-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_2762756-2870952 -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_11-snap.710-T1 Valid prediction for snap_scaffold_11-snap.722-T1 Valid prediction for GlimmerHMM_glimmerT_26742-T1 Valid prediction for GlimmerHMM_glimmerT_26729-T1 Valid prediction for Augustus_model.g17690.t1 Valid prediction for Augustus_model.g17687.t1 Valid prediction for GlimmerHMM_glimmerT_26739-T1 Valid prediction for CodingQuarry_transcript_8007-T1 Valid prediction for snap_scaffold_11-snap.713-T1 Valid prediction for snap_scaffold_11-snap.715-T1 Valid prediction for snap_scaffold_11-snap.706-T1 Valid prediction for GlimmerHMM_glimmerT_26737-T1 Valid prediction for snap_scaffold_11-snap.719-T1 Valid prediction for Augustus_model.g17698.t1 Valid prediction for snap_scaffold_11-snap.698-T1 Couldn't classify 75870, 76052 Sorry, prediction pasa_asmbl_5384.p1 fails validation. (ATG) CA 75238-75354 GT AGG (GTG) AG 75870-76052 AA CCA -recovered pasa_asmbl_5384.p1, initial, 75238, 75354 Valid prediction for snap_scaffold_11-snap.718-T1 Valid prediction for snap_scaffold_11-snap.705-T1 Valid prediction for HiQ_model.g17693.t1 Valid prediction for GlimmerHMM_glimmerT_26731-T1 Couldn't classify 12883, 13056 Sorry, prediction pasa_asmbl_5378.p1 fails validation. (GAC) TA 12883-13056 GT AGG (CCC) AG 13587-13713 GT CGG (ACA) AG 15244-15267 GT CGG (CAT) AG 15753-15958 CG GAC -recovered pasa_asmbl_5378.p1, terminal, 15753, 15958 -recovered pasa_asmbl_5378.p1, internal, 13587, 13713 -recovered pasa_asmbl_5378.p1, internal, 15244, 15267 Valid prediction for CodingQuarry_transcript_8006-T1 Valid prediction for GlimmerHMM_glimmerT_26738-T1 Valid prediction for pasa_asmbl_5385.p1 Valid prediction for Augustus_model.g17694.t1 Couldn't classify 91646, 91723 Sorry, prediction pasa_asmbl_5388.p1 fails validation. (GTC) GT 91646-91723 GT AGG (TTC) AG 91851-92004 GT AGG (TCT) AG 92332-92492 CC AAC -recovered pasa_asmbl_5388.p1, terminal, 92332, 92492 -recovered pasa_asmbl_5388.p1, internal, 91851, 92004 Valid prediction for snap_scaffold_11-snap.714-T1 Couldn't classify 88786, 88976 Couldn't classify 90147, 90268 Sorry, prediction pasa_asmbl_5387.p1 fails validation. (TGC) GC 88786-88976 GT GAG (GGA) AG 89264-89433 GT AGG (CTC) AG 89657-89812 GT AGG (CGT) AG 90147-90268 AT ACA -recovered pasa_asmbl_5387.p1, internal, 89264, 89433 -recovered pasa_asmbl_5387.p1, internal, 89657, 89812 Valid prediction for GlimmerHMM_glimmerT_26736-T1 Valid prediction for GlimmerHMM_glimmerT_26733-T1 Valid prediction for pasa_asmbl_5380.p1 Valid prediction for snap_scaffold_11-snap.724-T1 Valid prediction for snap_scaffold_11-snap.702-T1 Valid prediction for HiQ_model.g17695.t1 Valid prediction for snap_scaffold_11-snap.711-T1 Valid prediction for snap_scaffold_11-snap.704-T1 Valid prediction for GlimmerHMM_glimmerT_26735-T1 Couldn't classify 74197, 74674 Couldn't classify 74833, 74930 Sorry, prediction pasa_asmbl_6317.p1 fails validation. (TTT) AC 74197-74674 GT GGG (GCG) AG 74833-74930 GA TGG Valid prediction for snap_scaffold_11-snap.708-T1 Valid prediction for snap_scaffold_11-snap.725-T1 Valid prediction for snap_scaffold_11-snap.717-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_26734-T1 Valid prediction for Augustus_model.g17699.t1 Valid prediction for CodingQuarry_transcript_8004-T1 Valid prediction for snap_scaffold_11-snap.703-T1 Valid prediction for Augustus_model.g17689.t1 Valid prediction for snap_scaffold_11-snap.721-T1 Valid prediction for GlimmerHMM_glimmerT_26740-T1 Valid prediction for snap_scaffold_11-snap.701-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for CodingQuarry_transcript_8003-T1 Couldn't classify 62929, 62987 Sorry, prediction pasa_asmbl_6512.p1 fails validation. (AGG) CT 62929-62987 GT AGG (GTA) AG 63101-63178 GT CAG (GTG) AG 63630-63800 GT AGG (GAT) AG 64096-64197 GT GTG (GAG) AG 64416-64557 GC GAG -recovered pasa_asmbl_6512.p1, terminal, 64416, 64557 -recovered pasa_asmbl_6512.p1, internal, 63101, 63178 -recovered pasa_asmbl_6512.p1, internal, 63630, 63800 -recovered pasa_asmbl_6512.p1, internal, 64096, 64197 -recovered pasa_asmbl_6512.p1, internal, 64416, 64557 Couldn't classify 39480, 39533 Couldn't classify 42824, 42949 Sorry, prediction pasa_asmbl_6516.p1 fails validation. (ATT) GC 39480-39533 GT AGG (AGA) AG 40125-40378 GT AGG (GGA) AG 40883-40961 GT AAG (ATG) AG 41406-41516 GT CGG (GAG) AG 42824-42949 TA GGT -recovered pasa_asmbl_6516.p1, initial, 41406, 41516 -recovered pasa_asmbl_6516.p1, internal, 40125, 40378 -recovered pasa_asmbl_6516.p1, internal, 40883, 40961 -recovered pasa_asmbl_6516.p1, internal, 41406, 41516 Valid prediction for Augustus_model.g17688.t1 Valid prediction for Augustus_model.g17697.t1 Valid prediction for snap_scaffold_11-snap.700-T1 Valid prediction for snap_scaffold_11-snap.720-T1 Valid prediction for CodingQuarry_transcript_8005-T1 Couldn't classify 56690, 56803 Sorry, prediction pasa_asmbl_7361.p1 fails validation. (ATG) TC 45142-45169 GC AGG (GTG) AG 45308-45396 GT AGG (CAC) AG 45757-45855 GT TGG (GCC) AG 46129-46286 GT AGG (GTA) AG 46410-46509 GT AGG (GGT) AG 46613-46741 GT ATG (GAG) AG 47212-47392 GT TGG (GCT) AG 47530-47591 GT CTG (GAG) AG 47999-48109 GT AGG (GTG) AG 49170-49235 GT AGG (ATT) AG 49315-49416 GT AGG (GAA) AG 49497-49560 GT TGG (GGG) AG 49662-49786 GT ACG (GAG) AG 50120-50172 GT AAG (GAA) AG 50324-50426 GT AGG (GCT) AG 50530-50578 GT AGG (CAC) AG 50861-51015 GT GAG (GCC) AG 51625-51724 GT ACG (AAA) AG 51984-52087 GT AGG (ATG) AG 52191-52271 GT AGG (AAC) AG 52506-52687 GT AGG (CTT) AG 53038-53243 GT CAG (AAA) AG 53485-53575 GT AAG (GTA) AG 53749-53901 GT TAG (TGA) AG 54055-54155 GT CGG (TGG) AG 54709-54805 GT CCG (AAG) AG 55250-55398 GT CGG (AAA) AG 55743-55798 GT AGG (CTA) AG 55897-55993 GT GGG (TCC) AG 56462-56529 GT TGG (GTG) AG 56690-56803 GC TGG -recovered pasa_asmbl_7361.p1, initial, 45142, 45169 -recovered pasa_asmbl_7361.p1, initial, 52191, 52271 -recovered pasa_asmbl_7361.p1, internal, 45308, 45396 -recovered pasa_asmbl_7361.p1, internal, 45757, 45855 -recovered pasa_asmbl_7361.p1, internal, 46129, 46286 -recovered pasa_asmbl_7361.p1, internal, 46410, 46509 -recovered pasa_asmbl_7361.p1, internal, 46613, 46741 -recovered pasa_asmbl_7361.p1, internal, 47212, 47392 -recovered pasa_asmbl_7361.p1, internal, 47530, 47591 -recovered pasa_asmbl_7361.p1, internal, 47999, 48109 -recovered pasa_asmbl_7361.p1, internal, 49170, 49235 -recovered pasa_asmbl_7361.p1, internal, 49315, 49416 -recovered pasa_asmbl_7361.p1, internal, 49497, 49560 -recovered pasa_asmbl_7361.p1, internal, 49662, 49786 -recovered pasa_asmbl_7361.p1, internal, 50120, 50172 -recovered pasa_asmbl_7361.p1, internal, 50324, 50426 -recovered pasa_asmbl_7361.p1, internal, 50530, 50578 -recovered pasa_asmbl_7361.p1, internal, 50861, 51015 -recovered pasa_asmbl_7361.p1, internal, 51625, 51724 -recovered pasa_asmbl_7361.p1, internal, 51984, 52087 -recovered pasa_asmbl_7361.p1, internal, 52191, 52271 -recovered pasa_asmbl_7361.p1, internal, 52506, 52687 -recovered pasa_asmbl_7361.p1, internal, 53038, 53243 -recovered pasa_asmbl_7361.p1, internal, 53485, 53575 -recovered pasa_asmbl_7361.p1, internal, 53749, 53901 -recovered pasa_asmbl_7361.p1, internal, 54055, 54155 -recovered pasa_asmbl_7361.p1, internal, 54709, 54805 -recovered pasa_asmbl_7361.p1, internal, 55250, 55398 -recovered pasa_asmbl_7361.p1, internal, 55743, 55798 -recovered pasa_asmbl_7361.p1, internal, 55897, 55993 -recovered pasa_asmbl_7361.p1, internal, 56462, 56529 -recovered pasa_asmbl_7361.p1, internal, 56690, 56803 Couldn't classify 57298, 57365 Couldn't classify 59090, 59199 Sorry, prediction pasa_asmbl_6513.p1 fails validation. (GAG) GG 57298-57365 GT GGG (GTT) AG 58506-58642 GT AGG (TAA) AG 59090-59199 TA GGT -recovered pasa_asmbl_6513.p1, internal, 58506, 58642 Valid prediction for snap_scaffold_11-snap.707-T1 Valid prediction for GlimmerHMM_glimmerT_26732-T1 Valid prediction for snap_scaffold_11-snap.726-T1 Valid prediction for snap_scaffold_11-snap.712-T1 Valid prediction for GlimmerHMM_glimmerT_26741-T1 Valid prediction for GlimmerHMM_glimmerT_26743-T1 Valid prediction for snap_scaffold_11-snap.723-T1 Valid prediction for snap_scaffold_11-snap.699-T1 Valid prediction for HiQ_model.g17691.t1 Valid prediction for pasa_asmbl_6517.p1 Valid prediction for snap_scaffold_11-snap.709-T1 Valid prediction for CodingQuarry_transcript_8002-T1 Valid prediction for HiQ_model.g17696.t1 Valid prediction for GlimmerHMM_glimmerT_26730-T1 Valid prediction for Augustus_model.g17692.t1 Valid prediction for snap_scaffold_11-snap.716-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7663, rend_intergenic: 6051 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 19520, rend_intergenic: 18022 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21546, rend_intergenic: 19883 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28523, rend_intergenic: 24714 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53546, rend_intergenic: 43492 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 57366, rend_intergenic: 53798 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68025, rend_intergenic: 57853 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 72822, rend_intergenic: 70857 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 106584, rend_intergenic: 104536 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 108197 -exon list size: 324 building trellis 0.3 0.6 0.9 1.2 1.5 1.8 2.1 2.5 2.8 3.1 3.4 3.7 4.0 4.3 4.6 4.9 5.2 5.5 5.8 6.1 6.4 6.7 7.1 7.4 7.7 8.0 8.3 8.6 8.9 9.2 9.5 9.8 10.1 10.4 10.7 11.0 11.3 11.7 12.0 12.3 12.6 12.9 13.2 13.5 13.8 14.1 14.4 14.7 15.0 15.3 15.6 16.0 16.3 16.6 16.9 17.2 17.5 17.8 18.1 18.4 18.7 19.0 19.3 19.6 19.9 20.2 20.6 20.9 21.2 21.5 21.8 22.1 22.4 22.7 23.0 23.3 23.6 23.9 24.2 24.5 24.8 25.2 25.5 25.8 26.1 26.4 26.7 27.0 27.3 27.6 27.9 28.2 28.5 28.8 29.1 29.4 29.8 30.1 30.4 30.7 31.0 31.3 31.6 31.9 32.2 32.5 32.8 33.1 33.4 33.7 34.0 34.4 34.7 35.0 35.3 35.6 35.9 36.2 36.5 36.8 37.1 37.4 37.7 38.0 38.3 38.7 39.0 39.3 39.6 39.9 40.2 40.5 40.8 41.1 41.4 41.7 42.0 42.3 42.6 42.9 43.3 43.6 43.9 44.2 44.5 44.8 45.1 45.4 45.7 46.0 46.3 46.6 46.9 47.2 47.5 47.9 48.2 48.5 48.8 49.1 49.4 49.7 50.0 50.3 50.6 50.9 51.2 51.5 51.8 52.1 52.5 52.8 53.1 53.4 53.7 54.0 54.3 54.6 54.9 55.2 55.5 55.8 56.1 56.4 56.7 57.1 57.4 57.7 58.0 58.3 58.6 58.9 59.2 59.5 59.8 60.1 60.4 60.7 61.0 61.3 61.7 62.0 62.3 62.6 62.9 63.2 63.5 63.8 64.1 64.4 64.7 65.0 65.3 65.6 66.0 66.3 66.6 66.9 67.2 67.5 67.8 68.1 68.4 68.7 69.0 69.3 69.6 69.9 70.2 70.6 70.9 71.2 71.5 71.8 72.1 72.4 72.7 73.0 73.3 73.6 73.9 74.2 74.5 74.8 75.2 75.5 75.8 76.1 76.4 76.7 77.0 77.3 77.6 77.9 78.2 78.5 78.8 79.1 79.4 79.8 80.1 80.4 80.7 81.0 81.3 81.6 81.9 82.2 82.5 82.8 83.1 83.4 83.7 84.0 84.4 84.7 85.0 85.3 85.6 85.9 86.2 86.5 86.8 87.1 87.4 87.7 88.0 88.3 88.7 89.0 89.3 89.6 89.9 90.2 90.5 90.8 91.1 91.4 91.7 92.0 92.3 92.6 92.9 93.3 93.6 93.9 94.2 94.5 94.8 95.1 95.4 95.7 96.0 96.3 96.6 96.9 97.2 97.5 97.9 98.2 98.5 98.8 99.1 99.4 99.7 -found 15 predictions from path traversal Error with prediction: snap lend_intergenic: 7663, rend_intergenic: 6051 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 19520, rend_intergenic: 18022 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21546, rend_intergenic: 19883 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28523, rend_intergenic: 24714 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53546, rend_intergenic: 43492 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 57366, rend_intergenic: 53798 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68025, rend_intergenic: 57853 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 72822, rend_intergenic: 70857 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 106584, rend_intergenic: 104536 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 15 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 12843 -exon list size: 10 building trellis 8.3 16.7 25.0 33.3 41.7 50.0 58.3 66.7 75.0 83.3 91.7 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 94161 - 108197 -exon list size: 10 building trellis 8.3 16.7 25.0 33.3 41.7 50.0 58.3 66.7 75.0 83.3 91.7 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support