-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_7013718-7204401 -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 GlimmerHMM_glimmerT_29520-T1 Valid prediction for snap_scaffold_12-snap.1303-T1 Valid prediction for GlimmerHMM_glimmerT_29522-T1 Valid prediction for snap_scaffold_12-snap.1287-T1 Valid prediction for HiQ_model.g19465.t1 Valid prediction for GlimmerHMM_glimmerT_29503-T1 Valid prediction for snap_scaffold_12-snap.1275-T1 Valid prediction for pasa_asmbl_7721.p1 Valid prediction for GlimmerHMM_glimmerT_29495-T1 Valid prediction for CodingQuarry_transcript_10265-T1 Couldn't classify 16374, 16739 Sorry, prediction pasa_asmbl_7708.p2 fails validation. (ATG) AG 16374-16739 AC ACA Valid prediction for snap_scaffold_12-snap.1294-T1 Valid prediction for GlimmerHMM_glimmerT_29509-T1 Valid prediction for Augustus_model.g19476.t1 Valid prediction for Augustus_model.g19455.t1 Couldn't classify 94925, 95208 Sorry, prediction pasa_asmbl_7713.p1 fails validation. (GAA) TG 94925-95208 GT GAG (AGA) AG 95558-95723 GT CCG (GTG) AG 96014-96217 GC AGG (GAG) AG 96355-96583 GT AGG (CGA) AG 96810-96992 GT TGG (GTG) AG 97120-97236 GT ACG (AAT) AG 97351-97422 GT AGG (ATA) AG 97521-97606 GT AAG (GTG) AG 97751-97912 GT ATG (ATC) AG 98046-98190 GT TAG (GCT) AG 98349-98500 GT AGG (AAC) AG 99443-99625 GT AGG (GTC) AG 99890-100045 GA GAG add_exon() Sorry, pasa_asmbl_7713.p1 97351-97422-terminal-1 is invalid. -recovered pasa_asmbl_7713.p1, terminal, 97351, 97422 -recovered pasa_asmbl_7713.p1, terminal, 99890, 100045 -recovered pasa_asmbl_7713.p1, internal, 95558, 95723 -recovered pasa_asmbl_7713.p1, internal, 96014, 96217 -recovered pasa_asmbl_7713.p1, internal, 96355, 96583 -recovered pasa_asmbl_7713.p1, internal, 96810, 96992 -recovered pasa_asmbl_7713.p1, internal, 97120, 97236 -recovered pasa_asmbl_7713.p1, internal, 97351, 97422 -recovered pasa_asmbl_7713.p1, internal, 97521, 97606 -recovered pasa_asmbl_7713.p1, internal, 97751, 97912 -recovered pasa_asmbl_7713.p1, internal, 98046, 98190 -recovered pasa_asmbl_7713.p1, internal, 98349, 98500 -recovered pasa_asmbl_7713.p1, internal, 99443, 99625 Valid prediction for GlimmerHMM_glimmerT_29502-T1 Valid prediction for Augustus_model.g19457.t1 Valid prediction for snap_scaffold_12-snap.1279-T1 Valid prediction for GlimmerHMM_glimmerT_29508-T1 Valid prediction for Augustus_model.g19467.t1 Valid prediction for Augustus_model.g19458.t1 Valid prediction for snap_scaffold_12-snap.1297-T1 Couldn't classify 82331, 82493 Couldn't classify 83060, 83207 Sorry, prediction pasa_asmbl_7710.p1 fails validation. (GGC) AT 82331-82493 AT CAA (AGT) AC 83060-83207 GT AAG (GAA) AG 83342-83498 GT GAG (GCT) AG 84124-84252 GT AAG (AAC) AG 84423-84542 GT AGG (TTG) AG 84750-84853 GT AGG (ACT) AG 84983-85129 GT GAG (CAG) AG 85255-85374 GT AGG (GAG) AG 85555-85632 GT TTG (GGT) AG 86414-86453 GT AGG (ACG) AG 86642-86808 GT AGG (CAG) AG 87031-87651 GT AGG (TGC) AG 87813-87969 AG GAA -recovered pasa_asmbl_7710.p1, terminal, 87813, 87969 -recovered pasa_asmbl_7710.p1, internal, 83342, 83498 -recovered pasa_asmbl_7710.p1, internal, 84124, 84252 -recovered pasa_asmbl_7710.p1, internal, 84423, 84542 -recovered pasa_asmbl_7710.p1, internal, 84750, 84853 -recovered pasa_asmbl_7710.p1, internal, 84983, 85129 -recovered pasa_asmbl_7710.p1, internal, 85255, 85374 -recovered pasa_asmbl_7710.p1, internal, 85555, 85632 -recovered pasa_asmbl_7710.p1, internal, 86414, 86453 -recovered pasa_asmbl_7710.p1, internal, 86642, 86808 -recovered pasa_asmbl_7710.p1, internal, 87031, 87651 Valid prediction for snap_scaffold_12-snap.1281-T1 Valid prediction for snap_scaffold_12-snap.1300-T1 Valid prediction for Augustus_model.g19459.t1 Valid prediction for snap_scaffold_12-snap.1293-T1 Valid prediction for snap_scaffold_12-snap.1276-T1 Valid prediction for snap_scaffold_12-snap.1286-T1 Valid prediction for snap_scaffold_12-snap.1288-T1 Valid prediction for snap_scaffold_12-snap.1265-T1 Valid prediction for GlimmerHMM_glimmerT_29497-T1 Valid prediction for snap_scaffold_12-snap.1264-T1 Valid prediction for Augustus_model.g19464.t1 Valid prediction for GlimmerHMM_glimmerT_29499-T1 Valid prediction for Augustus_model.g19460.t1 Valid prediction for snap_scaffold_12-snap.1290-T1 Valid prediction for CodingQuarry_transcript_10262-T1 Couldn't classify 134589, 136304 Sorry, prediction pasa_asmbl_7719.p1 fails validation. (CGG) AC 134589-136304 CA AGC Valid prediction for Augustus_model.g19456.t1 Valid prediction for Augustus_model.g19468.t1 Valid prediction for snap_scaffold_12-snap.1268-T1 Valid prediction for GlimmerHMM_glimmerT_29514-T1 Valid prediction for snap_scaffold_12-snap.1285-T1 Couldn't classify 132864, 132871 Sorry, prediction pasa_asmbl_7718.p1 fails validation. (ATC) AG 132864-132871 GT TGG (TGC) AG 132988-133044 GT AGG (CTA) AG 133198-133324 GT AGG (GAT) AG 133407-133559 TG GAT -recovered pasa_asmbl_7718.p1, terminal, 133407, 133559 -recovered pasa_asmbl_7718.p1, internal, 132864, 132871 -recovered pasa_asmbl_7718.p1, internal, 132988, 133044 -recovered pasa_asmbl_7718.p1, internal, 133198, 133324 Couldn't classify 99362, 99625 Sorry, prediction pasa_asmbl_7715.p1 fails validation. (CTC) CT 99362-99625 GT AGG (GTC) AG 99890-100045 GA GAG -recovered pasa_asmbl_7715.p1, terminal, 99890, 100045 Valid prediction for pasa_asmbl_7717.p1 Valid prediction for snap_scaffold_12-snap.1282-T1 Valid prediction for CodingQuarry_transcript_10263-T1 Valid prediction for Augustus_model.g19472.t1 Valid prediction for GlimmerHMM_glimmerT_29513-T1 Couldn't classify 121798, 122265 Sorry, prediction pasa_asmbl_7716.p1 fails validation. (CCT) GC 121798-122265 TC GAT Valid prediction for snap_scaffold_12-snap.1306-T1 Valid prediction for GlimmerHMM_glimmerT_29512-T1 Couldn't classify 39821, 39909 Couldn't classify 41358, 41503 Sorry, prediction pasa_asmbl_8218.p2 fails validation. (TCC) GC 39821-39909 GT AGG (GGT) AG 40916-41043 GT AGG (CCC) AG 41358-41503 GA GTG -recovered pasa_asmbl_8218.p2, internal, 40916, 41043 Valid prediction for snap_scaffold_12-snap.1267-T1 Valid prediction for CodingQuarry_transcript_10261-T1 Valid prediction for GlimmerHMM_glimmerT_29507-T1 Valid prediction for GlimmerHMM_glimmerT_29511-T1 Valid prediction for pasa_asmbl_7709.p1 Valid prediction for GlimmerHMM_glimmerT_29519-T1 Valid prediction for GlimmerHMM_glimmerT_29504-T1 Valid prediction for Augustus_model.g19466.t1 Valid prediction for Augustus_model.g19462.t1 Valid prediction for HiQ_model.g19471.t1 Couldn't classify 90869, 91001 Couldn't classify 92556, 92612 Sorry, prediction pasa_asmbl_7712.p1 fails validation. (TTC) TC 90869-91001 GT AGG (GGC) AG 91221-91324 GT AGG (GTA) AG 91416-91536 GT CGG (AGG) AG 91737-92028 GT AAG (GTT) AG 92232-92397 GT AGG (ATT) AG 92556-92612 AA CCA -recovered pasa_asmbl_7712.p1, internal, 91221, 91324 -recovered pasa_asmbl_7712.p1, internal, 91416, 91536 -recovered pasa_asmbl_7712.p1, internal, 91737, 92028 -recovered pasa_asmbl_7712.p1, internal, 92232, 92397 Valid prediction for Augustus_model.g19453.t1 Valid prediction for GlimmerHMM_glimmerT_29498-T1 Valid prediction for GlimmerHMM_glimmerT_29524-T1 Valid prediction for HiQ_model.g19474.t1 Valid prediction for GlimmerHMM_glimmerT_29506-T1 Valid prediction for snap_scaffold_12-snap.1280-T1 Valid prediction for snap_scaffold_12-snap.1278-T1 Valid prediction for GlimmerHMM_glimmerT_29496-T1 Valid prediction for GlimmerHMM_glimmerT_29505-T1 Valid prediction for snap_scaffold_12-snap.1269-T1 Valid prediction for Augustus_model.g19461.t1 Valid prediction for snap_scaffold_12-snap.1295-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_12-snap.1305-T1 Valid prediction for Augustus_model.g19475.t1 Valid prediction for snap_scaffold_12-snap.1296-T1 Valid prediction for GlimmerHMM_glimmerT_29518-T1 Valid prediction for snap_scaffold_12-snap.1298-T1 Valid prediction for snap_scaffold_12-snap.1263-T1 Valid prediction for snap_scaffold_12-snap.1291-T1 Valid prediction for snap_scaffold_12-snap.1289-T1 Valid prediction for snap_scaffold_12-snap.1262-T1 Valid prediction for snap_scaffold_12-snap.1274-T1 Valid prediction for Augustus_model.g19452.t1 Valid prediction for snap_scaffold_12-snap.1270-T1 Valid prediction for Augustus_model.g19463.t1 Valid prediction for HiQ_model.g19469.t1 Valid prediction for GlimmerHMM_glimmerT_29515-T1 Valid prediction for GlimmerHMM_glimmerT_29500-T1 Valid prediction for snap_scaffold_12-snap.1272-T1 Valid prediction for snap_scaffold_12-snap.1266-T1 Valid prediction for snap_scaffold_12-snap.1283-T1 Valid prediction for GlimmerHMM_glimmerT_29510-T1 Valid prediction for snap_scaffold_12-snap.1273-T1 Couldn't classify 26673, 26723 Sorry, prediction pasa_asmbl_8559.p1 fails validation. (AGA) AC 26673-26723 GT AGG (TAT) AG 27049-27156 GT AGG (TAC) AG 27377-27508 GT TGG (GAT) AG 27781-27827 GT CGG (GCC) AG 27921-28045 GT AGG (GCT) AG 28290-28396 GT ATG (GAA) AG 28557-28772 GT AGG (CTG) AG 28854-28978 GT AGG (GTT) AG 29163-29304 GT AGG (GTG) AG 29466-29645 TC GAT -recovered pasa_asmbl_8559.p1, terminal, 29466, 29645 -recovered pasa_asmbl_8559.p1, internal, 27049, 27156 -recovered pasa_asmbl_8559.p1, internal, 27377, 27508 -recovered pasa_asmbl_8559.p1, internal, 27781, 27827 -recovered pasa_asmbl_8559.p1, internal, 27921, 28045 -recovered pasa_asmbl_8559.p1, internal, 28290, 28396 -recovered pasa_asmbl_8559.p1, internal, 28557, 28772 -recovered pasa_asmbl_8559.p1, internal, 28854, 28978 -recovered pasa_asmbl_8559.p1, internal, 29163, 29304 Valid prediction for CodingQuarry_transcript_10264-T1 Valid prediction for GlimmerHMM_glimmerT_29517-T1 Valid prediction for Augustus_model.g19477.t1 Valid prediction for snap_scaffold_12-snap.1284-T1 Valid prediction for snap_scaffold_12-snap.1304-T1 Couldn't classify 32934, 32971 Sorry, prediction pasa_asmbl_8557.p1 fails validation. (GCA) AA 32934-32971 GT GTG (CCT) AG 33505-33665 GT AGG (GTG) AG 33769-34070 GT AAG (AGA) AG 34306-34398 GT AGG (GGT) AG 34518-34602 GT CAG (TCT) AG 34764-34898 GT GAG (CCC) AG 35026-35157 GT CGG (GTC) AG 35421-35533 GT ACG (GAC) AG 35656-35737 GT GGG (GAA) AG 35933-36018 CG GAC -recovered pasa_asmbl_8557.p1, terminal, 35933, 36018 -recovered pasa_asmbl_8557.p1, internal, 33505, 33665 -recovered pasa_asmbl_8557.p1, internal, 33769, 34070 -recovered pasa_asmbl_8557.p1, internal, 34306, 34398 -recovered pasa_asmbl_8557.p1, internal, 34518, 34602 -recovered pasa_asmbl_8557.p1, internal, 34764, 34898 -recovered pasa_asmbl_8557.p1, internal, 35026, 35157 -recovered pasa_asmbl_8557.p1, internal, 35421, 35533 -recovered pasa_asmbl_8557.p1, internal, 35656, 35737 Valid prediction for GlimmerHMM_glimmerT_29525-T1 Valid prediction for snap_scaffold_12-snap.1271-T1 Valid prediction for snap_scaffold_12-snap.1302-T1 Valid prediction for snap_scaffold_12-snap.1301-T1 Valid prediction for GlimmerHMM_glimmerT_29523-T1 Valid prediction for Augustus_model.g19454.t1 Valid prediction for snap_scaffold_12-snap.1299-T1 Valid prediction for snap_scaffold_12-snap.1277-T1 Valid prediction for HiQ_model.g19473.t1 Valid prediction for GlimmerHMM_glimmerT_29516-T1 Valid prediction for GlimmerHMM_glimmerT_29494-T1 Valid prediction for GlimmerHMM_glimmerT_29501-T1 Valid prediction for Augustus_model.g19470.t1 Valid prediction for pasa_asmbl_8556.p1 Valid prediction for GlimmerHMM_glimmerT_29521-T1 Valid prediction for snap_scaffold_12-snap.1292-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55611, rend_intergenic: 36070 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87969, rend_intergenic: 82187 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133559, rend_intergenic: 130463 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 142908, rend_intergenic: 139399 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 152750, rend_intergenic: 149616 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179421, rend_intergenic: 174213 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 182267, rend_intergenic: 180881 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 190684 -exon list size: 429 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 3.2 3.5 3.7 3.9 4.2 4.4 4.6 4.9 5.1 5.3 5.6 5.8 6.0 6.3 6.5 6.7 7.0 7.2 7.4 7.7 7.9 8.1 8.4 8.6 8.8 9.0 9.3 9.5 9.7 10.0 10.2 10.4 10.7 10.9 11.1 11.4 11.6 11.8 12.1 12.3 12.5 12.8 13.0 13.2 13.5 13.7 13.9 14.2 14.4 14.6 14.8 15.1 15.3 15.5 15.8 16.0 16.2 16.5 16.7 16.9 17.2 17.4 17.6 17.9 18.1 18.3 18.6 18.8 19.0 19.3 19.5 19.7 20.0 20.2 20.4 20.6 20.9 21.1 21.3 21.6 21.8 22.0 22.3 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 27.1 27.4 27.6 27.8 28.1 28.3 28.5 28.8 29.0 29.2 29.5 29.7 29.9 30.2 30.4 30.6 30.9 31.1 31.3 31.6 31.8 32.0 32.3 32.5 32.7 32.9 33.2 33.4 33.6 33.9 34.1 34.3 34.6 34.8 35.0 35.3 35.5 35.7 36.0 36.2 36.4 36.7 36.9 37.1 37.4 37.6 37.8 38.1 38.3 38.5 38.7 39.0 39.2 39.4 39.7 39.9 40.1 40.4 40.6 40.8 41.1 41.3 41.5 41.8 42.0 42.2 42.5 42.7 42.9 43.2 43.4 43.6 43.9 44.1 44.3 44.5 44.8 45.0 45.2 45.5 45.7 45.9 46.2 46.4 46.6 46.9 47.1 47.3 47.6 47.8 48.0 48.3 48.5 48.7 49.0 49.2 49.4 49.7 49.9 50.1 50.3 50.6 50.8 51.0 51.3 51.5 51.7 52.0 52.2 52.4 52.7 52.9 53.1 53.4 53.6 53.8 54.1 54.3 54.5 54.8 55.0 55.2 55.5 55.7 55.9 56.1 56.4 56.6 56.8 57.1 57.3 57.5 57.8 58.0 58.2 58.5 58.7 58.9 59.2 59.4 59.6 59.9 60.1 60.3 60.6 60.8 61.0 61.3 61.5 61.7 61.9 62.2 62.4 62.6 62.9 63.1 63.3 63.6 63.8 64.0 64.3 64.5 64.7 65.0 65.2 65.4 65.7 65.9 66.1 66.4 66.6 66.8 67.1 67.3 67.5 67.7 68.0 68.2 68.4 68.7 68.9 69.1 69.4 69.6 69.8 70.1 70.3 70.5 70.8 71.0 71.2 71.5 71.7 71.9 72.2 72.4 72.6 72.9 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 77.7 78.0 78.2 78.4 78.7 78.9 79.1 79.4 79.6 79.8 80.0 80.3 80.5 80.7 81.0 81.2 81.4 81.7 81.9 82.1 82.4 82.6 82.8 83.1 83.3 83.5 83.8 84.0 84.2 84.5 84.7 84.9 85.2 85.4 85.6 85.8 86.1 86.3 86.5 86.8 87.0 87.2 87.5 87.7 87.9 88.2 88.4 88.6 88.9 89.1 89.3 89.6 89.8 90.0 90.3 90.5 90.7 91.0 91.2 91.4 91.6 91.9 92.1 92.3 92.6 92.8 93.0 93.3 93.5 93.7 94.0 94.2 94.4 94.7 94.9 95.1 95.4 95.6 95.8 96.1 96.3 96.5 96.8 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 35 predictions from path traversal Error with prediction: snap lend_intergenic: 55611, rend_intergenic: 36070 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87969, rend_intergenic: 82187 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133559, rend_intergenic: 130463 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 142908, rend_intergenic: 139399 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 152750, rend_intergenic: 149616 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179421, rend_intergenic: 174213 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 182267, rend_intergenic: 180881 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