG	GAG
add_exon() Sorry, pasa_asmbl_42547.p1 207469-207606-initial-1 is invalid.
-recovered pasa_asmbl_42547.p1, initial, 207469, 207606
-recovered pasa_asmbl_42547.p1, terminal, 207925, 208096
-recovered pasa_asmbl_42547.p1, internal, 205236, 205320
-recovered pasa_asmbl_42547.p1, internal, 206698, 206871
-recovered pasa_asmbl_42547.p1, internal, 207234, 207311
-recovered pasa_asmbl_42547.p1, internal, 207469, 207606
-recovered pasa_asmbl_42547.p1, internal, 207713, 207818
Valid prediction for pasa_asmbl_42555.p1
Valid prediction for GlimmerHMM_glimmerT_9326-T1
Valid prediction for Augustus_model.g6013.t1
Valid prediction for snap_scaffold_4-snap.1150-T1
Valid prediction for pasa_asmbl_42546.p1
Valid prediction for snap_scaffold_4-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_9327-T1
Valid prediction for CodingQuarry_transcript_48974-T1
Valid prediction for snap_scaffold_4-snap.1131-T1
Valid prediction for snap_scaffold_4-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_9333-T1
Valid prediction for snap_scaffold_4-snap.1149-T1
Valid prediction for GlimmerHMM_glimmerT_9336-T1
Valid prediction for snap_scaffold_4-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_9330-T1
Valid prediction for GlimmerHMM_glimmerT_9340-T1
Valid prediction for GlimmerHMM_glimmerT_9346-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69001, rend_intergenic: 63694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79506, rend_intergenic: 75918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128287, rend_intergenic: 121839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239953
-exon list size: 452


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 69001, rend_intergenic: 63694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79506, rend_intergenic: 75918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128287, rend_intergenic: 121839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support