-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_3081387-3270428 -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 snap_scaffold_6-snap.729-T1 Valid prediction for snap_scaffold_6-snap.746-T1 Valid prediction for Augustus_model.g9472.t1 Valid prediction for snap_scaffold_6-snap.747-T1 Valid prediction for snap_scaffold_6-snap.755-T1 Valid prediction for snap_scaffold_6-snap.756-T1 Valid prediction for snap_scaffold_6-snap.752-T1 Valid prediction for snap_scaffold_6-snap.738-T1 Valid prediction for Augustus_model.g9478.t1 Valid prediction for snap_scaffold_6-snap.735-T1 Valid prediction for GlimmerHMM_glimmerT_14288-T1 Valid prediction for snap_scaffold_6-snap.730-T1 Valid prediction for GlimmerHMM_glimmerT_14290-T1 Valid prediction for Augustus_model.g9477.t1 Valid prediction for GlimmerHMM_glimmerT_14294-T1 Valid prediction for snap_scaffold_6-snap.741-T1 Valid prediction for GlimmerHMM_glimmerT_14295-T1 Valid prediction for GlimmerHMM_glimmerT_14274-T1 Valid prediction for GlimmerHMM_glimmerT_14296-T1 Valid prediction for snap_scaffold_6-snap.733-T1 Valid prediction for snap_scaffold_6-snap.759-T1 Valid prediction for Augustus_model.g9465.t1 Valid prediction for GlimmerHMM_glimmerT_14276-T1 Valid prediction for snap_scaffold_6-snap.725-T1 Valid prediction for snap_scaffold_6-snap.757-T1 Couldn't classify 110207, 110347 Sorry, prediction pasa_asmbl_46814.p1 fails validation. (CGA) TA 110207-110347 GT AAG (GTG) AG 110615-110863 GA GAG -recovered pasa_asmbl_46814.p1, terminal, 110615, 110863 Valid prediction for Augustus_model.g9463.t1 Valid prediction for GlimmerHMM_glimmerT_14277-T1 Valid prediction for CodingQuarry_transcript_54972-T1 Valid prediction for CodingQuarry_transcript_54971-T1 Valid prediction for snap_scaffold_6-snap.743-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_14284-T1 Valid prediction for snap_scaffold_6-snap.740-T1 Valid prediction for GlimmerHMM_glimmerT_14292-T1 Valid prediction for snap_scaffold_6-snap.726-T1 Couldn't classify 28574, 28684 Couldn't classify 29485, 29629 Sorry, prediction pasa_asmbl_46812.p1 fails validation. (GTC) TG 28574-28684 GT AGG (ATC) AG 29281-29402 GT TGG (GTG) AG 29485-29629 GC AGG -recovered pasa_asmbl_46812.p1, internal, 29281, 29402 -recovered pasa_asmbl_46812.p1, internal, 29485, 29629 Valid prediction for snap_scaffold_6-snap.751-T1 Valid prediction for Augustus_model.g9476.t1 Valid prediction for snap_scaffold_6-snap.739-T1 Valid prediction for Augustus_model.g9471.t1 Couldn't classify 143704, 143890 Sorry, prediction pasa_asmbl_46819.p1 fails validation. (TTA) AG 143704-143890 GT AGG (GGG) AG 144043-144200 GT TGG (GTC) AG 144807-144933 GT TGG (TGA) AG 145101-145276 GT AAG (GTC) AG 145384-145494 GT AAG (TTG) AG 145858-146099 GT AAG (AAA) AG 146706-146886 GT AGG (GGA) AG 147256-147457 GT TGG (TCT) AG 147723-147882 GT CGG (CTT) AG 147980-148142 GT CAG (GCA) AG 148375-148710 TC GAT -recovered pasa_asmbl_46819.p1, terminal, 148375, 148710 -recovered pasa_asmbl_46819.p1, internal, 143704, 143890 -recovered pasa_asmbl_46819.p1, internal, 144043, 144200 -recovered pasa_asmbl_46819.p1, internal, 144807, 144933 -recovered pasa_asmbl_46819.p1, internal, 145101, 145276 -recovered pasa_asmbl_46819.p1, internal, 145384, 145494 -recovered pasa_asmbl_46819.p1, internal, 145858, 146099 -recovered pasa_asmbl_46819.p1, internal, 146706, 146886 -recovered pasa_asmbl_46819.p1, internal, 147256, 147457 -recovered pasa_asmbl_46819.p1, internal, 147723, 147882 -recovered pasa_asmbl_46819.p1, internal, 147980, 148142 Valid prediction for GlimmerHMM_glimmerT_14297-T1 Valid prediction for Augustus_model.g9467.t1 Valid prediction for GlimmerHMM_glimmerT_14273-T1 Valid prediction for GlimmerHMM_glimmerT_14281-T1 Valid prediction for pasa_asmbl_46822.p1 Valid prediction for snap_scaffold_6-snap.723-T1 Valid prediction for HiQ_model.g9475.t1 Valid prediction for snap_scaffold_6-snap.749-T1 Valid prediction for snap_scaffold_6-snap.742-T1 Valid prediction for snap_scaffold_6-snap.758-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_6-snap.727-T1 Valid prediction for GlimmerHMM_glimmerT_14279-T1 Valid prediction for Augustus_model.g9468.t1 Valid prediction for GlimmerHMM_glimmerT_14283-T1 Valid prediction for GlimmerHMM_glimmerT_14271-T1 Valid prediction for GlimmerHMM_glimmerT_14286-T1 Valid prediction for snap_scaffold_6-snap.732-T1 Valid prediction for GlimmerHMM_glimmerT_14272-T1 Valid prediction for snap_scaffold_6-snap.734-T1 Valid prediction for snap_scaffold_6-snap.763-T1 Valid prediction for snap_scaffold_6-snap.745-T1 Valid prediction for GlimmerHMM_glimmerT_14275-T1 Valid prediction for GlimmerHMM_glimmerT_14298-T1 Valid prediction for GlimmerHMM_glimmerT_14289-T1 Valid prediction for snap_scaffold_6-snap.736-T1 Valid prediction for Augustus_model.g9470.t1 Valid prediction for GlimmerHMM_glimmerT_14287-T1 Valid prediction for CodingQuarry_transcript_54970-T1 Couldn't classify 7034, 7114 Sorry, prediction pasa_asmbl_48234.p1 fails validation. (TAC) CG 7034-7114 GT AGG (AAT) AG 7316-7507 GT AGG (GCT) AG 7701-7789 GT GGG (GTA) AG 7872-7988 GT GGG (TCT) AG 8289-8402 GT AGG (AGC) AG 8541-8688 GT AGG (AGT) AG 8872-8967 GT AGG (GTG) AG 9059-9196 GT AGG (GTG) AG 9449-9624 GT AGG (GGA) AG 9893-10045 GT AGG (AAT) AG 10559-10661 GT AGG (GAC) AG 10736-10868 GT CAG (AGG) AG 11300-11413 GT TGG (TGG) AG 11533-11585 GT AGG (ATC) AG 12218-12315 GT AGG (CCG) AG 12483-12570 TG GAT -recovered pasa_asmbl_48234.p1, terminal, 12483, 12570 -recovered pasa_asmbl_48234.p1, internal, 7316, 7507 -recovered pasa_asmbl_48234.p1, internal, 7701, 7789 -recovered pasa_asmbl_48234.p1, internal, 7872, 7988 -recovered pasa_asmbl_48234.p1, internal, 8289, 8402 -recovered pasa_asmbl_48234.p1, internal, 8541, 8688 -recovered pasa_asmbl_48234.p1, internal, 8872, 8967 -recovered pasa_asmbl_48234.p1, internal, 9059, 9196 -recovered pasa_asmbl_48234.p1, internal, 9449, 9624 -recovered pasa_asmbl_48234.p1, internal, 9893, 10045 -recovered pasa_asmbl_48234.p1, internal, 10559, 10661 -recovered pasa_asmbl_48234.p1, internal, 10736, 10868 -recovered pasa_asmbl_48234.p1, internal, 11300, 11413 -recovered pasa_asmbl_48234.p1, internal, 11533, 11585 -recovered pasa_asmbl_48234.p1, internal, 12218, 12315 Valid prediction for snap_scaffold_6-snap.724-T1 Valid prediction for snap_scaffold_6-snap.731-T1 Valid prediction for snap_scaffold_6-snap.760-T1 Valid prediction for snap_scaffold_6-snap.754-T1 Valid prediction for GlimmerHMM_glimmerT_14280-T1 Valid prediction for GlimmerHMM_glimmerT_14285-T1 Valid prediction for snap_scaffold_6-snap.750-T1 Valid prediction for Augustus_model.g9473.t1 Valid prediction for snap_scaffold_6-snap.728-T1 Valid prediction for HiQ_model.g9474.t1 Valid prediction for pasa_asmbl_48231.p1 Valid prediction for snap_scaffold_6-snap.744-T1 Couldn't classify 71840, 71975 Couldn't classify 73524, 73628 Sorry, prediction pasa_asmbl_49349.p1 fails validation. (GGT) GA 71840-71975 GT AGG (GGA) AG 73254-73384 GT AGG (GCC) AG 73524-73628 AG TGA -recovered pasa_asmbl_49349.p1, internal, 73254, 73384 Couldn't classify 62103, 62323 Couldn't classify 63782, 63862 Sorry, prediction pasa_asmbl_48228.p1 fails validation. (CGG) GC 62103-62323 GT AGG (CTA) AG 62975-63101 GT AGG (CCT) AG 63349-63458 GT AGG (GTA) AG 63546-63654 GT ACG (CAA) AG 63782-63862 TT CCT -recovered pasa_asmbl_48228.p1, internal, 62975, 63101 -recovered pasa_asmbl_48228.p1, internal, 63349, 63458 -recovered pasa_asmbl_48228.p1, internal, 63546, 63654 Valid prediction for snap_scaffold_6-snap.762-T1 Valid prediction for Augustus_model.g9466.t1 Couldn't classify 57705, 57725 Couldn't classify 61792, 61943 Sorry, prediction pasa_asmbl_48229.p1 fails validation. (ATC) CC 57705-57725 GT TGG (GCA) AG 58218-58308 GT AGG (AGG) AG 58794-58906 GT AGG (AAC) AG 60201-60398 GT AGG (TTG) AG 60559-60718 GT TGG (GTA) AG 61437-61514 GT TAG (CAG) AG 61792-61943 AT GCA add_exon() Sorry, pasa_asmbl_48229.p1 58218-58308-terminal-3 is invalid. -recovered pasa_asmbl_48229.p1, terminal, 58218, 58308 -recovered pasa_asmbl_48229.p1, internal, 58218, 58308 -recovered pasa_asmbl_48229.p1, internal, 58794, 58906 -recovered pasa_asmbl_48229.p1, internal, 60201, 60398 -recovered pasa_asmbl_48229.p1, internal, 60559, 60718 -recovered pasa_asmbl_48229.p1, internal, 61437, 61514 Valid prediction for GlimmerHMM_glimmerT_14278-T1 Valid prediction for Augustus_model.g9464.t1 Valid prediction for snap_scaffold_6-snap.753-T1 Valid prediction for GlimmerHMM_glimmerT_14270-T1 Couldn't classify 65737, 65829 Sorry, prediction pasa_asmbl_48227.p1 fails validation. (TTC) AG 65737-65829 GT AGG (GTA) AG 66422-66568 GT AGG (GCT) AG 67054-67240 GT CAG (TGA) AG 67329-67484 GT TGG (ATG) AG 67842-67956 GT AGG (AGA) AG 68697-68868 GT AGG (CGC) AG 69266-69427 GT AGG (GCC) AG 69790-69888 GT GAG (AAG) AG 70015-70245 GT AGG (GAC) AG 70469-70570 CA AGC add_exon() Sorry, pasa_asmbl_48227.p1 67842-67956-initial-1 is invalid. -recovered pasa_asmbl_48227.p1, initial, 67842, 67956 -recovered pasa_asmbl_48227.p1, terminal, 70469, 70570 -recovered pasa_asmbl_48227.p1, internal, 65737, 65829 -recovered pasa_asmbl_48227.p1, internal, 66422, 66568 -recovered pasa_asmbl_48227.p1, internal, 67054, 67240 -recovered pasa_asmbl_48227.p1, internal, 67329, 67484 -recovered pasa_asmbl_48227.p1, internal, 67842, 67956 -recovered pasa_asmbl_48227.p1, internal, 68697, 68868 -recovered pasa_asmbl_48227.p1, internal, 69266, 69427 -recovered pasa_asmbl_48227.p1, internal, 69790, 69888 -recovered pasa_asmbl_48227.p1, internal, 70015, 70245 Valid prediction for GlimmerHMM_glimmerT_14282-T1 Valid prediction for snap_scaffold_6-snap.737-T1 Valid prediction for snap_scaffold_6-snap.761-T1 Valid prediction for GlimmerHMM_glimmerT_14293-T1 Valid prediction for Augustus_model.g9462.t1 Valid prediction for Augustus_model.g9479.t1 Valid prediction for pasa_asmbl_48224.p1 Valid prediction for snap_scaffold_6-snap.748-T1 Valid prediction for GlimmerHMM_glimmerT_14291-T1 Valid prediction for Augustus_model.g9469.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5055, rend_intergenic: 3239 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 7644, rend_intergenic: 5267 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 16019, rend_intergenic: 12230 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21570, rend_intergenic: 16267 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28087, rend_intergenic: 21948 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31465, rend_intergenic: 28123 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33882, rend_intergenic: 32319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35762, rend_intergenic: 34129 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 44355, rend_intergenic: 35868 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 54717, rend_intergenic: 47178 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70792, rend_intergenic: 66438 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 83063, rend_intergenic: 71165 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 97649, rend_intergenic: 94411 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179547, rend_intergenic: 173303 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 189042 -exon list size: 425 building trellis 0.2 0.5 0.7 0.9 1.2 1.4 1.6 1.9 2.1 2.3 2.6 2.8 3.0 3.3 3.5 3.7 4.0 4.2 4.4 4.7 4.9 5.2 5.4 5.6 5.9 6.1 6.3 6.6 6.8 7.0 7.3 7.5 7.7 8.0 8.2 8.4 8.7 8.9 9.1 9.4 9.6 9.8 10.1 10.3 10.5 10.8 11.0 11.2 11.5 11.7 11.9 12.2 12.4 12.6 12.9 13.1 13.3 13.6 13.8 14.1 14.3 14.5 14.8 15.0 15.2 15.5 15.7 15.9 16.2 16.4 16.6 16.9 17.1 17.3 17.6 17.8 18.0 18.3 18.5 18.7 19.0 19.2 19.4 19.7 19.9 20.1 20.4 20.6 20.8 21.1 21.3 21.5 21.8 22.0 22.2 22.5 22.7 23.0 23.2 23.4 23.7 23.9 24.1 24.4 24.6 24.8 25.1 25.3 25.5 25.8 26.0 26.2 26.5 26.7 26.9 27.2 27.4 27.6 27.9 28.1 28.3 28.6 28.8 29.0 29.3 29.5 29.7 30.0 30.2 30.4 30.7 30.9 31.1 31.4 31.6 31.9 32.1 32.3 32.6 32.8 33.0 33.3 33.5 33.7 34.0 34.2 34.4 34.7 34.9 35.1 35.4 35.6 35.8 36.1 36.3 36.5 36.8 37.0 37.2 37.5 37.7 37.9 38.2 38.4 38.6 38.9 39.1 39.3 39.6 39.8 40.0 40.3 40.5 40.7 41.0 41.2 41.5 41.7 41.9 42.2 42.4 42.6 42.9 43.1 43.3 43.6 43.8 44.0 44.3 44.5 44.7 45.0 45.2 45.4 45.7 45.9 46.1 46.4 46.6 46.8 47.1 47.3 47.5 47.8 48.0 48.2 48.5 48.7 48.9 49.2 49.4 49.6 49.9 50.1 50.4 50.6 50.8 51.1 51.3 51.5 51.8 52.0 52.2 52.5 52.7 52.9 53.2 53.4 53.6 53.9 54.1 54.3 54.6 54.8 55.0 55.3 55.5 55.7 56.0 56.2 56.4 56.7 56.9 57.1 57.4 57.6 57.8 58.1 58.3 58.5 58.8 59.0 59.3 59.5 59.7 60.0 60.2 60.4 60.7 60.9 61.1 61.4 61.6 61.8 62.1 62.3 62.5 62.8 63.0 63.2 63.5 63.7 63.9 64.2 64.4 64.6 64.9 65.1 65.3 65.6 65.8 66.0 66.3 66.5 66.7 67.0 67.2 67.4 67.7 67.9 68.1 68.4 68.6 68.9 69.1 69.3 69.6 69.8 70.0 70.3 70.5 70.7 71.0 71.2 71.4 71.7 71.9 72.1 72.4 72.6 72.8 73.1 73.3 73.5 73.8 74.0 74.2 74.5 74.7 74.9 75.2 75.4 75.6 75.9 76.1 76.3 76.6 76.8 77.0 77.3 77.5 77.8 78.0 78.2 78.5 78.7 78.9 79.2 79.4 79.6 79.9 80.1 80.3 80.6 80.8 81.0 81.3 81.5 81.7 82.0 82.2 82.4 82.7 82.9 83.1 83.4 83.6 83.8 84.1 84.3 84.5 84.8 85.0 85.2 85.5 85.7 85.9 86.2 86.4 86.7 86.9 87.1 87.4 87.6 87.8 88.1 88.3 88.5 88.8 89.0 89.2 89.5 89.7 89.9 90.2 90.4 90.6 90.9 91.1 91.3 91.6 91.8 92.0 92.3 92.5 92.7 93.0 93.2 93.4 93.7 93.9 94.1 94.4 94.6 94.8 95.1 95.3 95.6 95.8 96.0 96.3 96.5 96.7 97.0 97.2 97.4 97.7 97.9 98.1 98.4 98.6 98.8 99.1 99.3 99.5 99.8 -found 32 predictions from path traversal Error with prediction: snap lend_intergenic: 5055, rend_intergenic: 3239 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 7644, rend_intergenic: 5267 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 16019, rend_intergenic: 12230 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21570, rend_intergenic: 16267 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28087, rend_intergenic: 21948 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31465, rend_intergenic: 28123 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33882, rend_intergenic: 32319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35762, rend_intergenic: 34129 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 44355, rend_intergenic: 35868 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 54717, rend_intergenic: 47178 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70792, rend_intergenic: 66438 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 83063, rend_intergenic: 71165 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 97649, rend_intergenic: 94411 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179547, rend_intergenic: 173303 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 19 predictions persist after filtering for low support