-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_7575262-7725276 -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_49777-T1 Valid prediction for GlimmerHMM_glimmerT_49780-T1 Valid prediction for GlimmerHMM_glimmerT_49761-T1 Valid prediction for GlimmerHMM_glimmerT_49785-T1 Valid prediction for Augustus_model.g33215.t1 Valid prediction for HiQ_model.g33212.t1 Valid prediction for GlimmerHMM_glimmerT_49765-T1 Valid prediction for snap_scaffold_22-snap.1501-T1 Couldn't classify 25375, 25522 Couldn't classify 26729, 26824 Couldn't classify 27039, 27192 Sorry, prediction CodingQuarry_transcript_34213-T1 fails validation. (ATG) TC 21491-21515 GT AGG (GTG) AG 21790-21909 GT GGG (AGA) AG 22226-22312 GT AGG (AGA) AG 22951-23038 GT AGG (TTG) AG 23585-23663 GT AGG (GAC) AG 24138-24219 GT AGG (ACA) AG 24422-24507 GT AGG (GCG) AG 24637-24729 GT AGG (CTG) AG 24957-25187 GT CGG (GGC) CA 25375-25522 GT AGG (GTA) AG 26049-26199 GT AAG (TGA) AG 26729-26824 GA AGG (GTT) GT 27039-27192 GT AGG (AGT) AG 27343-27525 GT CCG (GTG) AG 27744-27878 GT AGG (GAG) AG 28075-28254 GT AGG (CAC) AG 28652-28798 GT GGG (AAG) AG 29228-29293 GT TGG (GGT) AG 29412-29570 GT AGG (TCC) AG 29963-30121 AC AAA -recovered CodingQuarry_transcript_34213-T1, initial, 21491, 21515 -recovered CodingQuarry_transcript_34213-T1, terminal, 29963, 30121 -recovered CodingQuarry_transcript_34213-T1, internal, 21790, 21909 -recovered CodingQuarry_transcript_34213-T1, internal, 22226, 22312 -recovered CodingQuarry_transcript_34213-T1, internal, 22951, 23038 -recovered CodingQuarry_transcript_34213-T1, internal, 23585, 23663 -recovered CodingQuarry_transcript_34213-T1, internal, 24138, 24219 -recovered CodingQuarry_transcript_34213-T1, internal, 24422, 24507 -recovered CodingQuarry_transcript_34213-T1, internal, 24637, 24729 -recovered CodingQuarry_transcript_34213-T1, internal, 24957, 25187 -recovered CodingQuarry_transcript_34213-T1, internal, 26049, 26199 -recovered CodingQuarry_transcript_34213-T1, internal, 27343, 27525 -recovered CodingQuarry_transcript_34213-T1, internal, 27744, 27878 -recovered CodingQuarry_transcript_34213-T1, internal, 28075, 28254 -recovered CodingQuarry_transcript_34213-T1, internal, 28652, 28798 -recovered CodingQuarry_transcript_34213-T1, internal, 29228, 29293 -recovered CodingQuarry_transcript_34213-T1, internal, 29412, 29570 Valid prediction for snap_scaffold_22-snap.1511-T1 Valid prediction for snap_scaffold_22-snap.1528-T1 Valid prediction for GlimmerHMM_glimmerT_49786-T1 Valid prediction for snap_scaffold_22-snap.1521-T1 Valid prediction for GlimmerHMM_glimmerT_49776-T1 Valid prediction for snap_scaffold_22-snap.1502-T1 Valid prediction for snap_scaffold_22-snap.1526-T1 Valid prediction for GlimmerHMM_glimmerT_49778-T1 Valid prediction for GlimmerHMM_glimmerT_49772-T1 Couldn't classify 103603, 103860 Couldn't classify 109300, 109456 Sorry, prediction pasa_asmbl_30209.p1 fails validation. (GTC) AG 103603-103860 GT CGG (GAG) AG 104775-104844 GT AGG (GTG) AG 105287-105405 GT AGG (TTC) AG 107687-107820 GT AAG (ACT) AG 109300-109456 TC GCT -recovered pasa_asmbl_30209.p1, terminal, 104775, 104844 -recovered pasa_asmbl_30209.p1, internal, 103603, 103860 -recovered pasa_asmbl_30209.p1, internal, 104775, 104844 -recovered pasa_asmbl_30209.p1, internal, 105287, 105405 -recovered pasa_asmbl_30209.p1, internal, 107687, 107820 Valid prediction for snap_scaffold_22-snap.1513-T1 Valid prediction for snap_scaffold_22-snap.1532-T1 Valid prediction for snap_scaffold_22-snap.1523-T1 Valid prediction for snap_scaffold_22-snap.1517-T1 Valid prediction for snap_scaffold_22-snap.1525-T1 Valid prediction for GlimmerHMM_glimmerT_49779-T1 Valid prediction for GlimmerHMM_glimmerT_49768-T1 Valid prediction for snap_scaffold_22-snap.1514-T1 Valid prediction for snap_scaffold_22-snap.1534-T1 Couldn't classify 113465, 113676 Sorry, prediction pasa_asmbl_30213.p1 fails validation. (TTC) AG 113465-113676 GT GTG (GGA) AG 114096-114135 GT AGG (GTA) AG 114320-114385 GT CGG (GAC) AG 114483-114540 GT ACG (ACA) AG 114726-114790 GT ATG (ACC) AG 115358-115426 GT TGG (ACG) AG 115867-115945 GT AGG (GCT) AG 116284-116400 GT CAG (AGA) AG 118457-118515 GT AGG (TGG) AG 118616-118642 AG GAA -recovered pasa_asmbl_30213.p1, terminal, 118616, 118642 -recovered pasa_asmbl_30213.p1, internal, 113465, 113676 -recovered pasa_asmbl_30213.p1, internal, 114096, 114135 -recovered pasa_asmbl_30213.p1, internal, 114320, 114385 -recovered pasa_asmbl_30213.p1, internal, 114483, 114540 -recovered pasa_asmbl_30213.p1, internal, 114726, 114790 -recovered pasa_asmbl_30213.p1, internal, 115358, 115426 -recovered pasa_asmbl_30213.p1, internal, 115867, 115945 -recovered pasa_asmbl_30213.p1, internal, 116284, 116400 -recovered pasa_asmbl_30213.p1, internal, 118457, 118515 Valid prediction for Augustus_model.g33205.t1 Valid prediction for snap_scaffold_22-snap.1516-T1 Valid prediction for snap_scaffold_22-snap.1522-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for snap_scaffold_22-snap.1507-T1 Valid prediction for snap_scaffold_22-snap.1509-T1 Valid prediction for GlimmerHMM_glimmerT_49762-T1 Valid prediction for snap_scaffold_22-snap.1518-T1 Valid prediction for Augustus_model.g33213.t1 Valid prediction for CodingQuarry_transcript_34212-T1 Valid prediction for GlimmerHMM_glimmerT_49764-T1 Valid prediction for GlimmerHMM_glimmerT_49771-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: -)Couldn't classify 87202, 87237 Couldn't classify 90551, 90607 Sorry, prediction pasa_asmbl_29416.p1 fails validation. (AGC) AC 87202-87237 GT CGG (CAG) AG 88210-88293 GT TGG (GAG) AG 88448-88569 GT AGG (GCT) AG 89373-89508 GT AGG (GTC) AG 90551-90607 CT CCC -recovered pasa_asmbl_29416.p1, internal, 88210, 88293 -recovered pasa_asmbl_29416.p1, internal, 88448, 88569 -recovered pasa_asmbl_29416.p1, internal, 89373, 89508 Valid prediction for Augustus_model.g33208.t1 Valid prediction for Augustus_model.g33209.t1 Valid prediction for HiQ_model.g33207.t1 Valid prediction for Augustus_model.g33210.t1 Couldn't classify 104373, 104582 Sorry, prediction pasa_asmbl_29412.p1 fails validation. (GTG) GT 104373-104582 GT AGG (GTT) AG 104809-104982 GT TGG (GCT) AG 105292-105391 GT CAG (ACG) AG 105958-106007 GT AGG (GGG) AG 106293-106351 GT AGG (CCC) AG 106448-106556 GT AGG (GGT) AG 106738-106890 GT GGG (GAC) AG 107046-107170 GT GGG (GAT) AG 107327-107384 GT AGG (GAT) AG 107530-107613 AC AAA -recovered pasa_asmbl_29412.p1, terminal, 107530, 107613 -recovered pasa_asmbl_29412.p1, internal, 104809, 104982 -recovered pasa_asmbl_29412.p1, internal, 105292, 105391 -recovered pasa_asmbl_29412.p1, internal, 105958, 106007 -recovered pasa_asmbl_29412.p1, internal, 106293, 106351 -recovered pasa_asmbl_29412.p1, internal, 106448, 106556 -recovered pasa_asmbl_29412.p1, internal, 106738, 106890 -recovered pasa_asmbl_29412.p1, internal, 107046, 107170 -recovered pasa_asmbl_29412.p1, internal, 107327, 107384 Valid prediction for snap_scaffold_22-snap.1510-T1 Valid prediction for snap_scaffold_22-snap.1504-T1 Valid prediction for GlimmerHMM_glimmerT_49767-T1 Valid prediction for GlimmerHMM_glimmerT_49775-T1 Valid prediction for snap_scaffold_22-snap.1529-T1 Valid prediction for snap_scaffold_22-snap.1520-T1 Valid prediction for GlimmerHMM_glimmerT_49782-T1 Valid prediction for snap_scaffold_22-snap.1515-T1 Valid prediction for Augustus_model.g33204.t1 Valid prediction for snap_scaffold_22-snap.1505-T1 Valid prediction for GlimmerHMM_glimmerT_49783-T1 Valid prediction for snap_scaffold_22-snap.1508-T1 Valid prediction for Augustus_model.g33206.t1 Couldn't classify 103899, 104095 Sorry, prediction pasa_asmbl_29413.p2 fails validation. (ATG) CT 101989-102216 GT AGG (GTG) AG 103141-103447 GT TGG (CCC) AG 103899-104095 AT ACA -recovered pasa_asmbl_29413.p2, initial, 101989, 102216 -recovered pasa_asmbl_29413.p2, internal, 103141, 103447 Valid prediction for snap_scaffold_22-snap.1524-T1 Valid prediction for GlimmerHMM_glimmerT_49769-T1 Valid prediction for GlimmerHMM_glimmerT_49774-T1 Valid prediction for snap_scaffold_22-snap.1512-T1 Valid prediction for GlimmerHMM_glimmerT_49760-T1 Valid prediction for snap_scaffold_22-snap.1519-T1 Valid prediction for GlimmerHMM_glimmerT_49770-T1 Valid prediction for GlimmerHMM_glimmerT_49763-T1 Valid prediction for snap_scaffold_22-snap.1530-T1 Valid prediction for CodingQuarry_transcript_34216-T1 Valid prediction for snap_scaffold_22-snap.1535-T1 Valid prediction for snap_scaffold_22-snap.1531-T1 Valid prediction for snap_scaffold_22-snap.1527-T1 Valid prediction for CodingQuarry_transcript_34215-T1 Valid prediction for CodingQuarry_transcript_34217-T1 Valid prediction for GlimmerHMM_glimmerT_49781-T1 Valid prediction for snap_scaffold_22-snap.1503-T1 Valid prediction for GlimmerHMM_glimmerT_49773-T1 Valid prediction for snap_scaffold_22-snap.1506-T1 Valid prediction for snap_scaffold_22-snap.1533-T1 Couldn't classify 94136, 94269 Couldn't classify 95573, 95658 Sorry, prediction pasa_asmbl_29415.p2 fails validation. (GAG) CG 94136-94269 GT GGG (GAG) AG 94467-94705 GT AGG (TTC) AG 95225-95344 GT AGG (TGT) AG 95573-95658 GG TCG -recovered pasa_asmbl_29415.p2, internal, 94467, 94705 -recovered pasa_asmbl_29415.p2, internal, 95225, 95344 Valid prediction for GlimmerHMM_glimmerT_49766-T1 Valid prediction for GlimmerHMM_glimmerT_49784-T1 Valid prediction for pasa_asmbl_29418.p1 Valid prediction for pasa_asmbl_29421.p1 Valid prediction for HiQ_model.g33211.t1 Valid prediction for HiQ_model.g33214.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30121, rend_intergenic: 12244 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31710, rend_intergenic: 30677 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38909, rend_intergenic: 31931 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40037, rend_intergenic: 39967 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46906, rend_intergenic: 42403 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48018, rend_intergenic: 47023 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 66383, rend_intergenic: 55343 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68031, rend_intergenic: 66432 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81611, rend_intergenic: 69051 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87012, rend_intergenic: 81714 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99189, rend_intergenic: 91709 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 106275, rend_intergenic: 104258 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 109419, rend_intergenic: 106759 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 117355, rend_intergenic: 110201 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 132321, rend_intergenic: 129144 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134148, rend_intergenic: 132960 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 145824, rend_intergenic: 136752 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 150015 -exon list size: 411 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 1.9 2.2 2.4 2.7 2.9 3.1 3.4 3.6 3.9 4.1 4.4 4.6 4.8 5.1 5.3 5.6 5.8 6.1 6.3 6.5 6.8 7.0 7.3 7.5 7.7 8.0 8.2 8.5 8.7 9.0 9.2 9.4 9.7 9.9 10.2 10.4 10.7 10.9 11.1 11.4 11.6 11.9 12.1 12.3 12.6 12.8 13.1 13.3 13.6 13.8 14.0 14.3 14.5 14.8 15.0 15.3 15.5 15.7 16.0 16.2 16.5 16.7 16.9 17.2 17.4 17.7 17.9 18.2 18.4 18.6 18.9 19.1 19.4 19.6 19.9 20.1 20.3 20.6 20.8 21.1 21.3 21.5 21.8 22.0 22.3 22.5 22.8 23.0 23.2 23.5 23.7 24.0 24.2 24.5 24.7 24.9 25.2 25.4 25.7 25.9 26.2 26.4 26.6 26.9 27.1 27.4 27.6 27.8 28.1 28.3 28.6 28.8 29.1 29.3 29.5 29.8 30.0 30.3 30.5 30.8 31.0 31.2 31.5 31.7 32.0 32.2 32.4 32.7 32.9 33.2 33.4 33.7 33.9 34.1 34.4 34.6 34.9 35.1 35.4 35.6 35.8 36.1 36.3 36.6 36.8 37.0 37.3 37.5 37.8 38.0 38.3 38.5 38.7 39.0 39.2 39.5 39.7 40.0 40.2 40.4 40.7 40.9 41.2 41.4 41.6 41.9 42.1 42.4 42.6 42.9 43.1 43.3 43.6 43.8 44.1 44.3 44.6 44.8 45.0 45.3 45.5 45.8 46.0 46.2 46.5 46.7 47.0 47.2 47.5 47.7 47.9 48.2 48.4 48.7 48.9 49.2 49.4 49.6 49.9 50.1 50.4 50.6 50.8 51.1 51.3 51.6 51.8 52.1 52.3 52.5 52.8 53.0 53.3 53.5 53.8 54.0 54.2 54.5 54.7 55.0 55.2 55.4 55.7 55.9 56.2 56.4 56.7 56.9 57.1 57.4 57.6 57.9 58.1 58.4 58.6 58.8 59.1 59.3 59.6 59.8 60.0 60.3 60.5 60.8 61.0 61.3 61.5 61.7 62.0 62.2 62.5 62.7 63.0 63.2 63.4 63.7 63.9 64.2 64.4 64.6 64.9 65.1 65.4 65.6 65.9 66.1 66.3 66.6 66.8 67.1 67.3 67.6 67.8 68.0 68.3 68.5 68.8 69.0 69.2 69.5 69.7 70.0 70.2 70.5 70.7 70.9 71.2 71.4 71.7 71.9 72.2 72.4 72.6 72.9 73.1 73.4 73.6 73.8 74.1 74.3 74.6 74.8 75.1 75.3 75.5 75.8 76.0 76.3 76.5 76.8 77.0 77.2 77.5 77.7 78.0 78.2 78.5 78.7 78.9 79.2 79.4 79.7 79.9 80.1 80.4 80.6 80.9 81.1 81.4 81.6 81.8 82.1 82.3 82.6 82.8 83.1 83.3 83.5 83.8 84.0 84.3 84.5 84.7 85.0 85.2 85.5 85.7 86.0 86.2 86.4 86.7 86.9 87.2 87.4 87.7 87.9 88.1 88.4 88.6 88.9 89.1 89.3 89.6 89.8 90.1 90.3 90.6 90.8 91.0 91.3 91.5 91.8 92.0 92.3 92.5 92.7 93.0 93.2 93.5 93.7 93.9 94.2 94.4 94.7 94.9 95.2 95.4 95.6 95.9 96.1 96.4 96.6 96.9 97.1 97.3 97.6 97.8 98.1 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 21 predictions from path traversal Error with prediction: snap lend_intergenic: 30121, rend_intergenic: 12244 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31710, rend_intergenic: 30677 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38909, rend_intergenic: 31931 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40037, rend_intergenic: 39967 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46906, rend_intergenic: 42403 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48018, rend_intergenic: 47023 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 66383, rend_intergenic: 55343 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68031, rend_intergenic: 66432 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81611, rend_intergenic: 69051 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87012, rend_intergenic: 81714 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99189, rend_intergenic: 91709 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 106275, rend_intergenic: 104258 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 109419, rend_intergenic: 106759 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 117355, rend_intergenic: 110201 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 132321, rend_intergenic: 129144 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134148, rend_intergenic: 132960 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 145824, rend_intergenic: 136752 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 15 predictions persist after filtering for low support