REF_FASTA :/home/curtish/ics/consults/ross/ics63/ref_genomes/NC_006273.2_HCMV_Merlin.fa FASTQ_FWD :/scratch/user/curtish/ross/vicunaFall/../fastq/SR07/55073-1_S5_L001_R1_001.fastq FASTQ_REV :/scratch/user/curtish/ross/vicunaFall/../fastq/SR07/55073-1_S5_L001_R2_001.fastq VICUNA_MSA_FILE :/home/curtish/ics/consults/ross/ics63/vicuna/ViralReferenceGenomes/HCMV/HCMV_All_Reference.fasta VICUNA_DIR :/share/apps/ngs-ccts/VICUNA_v1.3 VICUNA_EXE :/share/apps/ngs-ccts/VICUNA_v1.3/bin/vicuna-omp-v1.0 VICUNA_FASTQ_DIR :/scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/input_pe_fastq VICUNA_OUT_DIR :/scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output VICUNA_CONF :/scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/vicuna_config.txt VANALYSIS_CONF :/scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/vanalysis_contig.txt VICUNA_RAW_CONTIGS :/scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/contig.fasta VFAT_DIR :/share/apps/ngs-ccts/VfatSoftwarePackage export OMP_NUM_THREADS=6 Sun Jun 1 22:40:15 CDT 2014 TS START VICUNA SR07-05-55073-1 # CMD: /share/apps/ngs-ccts/VICUNA_v1.3/bin/vicuna-omp-v1.0 /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/vicuna_config.txt -------------------------------------------------------- Program runs with the following Parameter setting: ===== Trimmer ===== vectorFileName trimLogFileName minMSize 9 minInternalMSize 15 maxOverhangSize 2 minReadSize 25 ===== Profiler ===== MSAFileName /home/curtish/ics/consults/ross/ics63/vicuna/ViralReferenceGenomes/HCMV/HCMV_All_Reference.fasta binNumber 20 kmerLength 15 (encode using 4 bytes) maxHD 1 minSpan 75 blockNumber 5 rMapFileName ===== Contiger ===== w1 12 w2 5 Divergence 8 max_read_overhang 2 min_profile_col_weight 5 min_consensus_base_ratio 85 max_contig_overhang 10 seed_kmer_len 12 min_contig_overlap 25 min_contig_links 3 min_identity 90 min_perc_polymorphism 5 max_variant_len 20 ===== Assembly ===== pFqDir /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/input_pe_fastq/ batchSize 1000000 LibSizeLowerBound 100 LibSizeUpperBound 800 min_output_contig_len 200 outputDIR /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/ -------------------------------------------------------- Indexing ... /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/input_pe_fastq//1_2.fastq /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/input_pe_fastq//1_1.fastq 1_2.fastq #reads: 770577 1_1.fastq #reads: 770577 Total # Input Reads: 1541154 Indexing done !!! *** 1.47605 mins *** ----------------------------------------------------------- Trimming ... no vector trimming applied. Writing trim logs to file: /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/trim.log Number of Reads Trimmed by Heads, Tails, Full, Total: 0(nan%total) 0(nan%total) 0(nan%total) 0 Number of low complexity reads: 178382 Number of trimmed read-pairs: 70762 ( inf %total) Trimming done !!! *** 0.117833 mins *** ----------------------------------------------------------- Profiler ... Profiling ... ... _kmers size = 6648536 ------------------------------------------------- Histogram for #bins each kmer belongs to #bins #kmer 1 265272 2 113528 3 66676 4 40172 5 26148 6 22184 7 19912 8 17320 9 19038 10 21150 11 26644 12 40044 13 76826 14 206080 15 1536 16 2060 17 566 18 1390 19 756 20 300 21 358 22 348 23 40 24 656 25 104 26 778 27 146 28 1128 29 14 30 58 31 26 32 4 33 8 34 32 35 6 36 18 37 10 38 8 39 10 40 40 41 8 42 8 43 8 45 4 47 4 48 12 50 2 52 2 55 4 56 2 62 2 67 4 68 2 78 2 85 4 88 2 91 4 94 2 ------------------------------------------------- Replicate profiles ... ... Total entry of _duplTb: 33242680 Read assignment ... ... rslv ambiguities ... # of reads assigned to each bin: Bin #reads 0 264175 1 209860 2 102885 3 14224 4 36631 5 66019 6 28536 7 33467 8 23591 9 14403 10 4034 11 17663 12 19553 13 21188 14 165628 15 11096 16 10096 17 26837 18 8351 19 2745 --------------------------------------------- Stat ... # reads that are mapped as pairs: 1022984 # mapped reads: 1080982 --------------------------------------------- Profiling done !!! *** 7.96721 mins *** ----------------------------------------------------------- Building Contigs ... create super shingles for 1080982 reads *** 0.422544 mins *** Clustering via super-shingles *** 0.0285734 mins *** Init contigs no. initial contigs: 86130 no. reads involved: 848659 *** 0.145152 mins *** seed_template = 1101101111100110000111111 STable size: 771468 no. contigs: 87189 no. reads involved: 947504 *** 0.631579 mins *** Validate contigs no. resulting contigs: 254447 no. reads involved: 897503 *** 1.26274 mins *** Merge contigs via rID *** 0.17024 mins *** Validate contigs no. resulting contigs: 89594 no. reads involved: 547862 Extend contigs no. contigs to be extended: 89594 no. reads involved in final contigs: 273741 *** 89.6479 mins *** Contiger done!!! *** 92.3103 mins *** ----------------------------------------------------------- Whole program takes *** 101.871 mins *** DONE! Mon Jun 2 00:22:08 CDT 2014 TS DONE VICUNA SR07-05-55073-1 Mon Jun 2 00:22:08 CDT 2014 TS START CONTIG.ALIGN_PATCH SR07-05-55073-1 # this fixes a bug in VICUNA where it doesn't handle FASTQs that have a whitespace in the read name. # since our FASTQs look like this # @M02079:63:000000000-A8UNW:1:1101:13336:1651 1:N:0:9 # it converts them to this # @M02079:63:000000000-A8UNW:1:1101:13336:1651#1:N:0:9 # we always do this, and it has worked fine on all past fastq sets. # CMD: /home/curtish/ics/consults/ross/hcmv/vicuna/fix_contig.align.sh /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/contig.align perl -i.original -pe s/ (.:.:\d+:[ACTGN0-9]+)/#$1/g; /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/contig.align Mon Jun 2 00:22:09 CDT 2014 TS DONE CONTIG.ALIGN_PATCH SR07-05-55073-1 Mon Jun 2 00:22:09 CDT 2014 TS START VANALYSIS SR07-05-55073-1 # CMD: /share/apps/ngs-ccts/VICUNA_v1.3/bin/vicuna_analysis /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/vanalysis_contig.txt -------------------------------------------------------- Program runs with the following Parameter setting: pFqDir /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/input_pe_fastq/ trim_log_file /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/trim.log aln_file /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/contig.align outputDIR /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/ num_region 1 cID Start End 2 0 500 lfv_freq 5 lfv_max_len 20 -------------------------------------------------------- Reading trim logs from file: /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/trim.log retrieved 178565 logs Indexing ... /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/input_pe_fastq//1_2.fastq /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/input_pe_fastq//1_1.fastq 1_2.fastq #reads: 770577 1_1.fastq #reads: 770577 Total # Input Reads: 1541154 Reading contig alignment file: /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output/contig.align cID: 0 cLen: 1868 rNum:7820 cID: 1 cLen: 1650 rNum:4385 cID: 2 cLen: 1292 rNum:7336 cID: 3 cLen: 1258 rNum:4731 cID: 4 cLen: 1194 rNum:6499 cID: 5 cLen: 1146 rNum:2022 cID: 6 cLen: 1113 rNum:1856 cID: 7 cLen: 1026 rNum:1911 cID: 8 cLen: 1009 rNum:2647 cID: 9 cLen: 1001 rNum:2049 cID: 10 cLen: 982 rNum:6130 cID: 11 cLen: 980 rNum:1045 cID: 12 cLen: 979 rNum:1405 cID: 13 cLen: 964 rNum:1528 cID: 14 cLen: 934 rNum:934 cID: 15 cLen: 926 rNum:3108 cID: 16 cLen: 905 rNum:6710 cID: 17 cLen: 901 rNum:3865 cID: 18 cLen: 874 rNum:675 cID: 19 cLen: 867 rNum:563 cID: 20 cLen: 861 rNum:4430 cID: 21 cLen: 813 rNum:1021 cID: 22 cLen: 794 rNum:307 cID: 23 cLen: 789 rNum:723 cID: 24 cLen: 784 rNum:1746 cID: 25 cLen: 781 rNum:8542 cID: 26 cLen: 779 rNum:1109 cID: 27 cLen: 778 rNum:1895 cID: 28 cLen: 766 rNum:465 cID: 29 cLen: 763 rNum:1391 cID: 30 cLen: 762 rNum:3562 cID: 31 cLen: 756 rNum:1226 cID: 32 cLen: 754 rNum:1606 cID: 33 cLen: 752 rNum:6735 cID: 34 cLen: 751 rNum:3768 cID: 35 cLen: 748 rNum:482 cID: 36 cLen: 744 rNum:586 cID: 37 cLen: 728 rNum:1434 cID: 38 cLen: 726 rNum:1148 cID: 39 cLen: 712 rNum:2160 cID: 40 cLen: 697 rNum:1029 cID: 41 cLen: 684 rNum:284 cID: 42 cLen: 683 rNum:461 cID: 43 cLen: 672 rNum:996 cID: 44 cLen: 659 rNum:694 cID: 45 cLen: 656 rNum:296 cID: 46 cLen: 655 rNum:602 cID: 47 cLen: 652 rNum:2967 cID: 48 cLen: 652 rNum:6065 cID: 49 cLen: 649 rNum:520 cID: 50 cLen: 648 rNum:413 cID: 51 cLen: 644 rNum:1357 cID: 52 cLen: 639 rNum:3164 cID: 53 cLen: 639 rNum:311 cID: 54 cLen: 628 rNum:6740 cID: 55 cLen: 622 rNum:585 cID: 56 cLen: 618 rNum:349 cID: 57 cLen: 616 rNum:738 cID: 58 cLen: 613 rNum:730 cID: 59 cLen: 612 rNum:3715 cID: 60 cLen: 612 rNum:3026 cID: 61 cLen: 601 rNum:1162 cID: 62 cLen: 592 rNum:2304 cID: 63 cLen: 585 rNum:591 cID: 64 cLen: 581 rNum:340 cID: 65 cLen: 580 rNum:302 cID: 66 cLen: 579 rNum:569 cID: 67 cLen: 578 rNum:509 cID: 68 cLen: 573 rNum:628 cID: 69 cLen: 568 rNum:707 cID: 70 cLen: 554 rNum:786 cID: 71 cLen: 554 rNum:1020 cID: 72 cLen: 551 rNum:292 cID: 73 cLen: 546 rNum:1716 cID: 74 cLen: 543 rNum:6564 cID: 75 cLen: 542 rNum:311 cID: 76 cLen: 533 rNum:634 cID: 77 cLen: 533 rNum:304 cID: 78 cLen: 529 rNum:1621 cID: 79 cLen: 526 rNum:1577 cID: 80 cLen: 524 rNum:775 cID: 81 cLen: 521 rNum:489 cID: 82 cLen: 516 rNum:657 cID: 83 cLen: 511 rNum:1928 cID: 84 cLen: 509 rNum:966 cID: 85 cLen: 497 rNum:328 cID: 86 cLen: 492 rNum:642 cID: 87 cLen: 491 rNum:430 cID: 88 cLen: 491 rNum:460 cID: 89 cLen: 491 rNum:2275 cID: 90 cLen: 488 rNum:459 cID: 91 cLen: 482 rNum:3107 cID: 92 cLen: 477 rNum:465 cID: 93 cLen: 471 rNum:378 cID: 94 cLen: 469 rNum:791 cID: 95 cLen: 465 rNum:495 cID: 96 cLen: 465 rNum:631 cID: 97 cLen: 464 rNum:1724 cID: 98 cLen: 463 rNum:410 cID: 99 cLen: 459 rNum:449 cID: 100 cLen: 455 rNum:237 cID: 101 cLen: 452 rNum:254 cID: 102 cLen: 451 rNum:253 cID: 103 cLen: 443 rNum:317 cID: 104 cLen: 441 rNum:3662 cID: 105 cLen: 440 rNum:289 cID: 106 cLen: 437 rNum:883 cID: 107 cLen: 433 rNum:1065 cID: 108 cLen: 433 rNum:2211 cID: 109 cLen: 424 rNum:4750 cID: 110 cLen: 423 rNum:358 cID: 111 cLen: 420 rNum:160 cID: 112 cLen: 413 rNum:4110 cID: 113 cLen: 412 rNum:775 cID: 114 cLen: 407 rNum:1270 cID: 115 cLen: 401 rNum:411 cID: 116 cLen: 398 rNum:593 cID: 117 cLen: 398 rNum:359 cID: 118 cLen: 396 rNum:741 cID: 119 cLen: 395 rNum:270 cID: 120 cLen: 394 rNum:229 cID: 121 cLen: 393 rNum:151 cID: 122 cLen: 391 rNum:1462 cID: 123 cLen: 390 rNum:2016 cID: 124 cLen: 390 rNum:318 cID: 125 cLen: 385 rNum:279 cID: 126 cLen: 383 rNum:409 cID: 127 cLen: 382 rNum:2004 cID: 128 cLen: 381 rNum:182 cID: 129 cLen: 378 rNum:213 cID: 130 cLen: 372 rNum:156 cID: 131 cLen: 371 rNum:201 cID: 132 cLen: 371 rNum:430 cID: 133 cLen: 370 rNum:807 cID: 134 cLen: 368 rNum:461 cID: 135 cLen: 366 rNum:1125 cID: 136 cLen: 365 rNum:695 cID: 137 cLen: 362 rNum:3492 cID: 138 cLen: 361 rNum:662 cID: 139 cLen: 360 rNum:352 cID: 140 cLen: 360 rNum:531 cID: 141 cLen: 360 rNum:1131 cID: 142 cLen: 356 rNum:183 cID: 143 cLen: 354 rNum:914 cID: 144 cLen: 351 rNum:140 cID: 145 cLen: 350 rNum:322 cID: 146 cLen: 350 rNum:479 cID: 147 cLen: 349 rNum:432 cID: 148 cLen: 345 rNum:1240 cID: 149 cLen: 344 rNum:245 cID: 150 cLen: 344 rNum:365 cID: 151 cLen: 342 rNum:802 cID: 152 cLen: 341 rNum:110 cID: 153 cLen: 339 rNum:188 cID: 154 cLen: 337 rNum:145 cID: 155 cLen: 333 rNum:244 cID: 156 cLen: 332 rNum:543 cID: 157 cLen: 332 rNum:90 cID: 158 cLen: 332 rNum:85 cID: 159 cLen: 332 rNum:596 cID: 160 cLen: 331 rNum:314 cID: 161 cLen: 327 rNum:49 cID: 162 cLen: 326 rNum:1962 cID: 163 cLen: 325 rNum:4105 cID: 164 cLen: 323 rNum:321 cID: 165 cLen: 323 rNum:1357 cID: 166 cLen: 322 rNum:1375 cID: 167 cLen: 318 rNum:285 cID: 168 cLen: 318 rNum:397 cID: 169 cLen: 315 rNum:1864 cID: 170 cLen: 314 rNum:239 cID: 171 cLen: 312 rNum:279 cID: 172 cLen: 311 rNum:71 cID: 173 cLen: 306 rNum:243 cID: 174 cLen: 304 rNum:145 cID: 175 cLen: 303 rNum:1003 cID: 176 cLen: 303 rNum:329 cID: 177 cLen: 302 rNum:183 cID: 178 cLen: 301 rNum:212 cID: 179 cLen: 301 rNum:401 cID: 180 cLen: 300 rNum:346 cID: 181 cLen: 299 rNum:162 cID: 182 cLen: 299 rNum:81 cID: 183 cLen: 298 rNum:217 cID: 184 cLen: 298 rNum:387 cID: 185 cLen: 297 rNum:189 cID: 186 cLen: 296 rNum:1275 cID: 187 cLen: 293 rNum:121 cID: 188 cLen: 292 rNum:121 cID: 189 cLen: 290 rNum:103 cID: 190 cLen: 288 rNum:305 cID: 191 cLen: 286 rNum:999 cID: 192 cLen: 283 rNum:103 cID: 193 cLen: 283 rNum:300 cID: 194 cLen: 282 rNum:119 cID: 195 cLen: 281 rNum:105 cID: 196 cLen: 280 rNum:312 cID: 197 cLen: 278 rNum:96 cID: 198 cLen: 277 rNum:275 cID: 199 cLen: 272 rNum:288 cID: 200 cLen: 272 rNum:293 cID: 201 cLen: 268 rNum:323 cID: 202 cLen: 267 rNum:167 cID: 203 cLen: 267 rNum:173 cID: 204 cLen: 266 rNum:184 cID: 205 cLen: 266 rNum:88 cID: 206 cLen: 265 rNum:89 cID: 207 cLen: 265 rNum:188 cID: 208 cLen: 263 rNum:119 cID: 209 cLen: 260 rNum:58 cID: 210 cLen: 260 rNum:150 cID: 211 cLen: 260 rNum:96 cID: 212 cLen: 259 rNum:1804 cID: 213 cLen: 258 rNum:418 cID: 214 cLen: 257 rNum:120 cID: 215 cLen: 254 rNum:162 cID: 216 cLen: 250 rNum:147 cID: 217 cLen: 249 rNum:416 cID: 218 cLen: 247 rNum:35 cID: 219 cLen: 246 rNum:731 cID: 220 cLen: 245 rNum:81 cID: 221 cLen: 244 rNum:145 cID: 222 cLen: 244 rNum:102 cID: 223 cLen: 240 rNum:168 cID: 224 cLen: 240 rNum:1578 cID: 225 cLen: 239 rNum:1471 cID: 226 cLen: 238 rNum:217 cID: 227 cLen: 238 rNum:455 cID: 228 cLen: 236 rNum:138 cID: 229 cLen: 234 rNum:97 cID: 230 cLen: 233 rNum:1260 cID: 231 cLen: 233 rNum:138 cID: 232 cLen: 232 rNum:130 cID: 233 cLen: 232 rNum:415 cID: 234 cLen: 230 rNum:77 cID: 235 cLen: 230 rNum:49 cID: 236 cLen: 230 rNum:151 cID: 237 cLen: 228 rNum:132 cID: 238 cLen: 228 rNum:77 cID: 239 cLen: 226 rNum:110 cID: 240 cLen: 225 rNum:113 cID: 241 cLen: 225 rNum:78 cID: 242 cLen: 224 rNum:206 cID: 243 cLen: 224 rNum:610 cID: 244 cLen: 223 rNum:300 cID: 245 cLen: 223 rNum:79 cID: 246 cLen: 222 rNum:248 cID: 247 cLen: 222 rNum:65 cID: 248 cLen: 220 rNum:75 cID: 249 cLen: 220 rNum:818 cID: 250 cLen: 219 rNum:47 cID: 251 cLen: 218 rNum:49 cID: 252 cLen: 216 rNum:443 cID: 253 cLen: 214 rNum:175 cID: 254 cLen: 212 rNum:58 cID: 255 cLen: 210 rNum:142 cID: 256 cLen: 210 rNum:176 cID: 257 cLen: 210 rNum:124 cID: 258 cLen: 209 rNum:190 cID: 259 cLen: 208 rNum:63 cID: 260 cLen: 208 rNum:1384 cID: 261 cLen: 207 rNum:113 cID: 262 cLen: 204 rNum:50 cID: 263 cLen: 204 rNum:112 cID: 264 cLen: 204 rNum:188 cID: 265 cLen: 203 rNum:84 cID: 266 cLen: 201 rNum:171 output to file: /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output//contig.0.txt Contig::create_profile p2 SC failed ERROR: /share/apps/ngs-ccts/VICUNA_v1.3/bin/vicuna_analysis /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/vanalysis_contig.txt ERROR: Mon Jun 2 00:22:13 CDT 2014 TS ERROR VANALYSIS SR07-05-55073-1