-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_9135929-9390889 -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_26-snap.2073-T1 Valid prediction for GlimmerHMM_glimmerT_56329-T1 Valid prediction for snap_scaffold_26-snap.2086-T1 Valid prediction for Augustus_model.g37329.t1 Valid prediction for snap_scaffold_26-snap.2099-T1 Valid prediction for snap_scaffold_26-snap.2093-T1 Valid prediction for GlimmerHMM_glimmerT_56351-T1 Valid prediction for GlimmerHMM_glimmerT_56332-T1 Couldn't classify 175606, 175637 Sorry, prediction pasa_asmbl_35224.p1 fails validation. (CGA) AC 175606-175637 GT TTG (AAT) AG 176461-176513 GT AGG (TGG) AG 178809-178855 GT AGG (CTA) AG 179004-179079 GT AGG (AAA) AG 179275-179382 GT AGG (TGA) AG 179487-179554 GT AGG (GGA) AG 179699-179743 GT AGG (ATG) AG 179899-179933 GT AGG (AGG) AG 180068-180149 GC AGG (GTG) AG 180253-180318 GT AGG (ACA) AG 180518-180667 GT TGG (GGC) AG 180827-180922 GT AGG -recovered pasa_asmbl_35224.p1, initial, 179899, 179933 add_exon() Sorry, pasa_asmbl_35224.p1 179004-179079-terminal-3 is invalid. -recovered pasa_asmbl_35224.p1, terminal, 179004, 179079 add_exon() Sorry, pasa_asmbl_35224.p1 179275-179382-terminal-1 is invalid. -recovered pasa_asmbl_35224.p1, terminal, 179275, 179382 -recovered pasa_asmbl_35224.p1, terminal, 180827, 180922 -recovered pasa_asmbl_35224.p1, internal, 176461, 176513 -recovered pasa_asmbl_35224.p1, internal, 178809, 178855 -recovered pasa_asmbl_35224.p1, internal, 179004, 179079 -recovered pasa_asmbl_35224.p1, internal, 179275, 179382 -recovered pasa_asmbl_35224.p1, internal, 179487, 179554 -recovered pasa_asmbl_35224.p1, internal, 179699, 179743 -recovered pasa_asmbl_35224.p1, internal, 179899, 179933 -recovered pasa_asmbl_35224.p1, internal, 180068, 180149 -recovered pasa_asmbl_35224.p1, internal, 180253, 180318 -recovered pasa_asmbl_35224.p1, internal, 180518, 180667 -recovered pasa_asmbl_35224.p1, internal, 180827, 180922 Valid prediction for GlimmerHMM_glimmerT_56334-T1 Valid prediction for GlimmerHMM_glimmerT_56353-T1 Valid prediction for snap_scaffold_26-snap.2069-T1 Valid prediction for snap_scaffold_26-snap.2103-T1 Valid prediction for CodingQuarry_transcript_40432-T1 Valid prediction for GlimmerHMM_glimmerT_56354-T1 Valid prediction for snap_scaffold_26-snap.2070-T1 Couldn't classify 178184, 178184 Sorry, prediction CodingQuarry_transcript_40434-T1 fails validation. (AGT) CA 178184-178184 GT AAG (TGG) AG 178809-178855 GT AGG (CTA) AG 179004-179079 GT AGG (AAA) AG 179275-179382 GT AGG (TGA) AG 179487-179554 GT AGG (GGA) AG 179699-179743 GT AGG (ATG) AG 179899-179933 GT AGG (AGG) AG 180068-180149 GC AGG (GTG) AG 180253-180318 GT AGG (ACA) AG 180518-180685 CA GAC -recovered CodingQuarry_transcript_40434-T1, initial, 179899, 179933 add_exon() Sorry, CodingQuarry_transcript_40434-T1 179004-179079-terminal-3 is invalid. -recovered CodingQuarry_transcript_40434-T1, terminal, 179004, 179079 add_exon() Sorry, CodingQuarry_transcript_40434-T1 179275-179382-terminal-1 is invalid. -recovered CodingQuarry_transcript_40434-T1, terminal, 179275, 179382 -recovered CodingQuarry_transcript_40434-T1, terminal, 180518, 180685 -recovered CodingQuarry_transcript_40434-T1, internal, 178809, 178855 -recovered CodingQuarry_transcript_40434-T1, internal, 179004, 179079 -recovered CodingQuarry_transcript_40434-T1, internal, 179275, 179382 -recovered CodingQuarry_transcript_40434-T1, internal, 179487, 179554 -recovered CodingQuarry_transcript_40434-T1, internal, 179699, 179743 -recovered CodingQuarry_transcript_40434-T1, internal, 179899, 179933 -recovered CodingQuarry_transcript_40434-T1, internal, 180068, 180149 -recovered CodingQuarry_transcript_40434-T1, internal, 180253, 180318 Valid prediction for GlimmerHMM_glimmerT_56341-T1 Valid prediction for Augustus_model.g37346.t1 Valid prediction for Augustus_model.g37347.t1 Valid prediction for HiQ_model.g37343.t1 Valid prediction for Augustus_model.g37336.t1 Valid prediction for Augustus_model.g37331.t1 Couldn't classify 19295, 19478 Sorry, prediction pasa_asmbl_35211.p1 fails validation. (ATG) CC 12891-12929 GT AGG (ACA) AG 13125-13216 GT TGG (GTT) AG 13535-13646 GT AGG (TCT) AG 14237-14378 GT AGG (GGC) AG 14484-14634 GT GGG (TTT) AG 14753-14891 GT AGG (GTC) AG 15291-15434 GT AGG (AAA) AG 15631-15874 GT TGG (AGA) AG 16038-16154 GT AGG (ACC) AG 16341-16507 GT AGG (CTG) AG 16737-16965 GT AGG (GTG) AG 17321-17489 GT AAG (GAA) AG 17593-17680 GT TGG (TAC) AG 18164-18296 GT GAG (GAT) AG 18707-18895 GT GGG (AGT) AG 19091-19193 GT CCG (GTC) AG 19295-19478 GG ATG -recovered pasa_asmbl_35211.p1, initial, 12891, 12929 -recovered pasa_asmbl_35211.p1, internal, 13125, 13216 -recovered pasa_asmbl_35211.p1, internal, 13535, 13646 -recovered pasa_asmbl_35211.p1, internal, 14237, 14378 -recovered pasa_asmbl_35211.p1, internal, 14484, 14634 -recovered pasa_asmbl_35211.p1, internal, 14753, 14891 -recovered pasa_asmbl_35211.p1, internal, 15291, 15434 -recovered pasa_asmbl_35211.p1, internal, 15631, 15874 -recovered pasa_asmbl_35211.p1, internal, 16038, 16154 -recovered pasa_asmbl_35211.p1, internal, 16341, 16507 -recovered pasa_asmbl_35211.p1, internal, 16737, 16965 -recovered pasa_asmbl_35211.p1, internal, 17321, 17489 -recovered pasa_asmbl_35211.p1, internal, 17593, 17680 -recovered pasa_asmbl_35211.p1, internal, 18164, 18296 -recovered pasa_asmbl_35211.p1, internal, 18707, 18895 -recovered pasa_asmbl_35211.p1, internal, 19091, 19193 Valid prediction for Augustus_model.g37348.t1 Valid prediction for snap_scaffold_26-snap.2095-T1 Valid prediction for GlimmerHMM_glimmerT_56346-T1 Valid prediction for GlimmerHMM_glimmerT_56350-T1 Valid prediction for snap_scaffold_26-snap.2072-T1 Valid prediction for snap_scaffold_26-snap.2105-T1 Valid prediction for GlimmerHMM_glimmerT_56357-T1 Valid prediction for snap_scaffold_26-snap.2068-T1 Valid prediction for GlimmerHMM_glimmerT_56342-T1 Valid prediction for CodingQuarry_transcript_40433-T1 Valid prediction for GlimmerHMM_glimmerT_56339-T1 Valid prediction for GlimmerHMM_glimmerT_56355-T1 Valid prediction for GlimmerHMM_glimmerT_56352-T1 Valid prediction for GlimmerHMM_glimmerT_56344-T1 Valid prediction for snap_scaffold_26-snap.2102-T1 Valid prediction for Augustus_model.g37327.t1 Valid prediction for snap_scaffold_26-snap.2096-T1 Valid prediction for pasa_asmbl_35213.p1 Valid prediction for snap_scaffold_26-snap.2075-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_56338-T1 Valid prediction for Augustus_model.g37337.t1 Valid prediction for Augustus_model.g37334.t1 Valid prediction for snap_scaffold_26-snap.2097-T1 Valid prediction for snap_scaffold_26-snap.2091-T1 Valid prediction for snap_scaffold_26-snap.2085-T1 Couldn't classify 64607, 64780 Sorry, prediction pasa_asmbl_35773.p1 fails validation. (CTT) AC 64607-64780 GT AGG (TCC) AG 64937-65115 GT AGG (GCA) AG 67635-68700 AA GAA add_exon() Sorry, pasa_asmbl_35773.p1 64937-65115-terminal-2 is invalid. -recovered pasa_asmbl_35773.p1, terminal, 64937, 65115 -recovered pasa_asmbl_35773.p1, terminal, 67635, 68700 -recovered pasa_asmbl_35773.p1, internal, 64937, 65115 Valid prediction for snap_scaffold_26-snap.2104-T1 Valid prediction for snap_scaffold_26-snap.2082-T1 Valid prediction for snap_scaffold_26-snap.2088-T1 Valid prediction for Augustus_model.g37332.t1 Valid prediction for Augustus_model.g37340.t1 Valid prediction for GlimmerHMM_glimmerT_56347-T1 Valid prediction for Augustus_model.g37341.t1 Valid prediction for snap_scaffold_26-snap.2087-T1 Valid prediction for GlimmerHMM_glimmerT_56340-T1 Valid prediction for snap_scaffold_26-snap.2078-T1 Valid prediction for snap_scaffold_26-snap.2090-T1 Valid prediction for GlimmerHMM_glimmerT_56356-T1 Valid prediction for snap_scaffold_26-snap.2094-T1 Valid prediction for snap_scaffold_26-snap.2079-T1 Valid prediction for Augustus_model.g37330.t1 Valid prediction for GlimmerHMM_glimmerT_56331-T1 Valid prediction for snap_scaffold_26-snap.2092-T1 Valid prediction for snap_scaffold_26-snap.2077-T1 Valid prediction for GlimmerHMM_glimmerT_56333-T1 Valid prediction for GlimmerHMM_glimmerT_56348-T1 Valid prediction for GlimmerHMM_glimmerT_56336-T1 Valid prediction for GlimmerHMM_glimmerT_56345-T1 Couldn't classify 60001, 60075 Couldn't classify 63562, 64503 Sorry, prediction pasa_asmbl_35775.p1 fails validation. (TAT) GC 60001-60075 GT AGG (AAG) AG 60302-60421 GT AGG (GCC) AG 60517-60588 GT AGG (CTG) AG 61294-61439 GT ATG (GGC) AG 61601-61696 GT AGG (AGC) AG 61982-62081 GT AGG (CAG) AG 62218-62370 GT AGG (AGA) AG 62465-62554 GT GCG (GAG) AG 63562-64503 AG AAA -recovered pasa_asmbl_35775.p1, internal, 60302, 60421 -recovered pasa_asmbl_35775.p1, internal, 60517, 60588 -recovered pasa_asmbl_35775.p1, internal, 61294, 61439 -recovered pasa_asmbl_35775.p1, internal, 61601, 61696 -recovered pasa_asmbl_35775.p1, internal, 61982, 62081 -recovered pasa_asmbl_35775.p1, internal, 62218, 62370 -recovered pasa_asmbl_35775.p1, internal, 62465, 62554 Valid prediction for snap_scaffold_26-snap.2071-T1 Valid prediction for Augustus_model.g37339.t1 Valid prediction for snap_scaffold_26-snap.2083-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for Augustus_model.g37344.t1 Valid prediction for Augustus_model.g37328.t1 Valid prediction for Augustus_model.g37345.t1 Valid prediction for GlimmerHMM_glimmerT_56337-T1 Valid prediction for GlimmerHMM_glimmerT_56328-T1 Valid prediction for GlimmerHMM_glimmerT_56335-T1 Valid prediction for GlimmerHMM_glimmerT_56343-T1 Valid prediction for snap_scaffold_26-snap.2074-T1 Valid prediction for snap_scaffold_26-snap.2081-T1 Valid prediction for Augustus_model.g37342.t1 Valid prediction for snap_scaffold_26-snap.2084-T1 Valid prediction for Augustus_model.g37338.t1 Valid prediction for snap_scaffold_26-snap.2080-T1 Valid prediction for snap_scaffold_26-snap.2100-T1 Valid prediction for GlimmerHMM_glimmerT_56349-T1 Valid prediction for snap_scaffold_26-snap.2076-T1 Valid prediction for snap_scaffold_26-snap.2101-T1 Couldn't classify 139237, 139334 Sorry, prediction pasa_asmbl_35772.p2 fails validation. (AGT) TC 139237-139334 GT GAG (CTG) AG 141742-141826 GT TGG (CTG) AG 142851-143015 AG GAA -recovered pasa_asmbl_35772.p2, terminal, 142851, 143015 -recovered pasa_asmbl_35772.p2, internal, 141742, 141826 Valid prediction for snap_scaffold_26-snap.2089-T1 Valid prediction for GlimmerHMM_glimmerT_56330-T1 Valid prediction for Augustus_model.g37335.t1 Valid prediction for snap_scaffold_26-snap.2098-T1 Couldn't classify 82744, 82817 Couldn't classify 84877, 85089 Sorry, prediction pasa_asmbl_35883.p1 fails validation. (GTA) AC 82744-82817 GT CAG (TGC) AG 84011-84083 GT AGG (ATA) AG 84877-85089 CT TCC -recovered pasa_asmbl_35883.p1, internal, 84011, 84083 Valid prediction for Augustus_model.g37333.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 185866, rend_intergenic: 182769 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 188537, rend_intergenic: 186262 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 204277, rend_intergenic: 201339 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 231042, rend_intergenic: 221735 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 245856, rend_intergenic: 231109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 249808, rend_intergenic: 245898 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 254961 -exon list size: 387 building trellis 0.3 0.5 0.8 1.0 1.3 1.5 1.8 2.1 2.3 2.6 2.8 3.1 3.3 3.6 3.9 4.1 4.4 4.6 4.9 5.1 5.4 5.7 5.9 6.2 6.4 6.7 6.9 7.2 7.5 7.7 8.0 8.2 8.5 8.7 9.0 9.3 9.5 9.8 10.0 10.3 10.5 10.8 11.1 11.3 11.6 11.8 12.1 12.3 12.6 12.9 13.1 13.4 13.6 13.9 14.1 14.4 14.7 14.9 15.2 15.4 15.7 15.9 16.2 16.5 16.7 17.0 17.2 17.5 17.7 18.0 18.3 18.5 18.8 19.0 19.3 19.5 19.8 20.1 20.3 20.6 20.8 21.1 21.3 21.6 21.9 22.1 22.4 22.6 22.9 23.1 23.4 23.7 23.9 24.2 24.4 24.7 24.9 25.2 25.4 25.7 26.0 26.2 26.5 26.7 27.0 27.2 27.5 27.8 28.0 28.3 28.5 28.8 29.0 29.3 29.6 29.8 30.1 30.3 30.6 30.8 31.1 31.4 31.6 31.9 32.1 32.4 32.6 32.9 33.2 33.4 33.7 33.9 34.2 34.4 34.7 35.0 35.2 35.5 35.7 36.0 36.2 36.5 36.8 37.0 37.3 37.5 37.8 38.0 38.3 38.6 38.8 39.1 39.3 39.6 39.8 40.1 40.4 40.6 40.9 41.1 41.4 41.6 41.9 42.2 42.4 42.7 42.9 43.2 43.4 43.7 44.0 44.2 44.5 44.7 45.0 45.2 45.5 45.8 46.0 46.3 46.5 46.8 47.0 47.3 47.6 47.8 48.1 48.3 48.6 48.8 49.1 49.4 49.6 49.9 50.1 50.4 50.6 50.9 51.2 51.4 51.7 51.9 52.2 52.4 52.7 53.0 53.2 53.5 53.7 54.0 54.2 54.5 54.8 55.0 55.3 55.5 55.8 56.0 56.3 56.6 56.8 57.1 57.3 57.6 57.8 58.1 58.4 58.6 58.9 59.1 59.4 59.6 59.9 60.2 60.4 60.7 60.9 61.2 61.4 61.7 62.0 62.2 62.5 62.7 63.0 63.2 63.5 63.8 64.0 64.3 64.5 64.8 65.0 65.3 65.6 65.8 66.1 66.3 66.6 66.8 67.1 67.4 67.6 67.9 68.1 68.4 68.6 68.9 69.2 69.4 69.7 69.9 70.2 70.4 70.7 71.0 71.2 71.5 71.7 72.0 72.2 72.5 72.8 73.0 73.3 73.5 73.8 74.0 74.3 74.6 74.8 75.1 75.3 75.6 75.8 76.1 76.3 76.6 76.9 77.1 77.4 77.6 77.9 78.1 78.4 78.7 78.9 79.2 79.4 79.7 79.9 80.2 80.5 80.7 81.0 81.2 81.5 81.7 82.0 82.3 82.5 82.8 83.0 83.3 83.5 83.8 84.1 84.3 84.6 84.8 85.1 85.3 85.6 85.9 86.1 86.4 86.6 86.9 87.1 87.4 87.7 87.9 88.2 88.4 88.7 88.9 89.2 89.5 89.7 90.0 90.2 90.5 90.7 91.0 91.3 91.5 91.8 92.0 92.3 92.5 92.8 93.1 93.3 93.6 93.8 94.1 94.3 94.6 94.9 95.1 95.4 95.6 95.9 96.1 96.4 96.7 96.9 97.2 97.4 97.7 97.9 98.2 98.5 98.7 99.0 99.2 99.5 99.7 -found 28 predictions from path traversal Error with prediction: snap lend_intergenic: 185866, rend_intergenic: 182769 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 188537, rend_intergenic: 186262 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 204277, rend_intergenic: 201339 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 231042, rend_intergenic: 221735 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 245856, rend_intergenic: 231109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 249808, rend_intergenic: 245898 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 25 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 12890 -exon list size: 2 building trellis 25.0 50.0 75.0 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support