-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_7295891-7494447 -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_14-snap.1536-T1 Valid prediction for GlimmerHMM_glimmerT_34168-T1 Valid prediction for snap_scaffold_14-snap.1525-T1 Valid prediction for pasa_asmbl_12152.p1 Valid prediction for HiQ_model.g22815.t1 Valid prediction for Augustus_model.g22827.t1 Valid prediction for HiQ_model.g22831.t1 Couldn't classify 143232, 143314 Sorry, prediction pasa_asmbl_12160.p1 fails validation. (ATG) TC 141365-141403 GT ACG (GTG) AG 141755-141827 GT AAG (AGA) AG 141927-142018 GT AGG (GTC) AG 142195-142288 GT TGG (TTT) AG 142377-142444 GT AAG (GAG) AG 142527-142608 GT GGG (GTA) AG 143040-143111 GT AGG (GCA) AG 143232-143314 AT GCA -recovered pasa_asmbl_12160.p1, initial, 141365, 141403 -recovered pasa_asmbl_12160.p1, internal, 141755, 141827 -recovered pasa_asmbl_12160.p1, internal, 141927, 142018 -recovered pasa_asmbl_12160.p1, internal, 142195, 142288 -recovered pasa_asmbl_12160.p1, internal, 142377, 142444 -recovered pasa_asmbl_12160.p1, internal, 142527, 142608 -recovered pasa_asmbl_12160.p1, internal, 143040, 143111 Valid prediction for CodingQuarry_transcript_15703-T1 Valid prediction for snap_scaffold_14-snap.1504-T1 Valid prediction for GlimmerHMM_glimmerT_34147-T1 Valid prediction for CodingQuarry_transcript_15708-T1 Valid prediction for snap_scaffold_14-snap.1539-T1 Valid prediction for snap_scaffold_14-snap.1531-T1 Valid prediction for snap_scaffold_14-snap.1537-T1 Couldn't classify 159984, 160106 Sorry, prediction pasa_asmbl_12725.p1 fails validation. (AGT) TC 159984-160106 GT AGG (TTC) AG 160193-160283 GT AGG (GTG) AG 160415-160695 GG GAG -recovered pasa_asmbl_12725.p1, terminal, 160415, 160695 -recovered pasa_asmbl_12725.p1, internal, 160193, 160283 Couldn't classify 143845, 143933 Sorry, prediction pasa_asmbl_12161.p1 fails validation. (TGT) AC 143845-143933 GT GAG (GTG) AG 144209-144287 GT TGG (AGG) AG 144400-144534 GT AGG (ATC) AG 144671-145330 CC GAC -recovered pasa_asmbl_12161.p1, terminal, 144671, 145330 -recovered pasa_asmbl_12161.p1, internal, 144209, 144287 -recovered pasa_asmbl_12161.p1, internal, 144400, 144534 Couldn't classify 149890, 149983 Sorry, prediction pasa_asmbl_12164.p1 fails validation. (CTG) GG 149890-149983 GT AGG (GGG) AG 150104-150232 GT AGG (GCA) AG 150509-150672 GT AGG (ACT) AG 150903-151079 GT AGG (GCC) AG 151165-151356 AA AGA -recovered pasa_asmbl_12164.p1, terminal, 151165, 151356 -recovered pasa_asmbl_12164.p1, internal, 150104, 150232 -recovered pasa_asmbl_12164.p1, internal, 150509, 150672 -recovered pasa_asmbl_12164.p1, internal, 150903, 151079 Valid prediction for Augustus_model.g22823.t1 Valid prediction for snap_scaffold_14-snap.1510-T1 Valid prediction for GlimmerHMM_glimmerT_34158-T1 Valid prediction for CodingQuarry_transcript_15699-T1 Valid prediction for GlimmerHMM_glimmerT_34150-T1 Valid prediction for CodingQuarry_transcript_15704-T1 Valid prediction for snap_scaffold_14-snap.1535-T1 Valid prediction for snap_scaffold_14-snap.1532-T1 Valid prediction for GlimmerHMM_glimmerT_34146-T1 Valid prediction for GlimmerHMM_glimmerT_34156-T1 Valid prediction for GlimmerHMM_glimmerT_34171-T1 Valid prediction for pasa_asmbl_12700.p1 Valid prediction for snap_scaffold_14-snap.1527-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for snap_scaffold_14-snap.1529-T1 Valid prediction for Augustus_model.g22822.t1 Valid prediction for snap_scaffold_14-snap.1519-T1 Couldn't classify 134375, 134438 Sorry, prediction pasa_asmbl_12158.p1 fails validation. (CTC) AC 134375-134438 GT TGG (AGA) AG 135568-135747 GT GGG (GTG) AG 136017-136460 GT AGG (GTG) AG 136592-136681 GT AGG (TGA) AG 137073-137093 GT AGG (AAG) AG 137412-137549 GT AGG (ATG) AG 137638-138728 GA AAG -recovered pasa_asmbl_12158.p1, terminal, 137638, 138728 -recovered pasa_asmbl_12158.p1, internal, 135568, 135747 -recovered pasa_asmbl_12158.p1, internal, 136017, 136460 -recovered pasa_asmbl_12158.p1, internal, 136592, 136681 -recovered pasa_asmbl_12158.p1, internal, 137073, 137093 -recovered pasa_asmbl_12158.p1, internal, 137412, 137549 Valid prediction for Augustus_model.g22825.t1 Valid prediction for Augustus_model.g22829.t1 Valid prediction for GlimmerHMM_glimmerT_34169-T1 Valid prediction for GlimmerHMM_glimmerT_34166-T1 Valid prediction for snap_scaffold_14-snap.1534-T1 Valid prediction for CodingQuarry_transcript_15707-T1 Valid prediction for snap_scaffold_14-snap.1517-T1 Valid prediction for Augustus_model.g22818.t1 Valid prediction for snap_scaffold_14-snap.1520-T1 Valid prediction for snap_scaffold_14-snap.1516-T1 Valid prediction for snap_scaffold_14-snap.1523-T1 Valid prediction for GlimmerHMM_glimmerT_34163-T1 Valid prediction for GlimmerHMM_glimmerT_34164-T1 Valid prediction for CodingQuarry_transcript_15710-T1 Valid prediction for snap_scaffold_14-snap.1507-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 CodingQuarry_transcript_15706-T1 Valid prediction for GlimmerHMM_glimmerT_34148-T1 Valid prediction for GlimmerHMM_glimmerT_34160-T1 Couldn't classify 9430, 9549 Sorry, prediction pasa_asmbl_13213.p1 fails validation. (CCC) CA 9430-9549 GT AGG (GGA) AG 9836-9982 GT AGG (GAC) AG 10952-11098 CC GAC -recovered pasa_asmbl_13213.p1, terminal, 10952, 11098 -recovered pasa_asmbl_13213.p1, internal, 9836, 9982 Valid prediction for snap_scaffold_14-snap.1514-T1 Valid prediction for pasa_asmbl_13192.p1 Valid prediction for snap_scaffold_14-snap.1530-T1 Valid prediction for CodingQuarry_transcript_15711-T1 Couldn't classify 134118, 134149 Couldn't classify 142453, 142562 Sorry, prediction pasa_asmbl_13196.p1 fails validation. (CTG) AG 134118-134149 GT CAG (GAA) AG 134456-134560 GT AGG (GAC) AG 137428-137684 GT TGG (CCG) AG 137775-137957 GT GGG (AGG) AG 139088-139267 GT AGG (GCA) AG 139384-139640 GT AGG (ACC) AG 140773-140908 GT AGG (CCG) AG 141002-141119 GT ATG (ATT) AG 141237-141312 GT CTG (GTG) AG 141431-141539 GT AGG (GAG) AG 141619-141735 GT CTG (GTG) AG 141845-141985 GT AGG (TGG) AG 142453-142562 CC GCC add_exon() Sorry, pasa_asmbl_13196.p1 134456-134560-terminal-1 is invalid. -recovered pasa_asmbl_13196.p1, terminal, 134456, 134560 -recovered pasa_asmbl_13196.p1, internal, 134118, 134149 -recovered pasa_asmbl_13196.p1, internal, 134456, 134560 -recovered pasa_asmbl_13196.p1, internal, 137428, 137684 -recovered pasa_asmbl_13196.p1, internal, 137775, 137957 -recovered pasa_asmbl_13196.p1, internal, 139088, 139267 -recovered pasa_asmbl_13196.p1, internal, 139384, 139640 -recovered pasa_asmbl_13196.p1, internal, 140773, 140908 -recovered pasa_asmbl_13196.p1, internal, 141002, 141119 -recovered pasa_asmbl_13196.p1, internal, 141237, 141312 -recovered pasa_asmbl_13196.p1, internal, 141431, 141539 -recovered pasa_asmbl_13196.p1, internal, 141619, 141735 -recovered pasa_asmbl_13196.p1, internal, 141845, 141985 Couldn't classify 20495, 20654 Sorry, prediction pasa_asmbl_13211.p1 fails validation. (CAG) AA 20495-20654 GT AGG (CGA) AG 20783-20963 GT GAG (GTG) AG 21098-21207 GT AGG (GTA) AG 21299-21380 GT GGG (GTT) AG 21463-21522 GT ATG (TGT) AG 21763-22072 CA GAC -recovered pasa_asmbl_13211.p1, terminal, 21763, 22072 -recovered pasa_asmbl_13211.p1, internal, 20783, 20963 -recovered pasa_asmbl_13211.p1, internal, 21098, 21207 -recovered pasa_asmbl_13211.p1, internal, 21299, 21380 -recovered pasa_asmbl_13211.p1, internal, 21463, 21522 Valid prediction for GlimmerHMM_glimmerT_34161-T1 Valid prediction for GlimmerHMM_glimmerT_34172-T1 Valid prediction for GlimmerHMM_glimmerT_34154-T1 Valid prediction for GlimmerHMM_glimmerT_34165-T1 Valid prediction for HiQ_model.g22830.t1 Valid prediction for snap_scaffold_14-snap.1511-T1 Couldn't classify 143349, 143834 Sorry, prediction pasa_asmbl_13194.p1 fails validation. (TCA) CC 143349-143834 GT AGG (AGG) AG 143969-144205 GT GGG (CAT) AG 144515-144724 CG AGC -recovered pasa_asmbl_13194.p1, terminal, 144515, 144724 -recovered pasa_asmbl_13194.p1, internal, 143969, 144205 Valid prediction for GlimmerHMM_glimmerT_34170-T1 Valid prediction for snap_scaffold_14-snap.1505-T1 Valid prediction for CodingQuarry_transcript_15701-T1 Valid prediction for CodingQuarry_transcript_15713-T1 Valid prediction for snap_scaffold_14-snap.1512-T1 Valid prediction for snap_scaffold_14-snap.1524-T1 Valid prediction for pasa_asmbl_13212.p1 Valid prediction for HiQ_model.g22826.t1 Valid prediction for GlimmerHMM_glimmerT_34157-T1 Valid prediction for Augustus_model.g22833.t1 Valid prediction for GlimmerHMM_glimmerT_34173-T1 Valid prediction for Augustus_model.g22821.t1 Valid prediction for CodingQuarry_transcript_15702-T1 Valid prediction for Augustus_model.g22816.t1 Valid prediction for GlimmerHMM_glimmerT_34174-T1 Valid prediction for GlimmerHMM_glimmerT_34152-T1 Valid prediction for CodingQuarry_transcript_15709-T1 Couldn't classify 142662, 143261 Sorry, prediction pasa_asmbl_13195.p1 fails validation. (GTG) GC 142662-143261 AG GGA Valid prediction for pasa_asmbl_13201.p1 Valid prediction for GlimmerHMM_glimmerT_34162-T1 Valid prediction for CodingQuarry_transcript_15712-T1 Valid prediction for snap_scaffold_14-snap.1515-T1 Valid prediction for snap_scaffold_14-snap.1513-T1 Valid prediction for CodingQuarry_transcript_15705-T1 Valid prediction for GlimmerHMM_glimmerT_34155-T1 Valid prediction for GlimmerHMM_glimmerT_34153-T1 Valid prediction for GlimmerHMM_glimmerT_34149-T1 Valid prediction for HiQ_model.g22832.t1 Valid prediction for GlimmerHMM_glimmerT_34151-T1 Valid prediction for GlimmerHMM_glimmerT_34159-T1 Valid prediction for snap_scaffold_14-snap.1526-T1 Valid prediction for snap_scaffold_14-snap.1518-T1 Valid prediction for GlimmerHMM_glimmerT_34167-T1 Valid prediction for snap_scaffold_14-snap.1538-T1 Valid prediction for pasa_asmbl_13203.p1 Valid prediction for snap_scaffold_14-snap.1509-T1 Valid prediction for snap_scaffold_14-snap.1528-T1 Valid prediction for HiQ_model.g22817.t1 Valid prediction for snap_scaffold_14-snap.1521-T1 Valid prediction for HiQ_model.g22824.t1 Valid prediction for snap_scaffold_14-snap.1508-T1 Valid prediction for HiQ_model.g22828.t1 Valid prediction for Augustus_model.g22819.t1 Valid prediction for snap_scaffold_14-snap.1522-T1 Valid prediction for CodingQuarry_transcript_15700-T1 Valid prediction for Augustus_model.g22820.t1 Valid prediction for snap_scaffold_14-snap.1533-T1 Valid prediction for snap_scaffold_14-snap.1506-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 53837, rend_intergenic: 53834 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20020, rend_intergenic: 17419 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24476, rend_intergenic: 22482 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51457, rend_intergenic: 25210 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90558, rend_intergenic: 55799 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125020, rend_intergenic: 114921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 138728, rend_intergenic: 128939 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 147766, rend_intergenic: 142147 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 156770, rend_intergenic: 153851 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 159505, rend_intergenic: 156794 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160613, rend_intergenic: 159510 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 164248, rend_intergenic: 162702 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 191423, rend_intergenic: 176519 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192844, rend_intergenic: 191931 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197665, rend_intergenic: 193280 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 198557 -exon list size: 470 building trellis 0.2 0.4 0.6 0.8 1.1 1.3 1.5 1.7 1.9 2.1 2.3 2.5 2.8 3.0 3.2 3.4 3.6 3.8 4.0 4.2 4.4 4.7 4.9 5.1 5.3 5.5 5.7 5.9 6.1 6.4 6.6 6.8 7.0 7.2 7.4 7.6 7.8 8.1 8.3 8.5 8.7 8.9 9.1 9.3 9.5 9.7 10.0 10.2 10.4 10.6 10.8 11.0 11.2 11.4 11.7 11.9 12.1 12.3 12.5 12.7 12.9 13.1 13.3 13.6 13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.3 15.5 15.7 15.9 16.1 16.3 16.5 16.7 16.9 17.2 17.4 17.6 17.8 18.0 18.2 18.4 18.6 18.9 19.1 19.3 19.5 19.7 19.9 20.1 20.3 20.6 20.8 21.0 21.2 21.4 21.6 21.8 22.0 22.2 22.5 22.7 22.9 23.1 23.3 23.5 23.7 23.9 24.2 24.4 24.6 24.8 25.0 25.2 25.4 25.6 25.8 26.1 26.3 26.5 26.7 26.9 27.1 27.3 27.5 27.8 28.0 28.2 28.4 28.6 28.8 29.0 29.2 29.4 29.7 29.9 30.1 30.3 30.5 30.7 30.9 31.1 31.4 31.6 31.8 32.0 32.2 32.4 32.6 32.8 33.1 33.3 33.5 33.7 33.9 34.1 34.3 34.5 34.7 35.0 35.2 35.4 35.6 35.8 36.0 36.2 36.4 36.7 36.9 37.1 37.3 37.5 37.7 37.9 38.1 38.3 38.6 38.8 39.0 39.2 39.4 39.6 39.8 40.0 40.3 40.5 40.7 40.9 41.1 41.3 41.5 41.7 41.9 42.2 42.4 42.6 42.8 43.0 43.2 43.4 43.6 43.9 44.1 44.3 44.5 44.7 44.9 45.1 45.3 45.6 45.8 46.0 46.2 46.4 46.6 46.8 47.0 47.2 47.5 47.7 47.9 48.1 48.3 48.5 48.7 48.9 49.2 49.4 49.6 49.8 50.0 50.2 50.4 50.6 50.8 51.1 51.3 51.5 51.7 51.9 52.1 52.3 52.5 52.8 53.0 53.2 53.4 53.6 53.8 54.0 54.2 54.4 54.7 54.9 55.1 55.3 55.5 55.7 55.9 56.1 56.4 56.6 56.8 57.0 57.2 57.4 57.6 57.8 58.1 58.3 58.5 58.7 58.9 59.1 59.3 59.5 59.7 60.0 60.2 60.4 60.6 60.8 61.0 61.2 61.4 61.7 61.9 62.1 62.3 62.5 62.7 62.9 63.1 63.3 63.6 63.8 64.0 64.2 64.4 64.6 64.8 65.0 65.3 65.5 65.7 65.9 66.1 66.3 66.5 66.7 66.9 67.2 67.4 67.6 67.8 68.0 68.2 68.4 68.6 68.9 69.1 69.3 69.5 69.7 69.9 70.1 70.3 70.6 70.8 71.0 71.2 71.4 71.6 71.8 72.0 72.2 72.5 72.7 72.9 73.1 73.3 73.5 73.7 73.9 74.2 74.4 74.6 74.8 75.0 75.2 75.4 75.6 75.8 76.1 76.3 76.5 76.7 76.9 77.1 77.3 77.5 77.8 78.0 78.2 78.4 78.6 78.8 79.0 79.2 79.4 79.7 79.9 80.1 80.3 80.5 80.7 80.9 81.1 81.4 81.6 81.8 82.0 82.2 82.4 82.6 82.8 83.1 83.3 83.5 83.7 83.9 84.1 84.3 84.5 84.7 85.0 85.2 85.4 85.6 85.8 86.0 86.2 86.4 86.7 86.9 87.1 87.3 87.5 87.7 87.9 88.1 88.3 88.6 88.8 89.0 89.2 89.4 89.6 89.8 90.0 90.3 90.5 90.7 90.9 91.1 91.3 91.5 91.7 91.9 92.2 92.4 92.6 92.8 93.0 93.2 93.4 93.6 93.9 94.1 94.3 94.5 94.7 94.9 95.1 95.3 95.6 95.8 96.0 96.2 96.4 96.6 96.8 97.0 97.2 97.5 97.7 97.9 98.1 98.3 98.5 98.7 98.9 99.2 99.4 99.6 99.8 -found 31 predictions from path traversal Error with prediction: GlimmerHMM lend_intergenic: 53837, rend_intergenic: 53834 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20020, rend_intergenic: 17419 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24476, rend_intergenic: 22482 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51457, rend_intergenic: 25210 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90558, rend_intergenic: 55799 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125020, rend_intergenic: 114921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 138728, rend_intergenic: 128939 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 147766, rend_intergenic: 142147 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 156770, rend_intergenic: 153851 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 159505, rend_intergenic: 156794 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160613, rend_intergenic: 159510 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 164248, rend_intergenic: 162702 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 191423, rend_intergenic: 176519 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192844, rend_intergenic: 191931 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197665, rend_intergenic: 193280 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 24 predictions persist after filtering for low support