00000000000000000000000000 00000000000000000000000000 000000000^^^^^^^^000000000 000000^^^^^^^^^^^^^^000000 00000^^^^^CENOTE^^^^^00000 00000^^^^^TAKER!^^^^^00000 00000^^^^^^^^^^^^^^^^00000 000000^^^^^^^^^^^^^^000000 000000000^^^^^^^^000000000 00000000000000000000000000 00000000000000000000000000(B Version 2.1.3 @@@@@@@@@@@@@@@@@@@@@@@@@ Your specified arguments: original contigs: /scratch/gdlab/kailun/Phageome/NEC/metaspades/scaffolds/1003-01.fasta forward reads: /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/no_reads reverse reads: /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/no_reads title of this run: 1003_01 Isolate source: unknown collection date: unknown metagenome_type: unknown SRA run number: unknown SRA experiment number: unknown SRA sample number: unknown Bioproject number: unknown template file: /opt/apps/labs/gdlab/envs/cenote-taker2/2.1.3/Cenote-Taker2/dummy_template.sbt minimum circular contig length: 1000 minimum linear contig length: 1000 virus domain database: standard min. viral hallmarks for linear: 1 min. viral hallmarks for circular: 1 handle known seqs: blast_knowns contig assembler: unknown_assembler DNA or RNA: DNA HHsuite tool: hhblits original or TPA: original Do BLASTP?: no_blastp Do Prophage Pruning?: True Filter out plasmids?: True Run BLASTN against nt? /scratch/ref/gdlab/blast_db/nt_2021_10_07 Location of Cenote scripts: /opt/apps/labs/gdlab/envs/cenote-taker2/2.1.3/Cenote-Taker2 Location of scratch directory: none GB of memory: 30 number of CPUs available for run: 12 Annotation mode? False @@@@@@@@@@@@@@@@@@@@@@@@@ scratch space will not be used in this run HHsuite database locations: /opt/apps/labs/gdlab/envs/cenote-taker2/2.1.3/Cenote-Taker2/NCBI_CD/NCBI_CD /opt/apps/labs/gdlab/envs/cenote-taker2/2.1.3/Cenote-Taker2/pfam_32_db/pfam /opt/apps/labs/gdlab/envs/cenote-taker2/2.1.3/Cenote-Taker2/pdb70/pdb70 no CRISPR file given time update: locating inputs: 10-08-21---10:36:40 /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/1003-01.fasta File with .fasta extension detected, attempting to keep contigs over 1000 nt and find circular sequences with apc.pl(B 1003_01560.fasta has DTRs/circularity 1003_01639.fasta has DTRs/circularity 1003_011105.fasta has DTRs/circularity 1003_01621.fasta has DTRs/circularity 1003_011714.fasta has DTRs/circularity 1003_011506.fasta has DTRs/circularity 1003_01885.fasta has DTRs/circularity 1003_011573.fasta has DTRs/circularity 1003_012099.fasta has DTRs/circularity 1003_011037.fasta has DTRs/circularity 1003_011033.fasta has DTRs/circularity 1003_011063.fasta has DTRs/circularity no reads provided or reads not found Circular fasta file(s) detected(B Putting non-circular contigs in a separate directory (B time update: running IRF for ITRs in non-circular contigs 10-08-21---11:11:46 1003_011043.fasta contains ITRs 1003_01902.fasta contains ITRs time update: running prodigal on linear contigs 10-08-21---11:14:39 time update: running linear contigs with hmmscan against virus hallmark gene database: standard 10-08-21---18:09:23 time update: Calling ORFs for circular/DTR sequences with prodigal 10-08-21---20:33:27 time update: running hmmscan on circular/DTR contigs 10-08-21---20:33:30 time update: Calling ORFs for ITR sequences with prodigal 10-08-21---20:33:42 time update: running hmmscan on ITR contigs 10-08-21---20:33:43  Starting pruning of non-DTR/circular contigs with viral domains (B pruning script opened fna files found ./1003_013165.fna is too short to prune chromosomal regions ./1003_013369.fna is too short to prune chromosomal regions ./1003_012143.fna is too short to prune chromosomal regions ./1003_012370.fna is too short to prune chromosomal regions ./1003_01925.fna is too short to prune chromosomal regions ./1003_013232.fna is too short to prune chromosomal regions ./1003_011240.fna is too short to prune chromosomal regions ./1003_01627.fna is too short to prune chromosomal regions ./1003_011199.fna is too short to prune chromosomal regions ./1003_011445.fna is too short to prune chromosomal regions ./1003_012286.fna is too short to prune chromosomal regions ./1003_011423.fna is too short to prune chromosomal regions ./1003_01716.fna is too short to prune chromosomal regions ./1003_011060.fna is too short to prune chromosomal regions ./1003_01615.fna is too short to prune chromosomal regions ./1003_012527.fna is too short to prune chromosomal regions ./1003_011851.fna is too short to prune chromosomal regions ./1003_01753.fna is too short to prune chromosomal regions ./1003_011005.fna is too short to prune chromosomal regions ./1003_011640.fna is too short to prune chromosomal regions ./1003_012580.fna is too short to prune chromosomal regions ./1003_013030.fna is too short to prune chromosomal regions ./1003_01613.fna is too short to prune chromosomal regions ./1003_012012.fna is too short to prune chromosomal regions ./1003_013887.fna is too short to prune chromosomal regions ./1003_013229.fna is too short to prune chromosomal regions ./1003_011297.fna is too short to prune chromosomal regions ./1003_01616.fna is too short to prune chromosomal regions ./1003_01848.fna is too short to prune chromosomal regions ./1003_01927.fna is too short to prune chromosomal regions ./1003_011961.fna is too short to prune chromosomal regions ./1003_01704.fna is too short to prune chromosomal regions ./1003_01933.fna is too short to prune chromosomal regions ./1003_011789.fna is too short to prune chromosomal regions ./1003_011352.fna is too short to prune chromosomal regions ./1003_012956.fna is too short to prune chromosomal regions ./1003_012729.fna is too short to prune chromosomal regions ./1003_01769.fna is too short to prune chromosomal regions ./1003_011054.fna is too short to prune chromosomal regions ./1003_013433.fna is too short to prune chromosomal regions ./1003_011142.fna is too short to prune chromosomal regions ./1003_011226.fna is too short to prune chromosomal regions ./1003_012808.fna is too short to prune chromosomal regions ./1003_01826.fna is too short to prune chromosomal regions ./1003_01648.fna is too short to prune chromosomal regions ./1003_011614.fna is too short to prune chromosomal regions ./1003_01875.fna is too short to prune chromosomal regions ./1003_01850.fna is too short to prune chromosomal regions ./1003_012287.fna is too short to prune chromosomal regions ./1003_012020.fna is too short to prune chromosomal regions ./1003_011099.fna is too short to prune chromosomal regions ./1003_011426.fna is too short to prune chromosomal regions ./1003_01806.fna is too short to prune chromosomal regions ./1003_011133.fna is too short to prune chromosomal regions ./1003_01856.fna is too short to prune chromosomal regions ./1003_01700.fna is too short to prune chromosomal regions ./1003_011360.fna is too short to prune chromosomal regions ./1003_011235.fna is too short to prune chromosomal regions ./1003_01644.fna is too short to prune chromosomal regions ./1003_011129.fna is too short to prune chromosomal regions ./1003_012015.fna is too short to prune chromosomal regions ./1003_01772.fna is too short to prune chromosomal regions ./1003_01647.fna is too short to prune chromosomal regions ./1003_013216.fna is too short to prune chromosomal regions ./1003_01843.fna is too short to prune chromosomal regions ./1003_01729.fna is too short to prune chromosomal regions ./1003_01724.fna is too short to prune chromosomal regions ./1003_012297.fna is too short to prune chromosomal regions ./1003_012813.fna is too short to prune chromosomal regions ./1003_01945.fna is too short to prune chromosomal regions ./1003_01811.fna is too short to prune chromosomal regions ./1003_011398.fna is too short to prune chromosomal regions ./1003_012069.fna is too short to prune chromosomal regions ./1003_013415.fna is too short to prune chromosomal regions ./1003_012954.fna is too short to prune chromosomal regions ./1003_011180.fna is too short to prune chromosomal regions ./1003_013472.fna is too short to prune chromosomal regions ./1003_01663.fna is too short to prune chromosomal regions ./1003_012234.fna is too short to prune chromosomal regions ./1003_013584.fna is too short to prune chromosomal regions ./1003_012117.fna is too short to prune chromosomal regions ./1003_01645.fna is too short to prune chromosomal regions ./1003_01952.fna is too short to prune chromosomal regions ./1003_013023.fna is too short to prune chromosomal regions ./1003_011296.fna is too short to prune chromosomal regions ./1003_011926.fna is too short to prune chromosomal regions ./1003_013511.fna is too short to prune chromosomal regions ./1003_01866.fna is too short to prune chromosomal regions time update: HMMSCAN of common viral domains beginning 10-08-21---20:34:04 time update: making tables for hmmscan and rpsblast outputs 10-08-21---21:21:35 time update: running RPSBLAST on each sequence 10-08-21---21:21:57 /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/1003_01/no_end_contigs_with_viral_domain/COMBINED_RESULTS_PRUNE.AA.rpsblast.out time update: parsing tables into virus_signal.seq files for hmmscan and rpsblast outputs 10-08-21---21:40:59 time update: Identifying virus chunks, chromosomal junctions, and pruning contigs as necessary 10-08-21---21:45:53 Running file: 1003_01100.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 119 + ... none 8400 2 183 - ... none 11600 3 347 + ... none 19800 4 611 - ... none 33000 5 1044 + ... none 54650 6 1150 - ... none 59950 7 1476 + ... none 76250 8 1702 - ... none 87550 8 1702 - ... none 87550 [10 rows x 6 columns] Running file: 1003_01101.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 146 - ... none 9750 2 316 + ... none 18250 3 378 - ... none 21350 4 2021 + ... none 103500 4 2021 + ... none 103500 [6 rows x 6 columns] Running file: 1003_01109.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 181 - ... none 11500 2 850 + ... none 44950 3 1674 - ... none 86150 3 1674 - ... none 86150 [5 rows x 6 columns] Running file: 1003_01111.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 326 + ... none 18750 2 486 - ... none 26750 3 1249 + ... none 64900 4 1293 - ... none 67100 5 1591 + ... none 82000 5 1591 + ... none 82000 [7 rows x 6 columns] Running file: 1003_01117.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 484 + ... none 26650 2 540 - ... none 29450 2 540 - ... none 29450 [4 rows x 6 columns] Running file: 1003_0111.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 86 + ... none 6750 2 233 - ... none 14100 3 912 + ... none 48050 4 1055 - ... none 55200 5 1673 + ... none 86100 6 1820 - ... none 93450 7 1955 + ... none 100200 8 2135 - ... none 109200 9 2503 + ... none 127600 10 2639 - ... none 134400 11 2774 + ... none 141150 12 2908 - ... none 147850 13 3190 + ... none 161950 14 3197 - ... none 162300 15 3713 + ... none 188100 16 4016 - ... none 203250 17 4597 + ... none 232300 18 4764 - ... none 240650 19 5259 + ... none 265400 20 5385 - ... none 271700 21 5615 + ... none 283200 22 5689 - ... none 286900 23 5935 + ... none 299200 24 6003 - ... none 302600 25 6118 + ... none 308350 26 6210 - ... none 312950 27 6499 + ... none 327400 28 6590 - ... none 331950 29 6919 + ... none 348400 30 7078 - ... none 356350 31 7173 + ... none 361100 32 7262 - ... none 365550 33 7267 + ... none 365800 34 7630 - ... none 383950 34 7630 - ... none 383950 [36 rows x 6 columns] Running file: 1003_01126.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 101 + ... none 7500 2 202 - ... none 12550 3 320 + ... none 18450 4 420 - ... none 23450 5 483 + ... none 26600 6 754 - ... none 40150 7 922 + ... none 48550 8 987 - ... none 51800 9 1110 + ... none 57950 10 1509 - ... none 77900 10 1509 - ... none 77900 [12 rows x 6 columns] Running file: 1003_01142.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 443 - ... none 24600 2 813 + ... none 43100 3 914 - ... none 48150 4 1232 + ... none 64050 5 1324 - ... none 68650 5 1324 - ... none 68650 [7 rows x 6 columns] Running file: 1003_01151.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 1062 + ... none 55550 2 1168 - ... none 60850 2 1168 - ... none 60850 [4 rows x 6 columns] Running file: 1003_01158.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 762 + ... none 40550 1 762 + ... none 40550 [3 rows x 6 columns] Running file: 1003_0115.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 311 + ... none 18000 2 370 - ... none 20950 3 468 + ... none 25850 4 507 - ... none 27800 5 1136 + ... none 59250 6 1168 - ... none 60850 7 1360 + ... none 70450 8 1613 - ... none 83100 9 1702 + ... none 87550 10 2472 - ... none 126050 10 2472 - ... none 126050 [12 rows x 6 columns] Running file: 1003_0116.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 1013 + ... none 53100 2 1149 - ... none 59900 3 1292 + ... none 67050 4 2296 - ... none 117250 5 3124 + ... none 158650 6 3324 - ... none 168650 7 4139 + ... none 209400 8 4201 - ... none 212500 9 4959 + ... none 250400 10 5746 - ... none 289750 11 6032 + ... none 304050 12 6113 - ... none 308100 12 6113 - ... none 308100 [14 rows x 6 columns] Running file: 1003_01180.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 754 + ... none 40150 2 889 - ... none 46900 2 889 - ... none 46900 [4 rows x 6 columns] Running file: 1003_01182.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 164 - ... none 10650 2 547 + ... none 29800 3 712 - ... none 38050 4 779 + ... none 41400 5 1036 - ... none 54250 5 1036 - ... none 54250 [7 rows x 6 columns] Running file: 1003_01185.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 166 + ... none 10750 2 211 - ... none 13000 3 737 + ... none 39300 4 780 - ... none 41450 4 780 - ... none 41450 [6 rows x 6 columns] Running file: 1003_01187.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 121 - ... none 8500 2 630 + ... none 33950 3 691 - ... none 37000 3 691 - ... none 37000 [5 rows x 6 columns] Running file: 1003_0118.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 329 + ... none 18900 2 407 - ... none 22800 3 2097 + ... none 107300 4 2181 - ... none 111500 5 2855 + ... none 145200 6 2922 - ... none 148550 7 3655 + ... none 185200 8 3981 - ... none 201500 9 4022 + ... none 203550 10 4043 - ... none 204600 11 5301 + ... none 267500 12 5357 - ... none 270300 13 5832 + ... none 294050 14 5885 - ... none 296700 14 5885 - ... none 296700 [16 rows x 6 columns] Running file: 1003_01196.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 296 - ... none 17250 1 296 - ... none 17250 [3 rows x 6 columns] Running file: 1003_01197.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 4 + ... none 2650 2 814 - ... none 43150 2 814 - ... none 43150 [4 rows x 6 columns] Running file: 1003_0119.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 31 - ... none 4000 2 1122 + ... none 58550 3 1264 - ... none 65650 4 1766 + ... none 90750 5 2012 - ... none 103050 6 3580 + ... none 181450 7 3693 - ... none 187100 8 4184 + ... none 211650 9 4414 - ... none 223150 10 4977 + ... none 251300 11 5342 - ... none 269550 11 5342 - ... none 269550 [13 rows x 6 columns] Running file: 1003_011.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 1312 + ... none 68050 2 1452 - ... none 75050 3 1669 + ... none 85900 4 1705 - ... none 87700 5 2315 + ... none 118200 6 2330 - ... none 118950 7 2621 + ... none 133500 8 2726 - ... none 138750 9 4147 + ... none 209800 10 4179 - ... none 211400 11 5797 + ... none 292300 12 5894 - ... none 297150 13 6610 + ... none 332950 14 6641 - ... none 334500 15 7613 + ... none 383100 16 7676 - ... none 386250 17 8336 + ... none 419250 18 8506 - ... none 427750 19 8835 + ... none 444200 20 8917 - ... none 448300 21 12826 + ... none 643750 22 13152 - ... none 660050 23 13831 + ... none 694000 24 13987 - ... none 701800 25 15251 + ... none 765000 26 15382 - ... none 771550 27 16553 + ... none 830100 28 16654 - ... none 835150 29 16759 + ... none 840400 30 16804 - ... none 842650 31 16970 + ... none 850950 32 17049 - ... none 854900 33 17349 + ... none 869900 34 17630 - ... none 883950 35 18331 + ... none 919000 36 18391 - ... none 922000 37 19722 + ... none 988550 38 19894 - ... none 997150 39 20085 + ... none 1006700 40 20139 - ... none 1009400 41 21931 + ... none 1099000 42 21978 - ... none 1101350 43 23026 + ... none 1153750 44 23059 - ... none 1155400 45 25691 + ... none 1287000 46 25720 - ... none 1288450 47 26892 + ... none 1347050 48 26965 - ... none 1350700 49 27319 + ... none 1368400 50 27389 - ... none 1371900 51 27849 + ... none 1394900 52 27937 - ... none 1399300 53 28068 + ... none 1405850 54 28216 - ... none 1413250 55 28359 + ... none 1420400 56 28476 - ... none 1426250 56 28476 - ... none 1426250 [58 rows x 6 columns] Running file: 1003_01207.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 281 - ... none 16500 2 343 + ... none 19600 3 550 - ... none 29950 3 550 - ... none 29950 [5 rows x 6 columns] Running file: 1003_0120.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 476 + ... none 26250 2 751 - ... none 40000 3 945 + ... none 49700 4 1013 - ... none 53100 5 1695 + ... none 87200 6 1919 - ... none 98400 7 2669 + ... none 135900 8 2712 - ... none 138050 9 3159 + ... none 160400 10 3240 - ... none 164450 11 3334 + ... none 169150 12 3571 - ... none 181000 13 4586 + ... none 231750 14 4667 - ... none 235800 15 5602 + ... none 282550 15 5602 + ... none 282550 [17 rows x 6 columns] Running file: 1003_01212.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_0121.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 1560 + ... none 80450 2 1677 - ... none 86300 3 1865 + ... none 95700 4 2139 - ... none 109400 5 2411 + ... none 123000 6 2551 - ... none 130000 7 2735 + ... none 139200 8 2891 - ... none 147000 9 3069 + ... none 155900 10 3180 - ... none 161450 11 3303 + ... none 167600 12 3331 - ... none 169000 13 3862 + ... none 195550 14 4573 - ... none 231100 15 4698 + ... none 237350 16 4779 - ... none 241400 17 5092 + ... none 257050 18 5254 - ... none 265150 19 5329 + ... none 268900 20 5489 - ... none 276900 20 5489 - ... none 276900 [22 rows x 6 columns] Running file: 1003_01223.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 680 - ... none 36450 1 680 - ... none 36450 [3 rows x 6 columns] Running file: 1003_01243.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01246.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01249.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_0124.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 1143 + ... none 59600 2 1173 - ... none 61100 3 1712 + ... none 88050 4 1832 - ... none 94050 5 2107 + ... none 107800 6 2247 - ... none 114800 7 3642 + ... none 184550 8 3658 - ... none 185350 9 3759 + ... none 190400 10 4013 - ... none 203100 11 4841 + ... none 244500 12 4983 - ... none 251600 12 4983 - ... none 251600 [14 rows x 6 columns] Running file: 1003_01254.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01255.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 237 - ... none 14300 2 686 + ... none 36750 2 686 + ... none 36750 [4 rows x 6 columns] Running file: 1003_0125.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 608 + ... none 32850 2 696 - ... none 37250 3 918 + ... none 48350 4 1349 - ... none 69900 5 1536 + ... none 79250 6 1754 - ... none 90150 7 4091 + ... none 207000 8 4317 - ... none 218300 9 4351 + ... none 220000 10 4415 - ... none 223200 10 4415 - ... none 223200 [12 rows x 6 columns] Running file: 1003_0127.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 1107 + ... none 57800 2 1392 - ... none 72050 3 1650 + ... none 84950 4 1783 - ... none 91600 5 1969 + ... none 100900 6 2124 - ... none 108650 7 2303 + ... none 117600 8 2415 - ... none 123200 9 2536 + ... none 129250 10 2563 - ... none 130600 11 3113 + ... none 158100 12 3210 - ... none 162950 13 3322 + ... none 168550 14 3402 - ... none 172550 15 3704 + ... none 187650 16 3864 - ... none 195650 17 3937 + ... none 199300 18 4097 - ... none 207300 18 4097 - ... none 207300 [20 rows x 6 columns] Running file: 1003_01289.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 180 - ... none 11450 2 478 + ... none 26350 2 478 + ... none 26350 [4 rows x 6 columns] Running file: 1003_0128.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 229 - ... none 13900 2 1577 + ... none 81300 3 1709 - ... none 87900 4 1778 + ... none 91350 5 2003 - ... none 102600 6 2854 + ... none 145150 7 3781 - ... none 191500 8 4124 + ... none 208650 9 4226 - ... none 213750 10 4465 + ... none 225700 11 4799 - ... none 242400 11 4799 - ... none 242400 [13 rows x 6 columns] Running file: 1003_01291.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_012.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 934 - ... none 49150 2 1722 + ... none 88550 3 1739 - ... none 89400 4 2553 + ... none 130100 5 2705 - ... none 137700 6 3077 + ... none 156300 7 3106 - ... none 157750 8 3129 + ... none 158900 9 3318 - ... none 168350 10 3476 + ... none 176250 11 3515 - ... none 178200 12 4349 + ... none 219900 13 4476 - ... none 226250 14 4543 + ... none 229600 15 4760 - ... none 240450 16 5602 + ... none 282550 17 5883 - ... none 296600 18 6333 + ... none 319100 19 6532 - ... none 329050 20 6579 + ... none 331400 21 6980 - ... none 351450 22 7213 + ... none 363100 23 7280 - ... none 366450 24 7485 + ... none 376700 25 7585 - ... none 381700 26 7683 + ... none 386600 27 7792 - ... none 392050 28 8355 + ... none 420200 29 8439 - ... none 424400 30 9103 + ... none 457600 31 9344 - ... none 469650 32 10455 + ... none 525200 33 10568 - ... none 530850 34 12507 + ... none 627800 35 12660 - ... none 635450 35 12660 - ... none 635450 [37 rows x 6 columns] Running file: 1003_01301.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 453 + ... none 25100 1 453 + ... none 25100 [3 rows x 6 columns] Running file: 1003_01304.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01307.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 311 - ... none 18000 1 311 - ... none 18000 [3 rows x 6 columns] Running file: 1003_01316.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01318.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_0131.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 49 - ... none 4900 2 309 + ... none 17900 3 391 - ... none 22000 4 697 + ... none 37300 5 765 - ... none 40700 6 1232 + ... none 64050 7 1403 - ... none 72600 8 1517 + ... none 78300 9 1550 - ... none 79950 10 1714 + ... none 88150 11 1919 - ... none 98400 12 3344 + ... none 169650 13 3511 - ... none 178000 14 3620 + ... none 183450 15 3712 - ... none 188050 15 3712 - ... none 188050 [17 rows x 6 columns] Running file: 1003_01336.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01338.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01347.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 240 - ... none 14450 1 240 - ... none 14450 [3 rows x 6 columns] Running file: 1003_0134.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 685 - ... none 36700 2 890 + ... none 46950 3 952 - ... none 50050 4 1133 + ... none 59100 5 1843 - ... none 94600 6 3473 + ... none 176100 7 3549 - ... none 179900 8 4050 + ... none 204950 8 4050 + ... none 204950 [10 rows x 6 columns] Running file: 1003_01358.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_0135.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 477 + ... none 26300 2 547 - ... none 29800 2 547 - ... none 29800 [4 rows x 6 columns] Running file: 1003_0136.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 988 + ... none 51850 2 1097 - ... none 57300 3 1205 + ... none 62700 4 1364 - ... none 70650 5 1944 + ... none 99650 6 2125 - ... none 108700 7 2886 + ... none 146750 8 2985 - ... none 151700 9 3493 + ... none 177100 10 4215 - ... none 213200 10 4215 - ... none 213200 [12 rows x 6 columns] Running file: 1003_01393.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_013.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 410 + ... none 22950 2 529 - ... none 28900 3 751 + ... none 40000 4 992 - ... none 52050 5 1067 + ... none 55800 6 1291 - ... none 67000 7 2128 + ... none 108850 8 2241 - ... none 114500 9 3384 + ... none 171650 10 3481 - ... none 176500 11 4388 + ... none 221850 12 4745 - ... none 239700 13 5186 + ... none 261750 14 5201 - ... none 262500 15 5509 + ... none 277900 16 5803 - ... none 292600 17 6546 + ... none 329750 18 6620 - ... none 333450 19 7653 + ... none 385100 20 7704 - ... none 387650 21 7820 + ... none 393450 22 7855 - ... none 395200 23 8156 + ... none 410250 24 8291 - ... none 417000 25 8625 + ... none 433700 26 8756 - ... none 440250 27 9160 + ... none 460450 28 9297 - ... none 467300 29 10055 + ... none 505200 30 10215 - ... none 513200 31 10656 + ... none 535250 31 10656 + ... none 535250 [33 rows x 6 columns] Running file: 1003_01405.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 133 - ... none 9100 1 133 - ... none 9100 [3 rows x 6 columns] Running file: 1003_01431.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01444.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01461.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 165 - ... none 10700 1 165 - ... none 10700 [3 rows x 6 columns] Running file: 1003_01462.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01490.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_014.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 4 - ... none 2650 2 1419 + ... none 73400 3 1503 - ... none 77600 4 2130 + ... none 108950 5 2180 - ... none 111450 6 2986 + ... none 151750 7 3395 - ... none 172200 8 4131 + ... none 209000 9 4327 - ... none 218800 10 4524 + ... none 228650 11 5084 - ... none 256650 12 9695 + ... none 487200 13 9861 - ... none 495500 13 9861 - ... none 495500 [15 rows x 6 columns] Running file: 1003_01500.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 39 + ... none 4400 1 39 + ... none 4400 [3 rows x 6 columns] Running file: 1003_01502.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01514.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01527.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01537.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01547.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01554.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_0155.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 123 + ... none 8600 2 199 - ... none 12400 3 855 + ... none 45200 4 1200 - ... none 62450 5 1762 + ... none 90550 6 1812 - ... none 93050 7 3289 + ... none 166900 7 3289 + ... none 166900 [9 rows x 6 columns] Running file: 1003_0157.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 597 + ... none 32300 2 809 - ... none 42900 3 1229 + ... none 63900 4 1327 - ... none 68800 5 2939 + ... none 149400 6 3345 - ... none 169700 6 3345 - ... none 169700 [8 rows x 6 columns] Running file: 1003_01586.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01591.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500 [2 rows x 6 columns] Running file: 1003_01595.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 0 1 - ... none 2500 [2 rows x 6 columns] Running file: 1003_015.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 2 - ... none 2550 2 122 + ... none 8550 3 180 - ... none 11450 4 2862 + ... none 145550 5 3319 - ... none 168400 6 3721 + ... none 188500 7 3962 - ... none 200550 8 4258 + ... none 215350 9 4408 - ... none 222850 10 4707 + ... none 237800 11 4838 - ... none 244350 12 5187 + ... none 261800 13 5219 - ... none 263400 14 6205 + ... none 312700 15 6295 - ... none 317200 16 8779 + ... none 441400 17 8844 - ... none 444650 18 9060 + ... none 455450 19 9099 - ... none 457400 19 9099 - ... none 457400 [21 rows x 6 columns] Running file: 1003_0162.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 800 + ... none 42450 2 959 - ... none 50400 3 1169 + ... none 60900 4 1196 - ... none 62250 5 1343 + ... none 69600 6 1380 - ... none 71450 7 1612 + ... none 83050 8 2440 - ... none 124450 8 2440 - ... none 124450 [10 rows x 6 columns] Running file: 1003_0165.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 225 + ... none 13700 2 309 - ... none 17900 3 712 + ... none 38050 4 1729 - ... none 88900 5 1888 + ... none 96850 6 2113 - ... none 108100 7 2458 + ... none 125350 8 2635 - ... none 134200 8 2635 - ... none 134200 [10 rows x 6 columns] Running file: 1003_0166.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 75 + ... none 6200 2 165 - ... none 10700 3 916 + ... none 48250 4 1630 - ... none 83950 4 1630 - ... none 83950 [6 rows x 6 columns] Running file: 1003_0170.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 839 + ... none 44400 2 2056 - ... none 105250 2 2056 - ... none 105250 [4 rows x 6 columns] Running file: 1003_0173.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 817 + ... none 43300 2 877 - ... none 46300 3 1251 + ... none 65000 4 1338 - ... none 69350 4 1338 - ... none 69350 [6 rows x 6 columns] Running file: 1003_0177.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 90 + ... none 6950 2 470 - ... none 25950 3 1334 + ... none 69150 4 1370 - ... none 70950 5 1913 + ... none 98100 6 1956 - ... none 100250 7 2500 + ... none 127450 8 2548 - ... none 129850 8 2548 - ... none 129850 [10 rows x 6 columns] Running file: 1003_017.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 121 - ... none 8500 2 240 + ... none 14450 3 269 - ... none 15900 4 791 + ... none 42000 5 1161 - ... none 60500 6 1264 + ... none 65650 7 1335 - ... none 69200 8 1649 + ... none 84900 9 1811 - ... none 93000 10 1893 + ... none 97100 11 2059 - ... none 105400 12 3139 + ... none 159400 13 3157 - ... none 160300 14 4637 + ... none 234300 15 4839 - ... none 244400 16 5031 + ... none 254000 17 5042 - ... none 254550 18 5243 + ... none 264600 19 5398 - ... none 272350 20 5619 + ... none 283400 21 5706 - ... none 287750 22 5957 + ... none 300300 23 6032 - ... none 304050 24 6560 + ... none 330450 25 6774 - ... none 341150 26 7716 + ... none 388250 27 7841 - ... none 394500 28 7900 + ... none 397450 29 7980 - ... none 401450 30 7989 + ... none 401900 31 8149 - ... none 409900 31 8149 - ... none 409900 [33 rows x 6 columns] Running file: 1003_0183.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 375 + ... none 21200 2 520 - ... none 28450 3 1094 + ... none 57150 4 1308 - ... none 67850 5 1544 + ... none 79650 6 1644 - ... none 84650 6 1644 - ... none 84650 [8 rows x 6 columns] Running file: 1003_0185.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 427 + ... none 23800 2 446 - ... none 24750 3 823 + ... none 43600 4 1015 - ... none 53200 5 1653 + ... none 85100 6 1793 - ... none 92100 7 1856 + ... none 95250 8 2121 - ... none 108500 9 2291 + ... none 117000 10 2354 - ... none 120150 10 2354 - ... none 120150 [12 rows x 6 columns] Running file: 1003_0186.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 84 - ... none 6650 2 1768 + ... none 90850 3 1859 - ... none 95400 4 2334 + ... none 119150 4 2334 + ... none 119150 [6 rows x 6 columns] Running file: 1003_018.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 445 - ... none 24700 2 561 + ... none 30500 3 674 - ... none 36150 4 832 + ... none 44050 5 946 - ... none 49750 6 1861 + ... none 95500 7 1977 - ... none 101300 8 3720 + ... none 188450 9 3852 - ... none 195050 10 3945 + ... none 199700 11 3975 - ... none 201200 12 4001 + ... none 202500 13 4382 - ... none 221550 14 4454 + ... none 225150 15 4612 - ... none 233050 16 5893 + ... none 297100 17 5982 - ... none 301550 18 6623 + ... none 333600 19 6705 - ... none 337700 20 7571 + ... none 381000 21 7613 - ... none 383100 22 8356 + ... none 420250 23 8463 - ... none 425600 23 8463 - ... none 425600 [25 rows x 6 columns] Running file: 1003_0190.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 440 + ... none 24450 2 499 - ... none 27400 3 931 + ... none 49000 4 1035 - ... none 54200 5 1969 + ... none 100900 6 2246 - ... none 114750 6 2246 - ... none 114750 [8 rows x 6 columns] Running file: 1003_0194.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 1 1806 - ... none 92750 1 1806 - ... none 92750 [3 rows x 6 columns] Running file: 1003_019.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 - ... none 2500 1 5045 + ... none 254700 2 5142 - ... none 259550 3 6115 + ... none 308200 4 6288 - ... none 316850 5 7091 + ... none 357000 6 7263 - ... none 365600 7 7583 + ... none 381600 8 7658 - ... none 385350 9 7670 + ... none 385950 10 7809 - ... none 392900 11 7925 + ... none 398700 12 8015 - ... none 403200 12 8015 - ... none 403200 [14 rows x 6 columns] time update: Making prophage table 10-08-21---22:16:17  FINISHED PRUNING CONTIGS WITH AT LEAST 1 VIRAL DOMAIN(S) (B Annotating DTR contigs time update: running BLASTX, DTR contigs 10-08-21---22:17:49 time update: running PHANOTATE, annotate DTR contigs 10-08-21---22:18:13 time update: running hmmscan1, annotate DTR contigs 10-08-21---22:18:19 time update: running hmmscan2, annotate DTR contigs 10-08-21---22:18:27 BLASTN databases not found, skipping BLASTN step time update: running RPSBLAST, annotate DTR contigs 10-08-21---22:18:39 /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/1003_01/DTR_contigs_with_viral_domain/COMBINED_RESULTS.rotate.AA.rpsblast.out time update: running tRNAscan-SE 10-08-21---22:20:47  Removing ORFS within ORFs that are 'hypothetical' (B  Grabbing ORFs wihout RPS-BLAST hits and separating them into individual files for HHsearch (B time update: running HHsearch or HHblits 10-08-21---22:21:22 /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/1003_01/DTR_contigs_with_viral_domain/1003_011063.rotate.out_all.hhr /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/1003_01/DTR_contigs_with_viral_domain/1003_01560.rotate.out_all.hhr  Combining tbl files from all search results AND fix overlapping ORF module (B No ITR contigs with minimum hallmark genes found. Annotating linear contigs time update: running BLASTX, annotate linear contigs 10-08-21---22:21:45 time update: running PHANOTATE, annotate linear contigs 10-08-21---22:50:39 time update: running Prodigal, annotate linear contigs 10-08-21---23:34:57 time update: running hmmscan1, annotating linear contigs 10-08-21---23:35:02 time update: running hmmscan2, annotating linear contigs 10-08-21---23:46:54 BLASTN databases not found, skipping BLASTN step time update: running RPSBLAST, annotating linear contigs 10-08-21---23:59:58 /scratch/gdlab/kailun/Phageome/NEC/CenoteTaker2_3/1003_01/no_end_contigs_with_viral_domain/COMBINED_RESULTS.rotate.AA.rpsblast.out time update: running tRNAscan-SE 10-09-21---00:01:35  Removing ORFS within ORFs that are 'hypothetical' (B  Grabbing ORFs wihout RPS-BLAST hits and separating them into individual files for HHsearch (B time update: running HHsearch or HHblits 10-09-21---00:56:04  Combining tbl files from all search results AND fix overlapping ORF module, linear contigs (B finalizing taxonomy for linear contigs No suitable ORF for taxonomy found for 1003_011060_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01111_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_011426_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_011614_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_011789_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01180_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_011926_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_012527_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_012_vs02, using BLASTX result. No suitable ORF for taxonomy found for 1003_0131_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01347_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_013887_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01502_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01527_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01615_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01753_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_0177_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_01866_vs01, using BLASTX result. No suitable ORF for taxonomy found for 1003_0190_vs01, using BLASTX result. time update: finished annotating linear contigs 10-09-21---01:19:58 time update: running tbl2asn 10-09-21---01:21:37 Making gtf tables from final feature tables time update: Finishing 10-09-21---01:22:37 Virus prediction summary:(B 182 virus contigs were detected/predicted. 2 contigs had DTRs/circularity. 0 contigs had ITRs. 180 were linear/had no end features Prophage pruning summary:(B 92 linear contigs > 10 kb were run through pruning module, and 67 virus sub-contigs (putative prophages/proviruses) were extracted from these. 25 virus contigs were kept intact. removing ancillary files output directory: 1003_01 (B  >>>>>>CENOTE-TAKER 2 HAS FINISHED TAKING CENOTES<<<<<< (B /opt/apps/labs/gdlab/envs/cenote-taker2/2.1.3/Cenote-Taker2 prodigal found BWA found samtools found mummer found circlator found blastp found blastn found blastx found rpsblast found bioawk found efetch found ktClassifyBLAST found hmmscan found bowtie2 found tRNAscan-SE found pileup.sh found tbl2asn found getorf found transeq found bedtools found Job completed successfully