-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_885317-1107081 -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 Augustus_model.g26440.t1 Valid prediction for Augustus_model.g26439.t1 Valid prediction for GlimmerHMM_glimmerT_39676-T1 Valid prediction for snap_scaffold_17-snap.208-T1 Valid prediction for snap_scaffold_17-snap.177-T1 Valid prediction for snap_scaffold_17-snap.168-T1 Valid prediction for GlimmerHMM_glimmerT_39701-T1 Valid prediction for snap_scaffold_17-snap.200-T1 Valid prediction for snap_scaffold_17-snap.204-T1 Valid prediction for Augustus_model.g26443.t1 Valid prediction for snap_scaffold_17-snap.172-T1 Valid prediction for snap_scaffold_17-snap.197-T1 Valid prediction for GlimmerHMM_glimmerT_39665-T1 Valid prediction for GlimmerHMM_glimmerT_39684-T1 Valid prediction for GlimmerHMM_glimmerT_39694-T1 Valid prediction for GlimmerHMM_glimmerT_39692-T1 Valid prediction for GlimmerHMM_glimmerT_39667-T1 Valid prediction for snap_scaffold_17-snap.175-T1 Couldn't classify 189512, 189874 Sorry, prediction pasa_asmbl_18584.p1 fails validation. (TCC) AG 189512-189874 GG AGG Valid prediction for snap_scaffold_17-snap.190-T1 Valid prediction for Augustus_model.g26428.t1 Couldn't classify 213074, 213134 Sorry, prediction pasa_asmbl_18586.p1 fails validation. (ATG) CC 211414-211452 GT GCG (ACC) AG 212617-212822 GT AGG (GGC) AG 213074-213134 AC GGA -recovered pasa_asmbl_18586.p1, initial, 211414, 211452 -recovered pasa_asmbl_18586.p1, internal, 212617, 212822 Valid prediction for Augustus_model.g26438.t1 Valid prediction for snap_scaffold_17-snap.185-T1 Valid prediction for Augustus_model.g26425.t1 Valid prediction for Augustus_model.g26432.t1 Valid prediction for snap_scaffold_17-snap.167-T1 Couldn't classify 213905, 213964 Sorry, prediction pasa_asmbl_18588.p1 fails validation. (AAG) TG 213905-213964 GT ATG (ATG) AG 214545-214706 GT AGG (GTG) AG 214984-215442 TC GAT -recovered pasa_asmbl_18588.p1, initial, 214545, 214706 -recovered pasa_asmbl_18588.p1, terminal, 214984, 215442 -recovered pasa_asmbl_18588.p1, internal, 214545, 214706 Valid prediction for snap_scaffold_17-snap.192-T1 Valid prediction for snap_scaffold_17-snap.194-T1 Valid prediction for GlimmerHMM_glimmerT_39664-T1 Couldn't classify 194605, 194651 Sorry, prediction pasa_asmbl_18585.p1 fails validation. (AGC) CC 194605-194651 GT AGG (GCG) AG 194902-195006 GT AGG (GCG) AG 195070-195193 GT AGG (TCT) AG 195438-195551 GT AGG (GTG) AG 195818-195969 GT AGG (ACA) AG 196174-196306 GT ATG (GTG) AG 196676-196796 GT AGG (GTT) AG 197002-197183 AC GAA -recovered pasa_asmbl_18585.p1, terminal, 197002, 197183 -recovered pasa_asmbl_18585.p1, internal, 194902, 195006 -recovered pasa_asmbl_18585.p1, internal, 195070, 195193 -recovered pasa_asmbl_18585.p1, internal, 195438, 195551 -recovered pasa_asmbl_18585.p1, internal, 195818, 195969 -recovered pasa_asmbl_18585.p1, internal, 196174, 196306 -recovered pasa_asmbl_18585.p1, internal, 196676, 196796 Valid prediction for snap_scaffold_17-snap.202-T1 Valid prediction for Augustus_model.g26422.t1 Valid prediction for HiQ_model.g26431.t1 Valid prediction for GlimmerHMM_glimmerT_39670-T1 Valid prediction for snap_scaffold_17-snap.182-T1 Valid prediction for snap_scaffold_17-snap.174-T1 Valid prediction for snap_scaffold_17-snap.201-T1 Valid prediction for snap_scaffold_17-snap.209-T1 Valid prediction for snap_scaffold_17-snap.187-T1 Valid prediction for GlimmerHMM_glimmerT_39685-T1 Valid prediction for GlimmerHMM_glimmerT_39695-T1 Valid prediction for GlimmerHMM_glimmerT_39679-T1 Valid prediction for snap_scaffold_17-snap.186-T1 Valid prediction for snap_scaffold_17-snap.206-T1 Valid prediction for GlimmerHMM_glimmerT_39699-T1 Valid prediction for GlimmerHMM_glimmerT_39697-T1 Valid prediction for GlimmerHMM_glimmerT_39668-T1 Couldn't classify 118051, 118152 Sorry, prediction pasa_asmbl_18582.p1 fails validation. (ATT) CG 118051-118152 GT AGG (GTG) AG 118818-119090 GT GGG (CTA) AG 119352-119546 GT AGG (TTC) AG 119836-120054 GT AGG (GTG) AG 120182-120453 GT TGG (GAC) AG 120879-121053 GG GAG -recovered pasa_asmbl_18582.p1, terminal, 120879, 121053 -recovered pasa_asmbl_18582.p1, internal, 118818, 119090 -recovered pasa_asmbl_18582.p1, internal, 119352, 119546 -recovered pasa_asmbl_18582.p1, internal, 119836, 120054 -recovered pasa_asmbl_18582.p1, internal, 120182, 120453 Valid prediction for Augustus_model.g26436.t1 Valid prediction for snap_scaffold_17-snap.207-T1 Valid prediction for Augustus_model.g26442.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 Augustus_model.g26435.t1 Valid prediction for snap_scaffold_17-snap.191-T1 Valid prediction for GlimmerHMM_glimmerT_39672-T1 Couldn't classify 74235, 74348 Couldn't classify 76258, 76387 Sorry, prediction pasa_asmbl_17664.p1 fails validation. (AAC) AG 74235-74348 GT AGG (GCA) AG 74680-74847 GT AGG (AAC) AG 75123-75281 GT GGG (ATG) AG 75461-75568 GT AGG (GGA) AG 75961-76082 GT AGG (GCC) AG 76258-76387 AG AGA -recovered pasa_asmbl_17664.p1, initial, 75461, 75568 -recovered pasa_asmbl_17664.p1, internal, 74235, 74348 -recovered pasa_asmbl_17664.p1, internal, 74680, 74847 -recovered pasa_asmbl_17664.p1, internal, 75123, 75281 -recovered pasa_asmbl_17664.p1, internal, 75461, 75568 -recovered pasa_asmbl_17664.p1, internal, 75961, 76082 Couldn't classify 117178, 117531 Sorry, prediction pasa_asmbl_17659.p1 fails validation. (AGC) GG 117178-117531 AC GCA Valid prediction for Augustus_model.g26426.t1 Couldn't classify 112553, 112584 Couldn't classify 117024, 117113 Sorry, prediction pasa_asmbl_17660.p1 fails validation. (CTG) AT 112553-112584 GT AGG (GAG) AG 114133-114201 GT AGG (GAC) AG 114646-114734 GT AAG (TGT) AG 115184-115257 GT AGG (TCG) AG 115431-115474 GT AAG (GAT) AG 115638-115882 GT AGG (GTC) AG 116078-116520 GT AGG (GGA) AG 117024-117113 GG AGG -recovered pasa_asmbl_17660.p1, internal, 114133, 114201 -recovered pasa_asmbl_17660.p1, internal, 114646, 114734 -recovered pasa_asmbl_17660.p1, internal, 115184, 115257 -recovered pasa_asmbl_17660.p1, internal, 115431, 115474 -recovered pasa_asmbl_17660.p1, internal, 115638, 115882 -recovered pasa_asmbl_17660.p1, internal, 116078, 116520 Couldn't classify 20239, 20364 Sorry, prediction CodingQuarry_transcript_21839-T1 fails validation. (ATG) GG 16869-17648 GT AGG (GCA) AG 18224-18281 GT AGG (GAG) AG 18605-18669 GT AGG (AAC) AG 19027-19185 GT AGG (AGT) AG 19334-19436 GT AGG (GGC) AG 19572-19714 GT AGG (GGT) AG 19781-19975 GT AGG (GAC) AG 20239-20364 CA AGC (GGC) AG 20398-20424 GT AGG (GTC) AG 20531-20605 AC AGA -recovered CodingQuarry_transcript_21839-T1, initial, 16869, 17648 add_exon() Sorry, CodingQuarry_transcript_21839-T1 18224-18281-terminal-3 is invalid. -recovered CodingQuarry_transcript_21839-T1, terminal, 18224, 18281 -recovered CodingQuarry_transcript_21839-T1, terminal, 20531, 20605 -recovered CodingQuarry_transcript_21839-T1, internal, 18224, 18281 -recovered CodingQuarry_transcript_21839-T1, internal, 18605, 18669 -recovered CodingQuarry_transcript_21839-T1, internal, 19027, 19185 -recovered CodingQuarry_transcript_21839-T1, internal, 19334, 19436 -recovered CodingQuarry_transcript_21839-T1, internal, 19572, 19714 -recovered CodingQuarry_transcript_21839-T1, internal, 19781, 19975 -recovered CodingQuarry_transcript_21839-T1, internal, 20398, 20424 Valid prediction for Augustus_model.g26434.t1 Valid prediction for Augustus_model.g26423.t1 Valid prediction for GlimmerHMM_glimmerT_39686-T1 Valid prediction for GlimmerHMM_glimmerT_39682-T1 Valid prediction for snap_scaffold_17-snap.199-T1 Valid prediction for snap_scaffold_17-snap.183-T1 Valid prediction for snap_scaffold_17-snap.188-T1 Valid prediction for GlimmerHMM_glimmerT_39687-T1 Valid prediction for GlimmerHMM_glimmerT_39688-T1 Valid prediction for GlimmerHMM_glimmerT_39678-T1 Valid prediction for GlimmerHMM_glimmerT_39680-T1 Valid prediction for snap_scaffold_17-snap.181-T1 Valid prediction for snap_scaffold_17-snap.205-T1 Valid prediction for pasa_asmbl_17672.p1 Valid prediction for GlimmerHMM_glimmerT_39683-T1 Valid prediction for GlimmerHMM_glimmerT_39700-T1 Couldn't classify 72098, 72166 Sorry, prediction pasa_asmbl_17666.p1 fails validation. (ATG) AG 71024-71116 GT CGG (ACC) AG 71273-71407 GT AGG (GAG) AG 71531-71591 GT CTG (ACT) AG 71732-71811 GT AGG (GAG) AG 72098-72166 GT GGG -recovered pasa_asmbl_17666.p1, initial, 71024, 71116 -recovered pasa_asmbl_17666.p1, internal, 71024, 71116 -recovered pasa_asmbl_17666.p1, internal, 71273, 71407 -recovered pasa_asmbl_17666.p1, internal, 71531, 71591 -recovered pasa_asmbl_17666.p1, internal, 71732, 71811 -recovered pasa_asmbl_17666.p1, internal, 72098, 72166 Valid prediction for GlimmerHMM_glimmerT_39698-T1 Valid prediction for CodingQuarry_transcript_21838-T1 Valid prediction for Augustus_model.g26430.t1 Valid prediction for Augustus_model.g26421.t1 Valid prediction for GlimmerHMM_glimmerT_39690-T1 Valid prediction for snap_scaffold_17-snap.203-T1 Couldn't classify 117591, 117836 Sorry, prediction pasa_asmbl_17658.p1 fails validation. (CCA) AT 117591-117836 GT AGG (AGT) AG 118474-118557 GT AGG (TTG) AG 118656-118845 GT AAG (TGT) AG 118995-119164 CC GAC -recovered pasa_asmbl_17658.p1, terminal, 118995, 119164 -recovered pasa_asmbl_17658.p1, internal, 118474, 118557 -recovered pasa_asmbl_17658.p1, internal, 118656, 118845 Valid prediction for snap_scaffold_17-snap.173-T1 Valid prediction for Augustus_model.g26437.t1 Valid prediction for GlimmerHMM_glimmerT_39669-T1 Valid prediction for HiQ_model.g26441.t1 Valid prediction for snap_scaffold_17-snap.198-T1 Valid prediction for Augustus_model.g26433.t1 Valid prediction for snap_scaffold_17-snap.169-T1 Valid prediction for snap_scaffold_17-snap.196-T1 Valid prediction for GlimmerHMM_glimmerT_39696-T1 Valid prediction for pasa_asmbl_17671.p1 Valid prediction for GlimmerHMM_glimmerT_39673-T1 Valid prediction for GlimmerHMM_glimmerT_39671-T1 Valid prediction for snap_scaffold_17-snap.184-T1 Valid prediction for snap_scaffold_17-snap.180-T1 Valid prediction for Augustus_model.g26427.t1 Valid prediction for GlimmerHMM_glimmerT_39681-T1 Valid prediction for Augustus_model.g26429.t1 Valid prediction for snap_scaffold_17-snap.176-T1 Valid prediction for snap_scaffold_17-snap.171-T1 Valid prediction for GlimmerHMM_glimmerT_39693-T1 Valid prediction for snap_scaffold_17-snap.189-T1 Valid prediction for GlimmerHMM_glimmerT_39691-T1 Couldn't classify 125855, 126160 Sorry, prediction pasa_asmbl_18581.p1 fails validation. (ATG) AG 125855-126160 GA CCG Valid prediction for snap_scaffold_17-snap.178-T1 Valid prediction for snap_scaffold_17-snap.195-T1 Valid prediction for GlimmerHMM_glimmerT_39675-T1 Valid prediction for GlimmerHMM_glimmerT_39666-T1 Valid prediction for Augustus_model.g26424.t1 Valid prediction for snap_scaffold_17-snap.193-T1 Valid prediction for snap_scaffold_17-snap.170-T1 Couldn't classify 124485, 124583 Sorry, prediction GlimmerHMM_glimmerT_39677-T1 fails validation. (ATG) CT 123411-123504 GT CGG (CTG) AG 123519-123700 GT GGG (GAA) AG 123959-124195 GT ATG (GCC) AG 124485-124583 NN ANN -recovered GlimmerHMM_glimmerT_39677-T1, initial, 123411, 123504 -recovered GlimmerHMM_glimmerT_39677-T1, internal, 123519, 123700 -recovered GlimmerHMM_glimmerT_39677-T1, internal, 123959, 124195 Couldn't classify 154317, 155342 Sorry, prediction pasa_asmbl_17655.p1 fails validation. (CAG) AC 154317-155342 GA AGG Valid prediction for snap_scaffold_17-snap.179-T1 Valid prediction for GlimmerHMM_glimmerT_39689-T1 Valid prediction for GlimmerHMM_glimmerT_39674-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 47248, rend_intergenic: 39874 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47901, rend_intergenic: 47631 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51119, rend_intergenic: 49005 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 130020, rend_intergenic: 126136 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140587, rend_intergenic: 133105 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 167899, rend_intergenic: 161548 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192303, rend_intergenic: 189864 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 204897, rend_intergenic: 200476 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 221765 -exon list size: 481 building trellis 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.7 1.9 2.1 2.3 2.5 2.7 2.9 3.1 3.3 3.5 3.7 3.9 4.1 4.3 4.6 4.8 5.0 5.2 5.4 5.6 5.8 6.0 6.2 6.4 6.6 6.8 7.0 7.2 7.5 7.7 7.9 8.1 8.3 8.5 8.7 8.9 9.1 9.3 9.5 9.7 9.9 10.1 10.4 10.6 10.8 11.0 11.2 11.4 11.6 11.8 12.0 12.2 12.4 12.6 12.8 13.0 13.3 13.5 13.7 13.9 14.1 14.3 14.5 14.7 14.9 15.1 15.3 15.5 15.7 15.9 16.1 16.4 16.6 16.8 17.0 17.2 17.4 17.6 17.8 18.0 18.2 18.4 18.6 18.8 19.0 19.3 19.5 19.7 19.9 20.1 20.3 20.5 20.7 20.9 21.1 21.3 21.5 21.7 21.9 22.2 22.4 22.6 22.8 23.0 23.2 23.4 23.6 23.8 24.0 24.2 24.4 24.6 24.8 25.1 25.3 25.5 25.7 25.9 26.1 26.3 26.5 26.7 26.9 27.1 27.3 27.5 27.7 28.0 28.2 28.4 28.6 28.8 29.0 29.2 29.4 29.6 29.8 30.0 30.2 30.4 30.6 30.8 31.1 31.3 31.5 31.7 31.9 32.1 32.3 32.5 32.7 32.9 33.1 33.3 33.5 33.7 34.0 34.2 34.4 34.6 34.8 35.0 35.2 35.4 35.6 35.8 36.0 36.2 36.4 36.6 36.9 37.1 37.3 37.5 37.7 37.9 38.1 38.3 38.5 38.7 38.9 39.1 39.3 39.5 39.8 40.0 40.2 40.4 40.6 40.8 41.0 41.2 41.4 41.6 41.8 42.0 42.2 42.4 42.7 42.9 43.1 43.3 43.5 43.7 43.9 44.1 44.3 44.5 44.7 44.9 45.1 45.3 45.5 45.8 46.0 46.2 46.4 46.6 46.8 47.0 47.2 47.4 47.6 47.8 48.0 48.2 48.4 48.7 48.9 49.1 49.3 49.5 49.7 49.9 50.1 50.3 50.5 50.7 50.9 51.1 51.3 51.6 51.8 52.0 52.2 52.4 52.6 52.8 53.0 53.2 53.4 53.6 53.8 54.0 54.2 54.5 54.7 54.9 55.1 55.3 55.5 55.7 55.9 56.1 56.3 56.5 56.7 56.9 57.1 57.3 57.6 57.8 58.0 58.2 58.4 58.6 58.8 59.0 59.2 59.4 59.6 59.8 60.0 60.2 60.5 60.7 60.9 61.1 61.3 61.5 61.7 61.9 62.1 62.3 62.5 62.7 62.9 63.1 63.4 63.6 63.8 64.0 64.2 64.4 64.6 64.8 65.0 65.2 65.4 65.6 65.8 66.0 66.3 66.5 66.7 66.9 67.1 67.3 67.5 67.7 67.9 68.1 68.3 68.5 68.7 68.9 69.2 69.4 69.6 69.8 70.0 70.2 70.4 70.6 70.8 71.0 71.2 71.4 71.6 71.8 72.0 72.3 72.5 72.7 72.9 73.1 73.3 73.5 73.7 73.9 74.1 74.3 74.5 74.7 74.9 75.2 75.4 75.6 75.8 76.0 76.2 76.4 76.6 76.8 77.0 77.2 77.4 77.6 77.8 78.1 78.3 78.5 78.7 78.9 79.1 79.3 79.5 79.7 79.9 80.1 80.3 80.5 80.7 81.0 81.2 81.4 81.6 81.8 82.0 82.2 82.4 82.6 82.8 83.0 83.2 83.4 83.6 83.9 84.1 84.3 84.5 84.7 84.9 85.1 85.3 85.5 85.7 85.9 86.1 86.3 86.5 86.7 87.0 87.2 87.4 87.6 87.8 88.0 88.2 88.4 88.6 88.8 89.0 89.2 89.4 89.6 89.9 90.1 90.3 90.5 90.7 90.9 91.1 91.3 91.5 91.7 91.9 92.1 92.3 92.5 92.8 93.0 93.2 93.4 93.6 93.8 94.0 94.2 94.4 94.6 94.8 95.0 95.2 95.4 95.7 95.9 96.1 96.3 96.5 96.7 96.9 97.1 97.3 97.5 97.7 97.9 98.1 98.3 98.6 98.8 99.0 99.2 99.4 99.6 99.8 -found 36 predictions from path traversal Error with prediction: snap lend_intergenic: 47248, rend_intergenic: 39874 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47901, rend_intergenic: 47631 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51119, rend_intergenic: 49005 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 130020, rend_intergenic: 126136 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140587, rend_intergenic: 133105 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 167899, rend_intergenic: 161548 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192303, rend_intergenic: 189864 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 204897, rend_intergenic: 200476 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 31 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 10973 -exon list size: 6 building trellis 12.5 25.0 37.5 50.0 62.5 75.0 87.5 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support