STAR version=2.7.11b STAR compilation time,server,dir=2025-01-09T12:32:06+0000 :/opt/conda/conda-bld/star_1736425784849/work/source ##### Command Line: /opt/conda/bin/STAR-avx2 --genomeDir star --readFilesIn input1/POC-201-TP1_1.merged.fastq.gz input2/POC-201-TP1_2.merged.fastq.gz --runThreadN 16 --outFileNamePrefix POC-201-TP1. --sjdbGTFfile Pocillopora_meandrina_HIv1.genes-validated.gtf --outSAMattrRGline ID:POC-201-TP1 SM:POC-201-TP1 PL:illumina --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --sjdbOverhang 149 --twopassMode Basic --outBAMsortingBinsN 50 --limitOutSJcollapsed 1000000 ##### Initial USER parameters from Command Line: outFileNamePrefix POC-201-TP1. ###### All USER parameters from Command Line: genomeDir star ~RE-DEFINED readFilesIn input1/POC-201-TP1_1.merged.fastq.gz input2/POC-201-TP1_2.merged.fastq.gz ~RE-DEFINED runThreadN 16 ~RE-DEFINED outFileNamePrefix POC-201-TP1. ~RE-DEFINED sjdbGTFfile Pocillopora_meandrina_HIv1.genes-validated.gtf ~RE-DEFINED outSAMattrRGline ID:POC-201-TP1 SM:POC-201-TP1 PL:illumina ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED sjdbOverhang 149 ~RE-DEFINED twopassMode Basic ~RE-DEFINED outBAMsortingBinsN 50 ~RE-DEFINED limitOutSJcollapsed 1000000 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 16 genomeDir star readFilesIn input1/POC-201-TP1_1.merged.fastq.gz input2/POC-201-TP1_2.merged.fastq.gz readFilesCommand zcat limitOutSJcollapsed 1000000 outFileNamePrefix POC-201-TP1. outSAMtype BAM SortedByCoordinate outSAMattrRGline ID:POC-201-TP1 SM:POC-201-TP1 PL:illumina outBAMsortingBinsN 50 sjdbGTFfile Pocillopora_meandrina_HIv1.genes-validated.gtf sjdbOverhang 149 twopassMode Basic ------------------------------- ##### Final effective command line: /opt/conda/bin/STAR-avx2 --runThreadN 16 --genomeDir star --readFilesIn input1/POC-201-TP1_1.merged.fastq.gz input2/POC-201-TP1_2.merged.fastq.gz --readFilesCommand zcat --limitOutSJcollapsed 1000000 --outFileNamePrefix POC-201-TP1. --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:POC-201-TP1 SM:POC-201-TP1 PL:illumina --outBAMsortingBinsN 50 --sjdbGTFfile Pocillopora_meandrina_HIv1.genes-validated.gtf --sjdbOverhang 149 --twopassMode Basic ---------------------------------------- Number of fastq files for each mate = 1 Input read files for mate 1 : -rw-r--r-- 1 strigg all 1090686876 May 6 09:13 input1/POC-201-TP1_1.merged.fastq.gz readsCommandsFile: exec > "POC-201-TP1._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "input1/POC-201-TP1_1.merged.fastq.gz" Input read files for mate 2 : -rw-r--r-- 1 strigg all 1103160128 May 6 09:13 input2/POC-201-TP1_2.merged.fastq.gz readsCommandsFile: exec > "POC-201-TP1._STARtmp/tmp.fifo.read2" echo FILE 0 zcat "input2/POC-201-TP1_2.merged.fastq.gz" WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10 WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters: ### /opt/conda/bin/STAR-avx2 --runMode genomeGenerate --runThreadN 16 --genomeDir star/ --genomeFastaFiles Pocillopora_meandrina_HIv1.assembly.fasta --genomeSAindexNbases 13 --limitGenomeGenerateRAM 160961273600 --sjdbGTFfile Pocillopora_meandrina_HIv1.genes-validated.gtf --sjdbOverhang 149 ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles Pocillopora_meandrina_HIv1.assembly.fasta ~RE-DEFINED genomeSAindexNbases 13 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED genomeTransformType None ~RE-DEFINED genomeTransformVCF - ~RE-DEFINED sjdbOverhang 149 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile Pocillopora_meandrina_HIv1.genes-validated.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 468067901 3541187796 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 212 1 Pocillopora_meandrina_HIv1___Sc0000000 21651136 0 2 Pocillopora_meandrina_HIv1___Sc0000001 21507942 21757952 3 Pocillopora_meandrina_HIv1___Sc0000002 19741974 43515904 4 Pocillopora_meandrina_HIv1___Sc0000003 19417450 63438848 5 Pocillopora_meandrina_HIv1___Sc0000004 14584444 83099648 6 Pocillopora_meandrina_HIv1___Sc0000005 14098929 97779712 7 Pocillopora_meandrina_HIv1___Sc0000006 14068054 111935488 8 Pocillopora_meandrina_HIv1___Sc0000007 13590779 126091264 9 Pocillopora_meandrina_HIv1___Sc0000008 12446599 139722752 10 Pocillopora_meandrina_HIv1___Sc0000009 11983232 152305664 11 Pocillopora_meandrina_HIv1___Sc0000010 11763137 164364288 12 Pocillopora_meandrina_HIv1___Sc0000011 10501528 176160768 13 Pocillopora_meandrina_HIv1___Sc0000012 10024633 186908672 14 Pocillopora_meandrina_HIv1___Sc0000013 9946974 197132288 15 Pocillopora_meandrina_HIv1___Sc0000014 9536826 207093760 16 Pocillopora_meandrina_HIv1___Sc0000015 9393205 216793088 17 Pocillopora_meandrina_HIv1___Sc0000016 9288165 226230272 18 Pocillopora_meandrina_HIv1___Sc0000017 9274345 235667456 19 Pocillopora_meandrina_HIv1___Sc0000018 8584156 245104640 20 Pocillopora_meandrina_HIv1___Sc0000019 7112774 253755392 21 Pocillopora_meandrina_HIv1___Sc0000020 6748058 261095424 22 Pocillopora_meandrina_HIv1___Sc0000021 6546105 267911168 23 Pocillopora_meandrina_HIv1___Sc0000022 6319256 274464768 24 Pocillopora_meandrina_HIv1___Sc0000023 5767069 281018368 25 Pocillopora_meandrina_HIv1___Sc0000024 5762297 286785536 26 Pocillopora_meandrina_HIv1___Sc0000025 5759531 292552704 27 Pocillopora_meandrina_HIv1___Sc0000026 5647578 298319872 28 Pocillopora_meandrina_HIv1___Sc0000027 5550630 304087040 29 Pocillopora_meandrina_HIv1___Sc0000028 5130920 309854208 30 Pocillopora_meandrina_HIv1___Sc0000029 4860867 315097088 31 Pocillopora_meandrina_HIv1___Sc0000030 4843735 320077824 32 Pocillopora_meandrina_HIv1___Sc0000031 4691590 325058560 33 Pocillopora_meandrina_HIv1___Sc0000032 3615800 329777152 34 Pocillopora_meandrina_HIv1___Sc0000033 3306609 333447168 35 Pocillopora_meandrina_HIv1___Sc0000034 3122802 336855040 36 Pocillopora_meandrina_HIv1___Sc0000035 3015365 340000768 37 Pocillopora_meandrina_HIv1___Sc0000036 3007169 343146496 38 Pocillopora_meandrina_HIv1___Sc0000037 2860435 346292224 39 Pocillopora_meandrina_HIv1___Sc0000038 2701138 349175808 40 Pocillopora_meandrina_HIv1___Sc0000039 2599273 352059392 41 Pocillopora_meandrina_HIv1___Sc0000040 2445666 354680832 42 Pocillopora_meandrina_HIv1___Sc0000041 2159376 357302272 43 Pocillopora_meandrina_HIv1___Sc0000042 1957488 359661568 44 Pocillopora_meandrina_HIv1___Sc0000043 1845599 361758720 45 Pocillopora_meandrina_HIv1___Sc0000044 1724711 363855872 46 Pocillopora_meandrina_HIv1___Sc0000045 1153740 365690880 47 Pocillopora_meandrina_HIv1___Sc0000046 755410 367001600 48 Pocillopora_meandrina_HIv1___Sc0000047 239089 367788032 49 Pocillopora_meandrina_HIv1___Sc0000048 214660 368050176 50 Pocillopora_meandrina_HIv1___Sc0000049 179266 368312320 51 Pocillopora_meandrina_HIv1___Sc0000050 177168 368574464 52 Pocillopora_meandrina_HIv1___Sc0000051 165057 368836608 53 Pocillopora_meandrina_HIv1___Sc0000052 155210 369098752 54 Pocillopora_meandrina_HIv1___Sc0000053 123249 369360896 55 Pocillopora_meandrina_HIv1___Sc0000054 122643 369623040 56 Pocillopora_meandrina_HIv1___Sc0000055 121609 369885184 57 Pocillopora_meandrina_HIv1___Sc0000056 112816 370147328 58 Pocillopora_meandrina_HIv1___Sc0000057 107171 370409472 59 Pocillopora_meandrina_HIv1___Sc0000058 98341 370671616 60 Pocillopora_meandrina_HIv1___Sc0000059 83292 370933760 61 Pocillopora_meandrina_HIv1___Sc0000060 79483 371195904 62 Pocillopora_meandrina_HIv1___Sc0000061 75390 371458048 63 Pocillopora_meandrina_HIv1___Sc0000062 74194 371720192 64 Pocillopora_meandrina_HIv1___Sc0000063 73457 371982336 65 Pocillopora_meandrina_HIv1___Sc0000064 72700 372244480 66 Pocillopora_meandrina_HIv1___Sc0000065 67986 372506624 67 Pocillopora_meandrina_HIv1___Sc0000066 66659 372768768 68 Pocillopora_meandrina_HIv1___Sc0000067 64947 373030912 69 Pocillopora_meandrina_HIv1___Sc0000068 64340 373293056 70 Pocillopora_meandrina_HIv1___Sc0000069 62616 373555200 71 Pocillopora_meandrina_HIv1___Sc0000070 60121 373817344 72 Pocillopora_meandrina_HIv1___Sc0000071 57157 374079488 73 Pocillopora_meandrina_HIv1___Sc0000072 56626 374341632 74 Pocillopora_meandrina_HIv1___Sc0000073 56082 374603776 75 Pocillopora_meandrina_HIv1___Sc0000074 55210 374865920 76 Pocillopora_meandrina_HIv1___Sc0000075 54685 375128064 77 Pocillopora_meandrina_HIv1___Sc0000076 54587 375390208 78 Pocillopora_meandrina_HIv1___Sc0000077 53379 375652352 79 Pocillopora_meandrina_HIv1___Sc0000078 51564 375914496 80 Pocillopora_meandrina_HIv1___Sc0000079 49664 376176640 81 Pocillopora_meandrina_HIv1___Sc0000080 47218 376438784 82 Pocillopora_meandrina_HIv1___Sc0000081 42490 376700928 83 Pocillopora_meandrina_HIv1___Sc0000082 32657 376963072 84 Pocillopora_meandrina_HIv1___Sc0000083 27992 377225216 85 Pocillopora_meandrina_HIv1___xfSc0000000 1601609 377487360 86 Pocillopora_meandrina_HIv1___xfSc0000001 1197718 379322368 87 Pocillopora_meandrina_HIv1___xfSc0000002 779520 380633088 88 Pocillopora_meandrina_HIv1___xfSc0000003 462347 381419520 89 Pocillopora_meandrina_HIv1___xfSc0000004 334777 381943808 90 Pocillopora_meandrina_HIv1___xfSc0000006 290100 382468096 91 Pocillopora_meandrina_HIv1___xfSc0000007 252258 382992384 92 Pocillopora_meandrina_HIv1___xfSc0000012 148278 383254528 93 Pocillopora_meandrina_HIv1___xfSc0000014 118081 383516672 94 Pocillopora_meandrina_HIv1___xfSc0000017 98555 383778816 95 Pocillopora_meandrina_HIv1___xfSc0000021 95778 384040960 96 Pocillopora_meandrina_HIv1___xfSc0000024 90744 384303104 97 Pocillopora_meandrina_HIv1___xfSc0000029 85532 384565248 98 Pocillopora_meandrina_HIv1___xfSc0000038 77395 384827392 99 Pocillopora_meandrina_HIv1___xfSc0000058 69718 385089536 100 Pocillopora_meandrina_HIv1___xfSc0000059 69426 385351680 101 Pocillopora_meandrina_HIv1___xfSc0000074 66573 385613824 102 Pocillopora_meandrina_HIv1___xfSc0000081 65415 385875968 103 Pocillopora_meandrina_HIv1___xfSc0000083 65317 386138112 104 Pocillopora_meandrina_HIv1___xfSc0000092 63607 386400256 105 Pocillopora_meandrina_HIv1___xfSc0000094 62842 386662400 106 Pocillopora_meandrina_HIv1___xfSc0000113 60556 386924544 107 Pocillopora_meandrina_HIv1___xfSc0000132 59032 387186688 108 Pocillopora_meandrina_HIv1___xfSc0000145 58221 387448832 109 Pocillopora_meandrina_HIv1___xfSc0000146 58151 387710976 110 Pocillopora_meandrina_HIv1___xfSc0000168 56681 387973120 111 Pocillopora_meandrina_HIv1___xfSc0000175 56271 388235264 112 Pocillopora_meandrina_HIv1___xfSc0000195 55223 388497408 113 Pocillopora_meandrina_HIv1___xfSc0000199 55095 388759552 114 Pocillopora_meandrina_HIv1___xfSc0000205 54658 389021696 115 Pocillopora_meandrina_HIv1___xfSc0000206 54623 389283840 116 Pocillopora_meandrina_HIv1___xfSc0000212 54299 389545984 117 Pocillopora_meandrina_HIv1___xfSc0000217 54168 389808128 118 Pocillopora_meandrina_HIv1___xfSc0000223 53823 390070272 119 Pocillopora_meandrina_HIv1___xfSc0000228 53382 390332416 120 Pocillopora_meandrina_HIv1___xfSc0000237 53049 390594560 121 Pocillopora_meandrina_HIv1___xfSc0000262 52308 390856704 122 Pocillopora_meandrina_HIv1___xfSc0000264 52264 391118848 123 Pocillopora_meandrina_HIv1___xfSc0000272 52107 391380992 124 Pocillopora_meandrina_HIv1___xfSc0000275 51938 391643136 125 Pocillopora_meandrina_HIv1___xfSc0000284 51483 391905280 126 Pocillopora_meandrina_HIv1___xfSc0000288 51367 392167424 127 Pocillopora_meandrina_HIv1___xfSc0000300 50845 392429568 128 Pocillopora_meandrina_HIv1___xfSc0000301 50809 392691712 129 Pocillopora_meandrina_HIv1___xfSc0000343 49544 392953856 130 Pocillopora_meandrina_HIv1___xfSc0000376 48519 393216000 131 Pocillopora_meandrina_HIv1___xfSc0000415 47398 393478144 132 Pocillopora_meandrina_HIv1___xfSc0000423 47202 393740288 133 Pocillopora_meandrina_HIv1___xfSc0000426 47096 394002432 134 Pocillopora_meandrina_HIv1___xfSc0000428 47057 394264576 135 Pocillopora_meandrina_HIv1___xfSc0000436 46816 394526720 136 Pocillopora_meandrina_HIv1___xfSc0000445 46561 394788864 137 Pocillopora_meandrina_HIv1___xfSc0000447 46542 395051008 138 Pocillopora_meandrina_HIv1___xfSc0000469 45938 395313152 139 Pocillopora_meandrina_HIv1___xfSc0000477 45781 395575296 140 Pocillopora_meandrina_HIv1___xfSc0000479 45736 395837440 141 Pocillopora_meandrina_HIv1___xfSc0000482 45585 396099584 142 Pocillopora_meandrina_HIv1___xfSc0000488 45379 396361728 143 Pocillopora_meandrina_HIv1___xfSc0000506 44781 396623872 144 Pocillopora_meandrina_HIv1___xfSc0000527 44235 396886016 145 Pocillopora_meandrina_HIv1___xfSc0000540 43935 397148160 146 Pocillopora_meandrina_HIv1___xfSc0000555 43535 397410304 147 Pocillopora_meandrina_HIv1___xfSc0000565 43357 397672448 148 Pocillopora_meandrina_HIv1___xfSc0000566 43316 397934592 149 Pocillopora_meandrina_HIv1___xfSc0000567 43305 398196736 150 Pocillopora_meandrina_HIv1___xfSc0000570 43295 398458880 151 Pocillopora_meandrina_HIv1___xfSc0000579 43029 398721024 152 Pocillopora_meandrina_HIv1___xfSc0000583 42958 398983168 153 Pocillopora_meandrina_HIv1___xfSc0000596 42675 399245312 154 Pocillopora_meandrina_HIv1___xfSc0000612 42423 399507456 155 Pocillopora_meandrina_HIv1___xfSc0000616 42355 399769600 156 Pocillopora_meandrina_HIv1___xfSc0000621 42164 400031744 157 Pocillopora_meandrina_HIv1___xfSc0000642 41754 400293888 158 Pocillopora_meandrina_HIv1___xfSc0000655 41446 400556032 159 Pocillopora_meandrina_HIv1___xfSc0000692 40426 400818176 160 Pocillopora_meandrina_HIv1___xfSc0000699 40296 401080320 161 Pocillopora_meandrina_HIv1___xfSc0000704 40233 401342464 162 Pocillopora_meandrina_HIv1___xfSc0000705 40197 401604608 163 Pocillopora_meandrina_HIv1___xfSc0000716 39998 401866752 164 Pocillopora_meandrina_HIv1___xfSc0000725 39827 402128896 165 Pocillopora_meandrina_HIv1___xfSc0000729 39775 402391040 166 Pocillopora_meandrina_HIv1___xfSc0000760 39228 402653184 167 Pocillopora_meandrina_HIv1___xfSc0000763 39151 402915328 168 Pocillopora_meandrina_HIv1___xfSc0000765 39117 403177472 169 Pocillopora_meandrina_HIv1___xfSc0000788 38513 403439616 170 Pocillopora_meandrina_HIv1___xfSc0000811 37888 403701760 171 Pocillopora_meandrina_HIv1___xfSc0000812 37881 403963904 172 Pocillopora_meandrina_HIv1___xfSc0000817 37779 404226048 173 Pocillopora_meandrina_HIv1___xfSc0000824 37656 404488192 174 Pocillopora_meandrina_HIv1___xfSc0000835 37434 404750336 175 Pocillopora_meandrina_HIv1___xfSc0000836 37372 405012480 176 Pocillopora_meandrina_HIv1___xfSc0000837 37368 405274624 177 Pocillopora_meandrina_HIv1___xfSc0000840 37283 405536768 178 Pocillopora_meandrina_HIv1___xfSc0000857 37006 405798912 179 Pocillopora_meandrina_HIv1___xfSc0000859 36995 406061056 180 Pocillopora_meandrina_HIv1___xfSc0000866 36925 406323200 181 Pocillopora_meandrina_HIv1___xfSc0000868 36831 406585344 182 Pocillopora_meandrina_HIv1___xfSc0000875 36611 406847488 183 Pocillopora_meandrina_HIv1___xfSc0000885 36416 407109632 184 Pocillopora_meandrina_HIv1___xfSc0000886 36355 407371776 185 Pocillopora_meandrina_HIv1___xfSc0000890 36339 407633920 186 Pocillopora_meandrina_HIv1___xfSc0000892 36267 407896064 187 Pocillopora_meandrina_HIv1___xfSc0000943 35168 408158208 188 Pocillopora_meandrina_HIv1___xfSc0000948 35100 408420352 189 Pocillopora_meandrina_HIv1___xfSc0000952 34934 408682496 190 Pocillopora_meandrina_HIv1___xfSc0000953 34905 408944640 191 Pocillopora_meandrina_HIv1___xfSc0000957 34773 409206784 192 Pocillopora_meandrina_HIv1___xfSc0000968 34345 409468928 193 Pocillopora_meandrina_HIv1___xfSc0000974 34140 409731072 194 Pocillopora_meandrina_HIv1___xfSc0000975 33988 409993216 195 Pocillopora_meandrina_HIv1___xfSc0000995 33324 410255360 196 Pocillopora_meandrina_HIv1___xfSc0001011 32918 410517504 197 Pocillopora_meandrina_HIv1___xfSc0001122 29140 410779648 198 Pocillopora_meandrina_HIv1___xfSc0001170 27381 411041792 199 Pocillopora_meandrina_HIv1___xfSc0001179 27200 411303936 200 Pocillopora_meandrina_HIv1___xfSc0001231 22938 411566080 201 Pocillopora_meandrina_HIv1___xfSc0001237 22715 411828224 202 Pocillopora_meandrina_HIv1___xpSc0001273 408270 412090368 203 Pocillopora_meandrina_HIv1___xpSc0001275 48561 412614656 204 Pocillopora_meandrina_HIv1___xpSc0001276 38618 412876800 205 Pocillopora_meandrina_HIv1___xpSc0001280 35955 413138944 206 Pocillopora_meandrina_HIv1___xpSc0001281 34238 413401088 207 Pocillopora_meandrina_HIv1___xpSc0001290 28931 413663232 208 Pocillopora_meandrina_HIv1___xpSc0001321 15304 413925376 209 Pocillopora_meandrina_HIv1___xpSc0001331 8958 414187520 210 Pocillopora_meandrina_HIv1___xpSc0001337 6786 414449664 211 Pocillopora_meandrina_HIv1___xpSc0001344 5647 414711808 212 Pocillopora_meandrina_HIv1___xpSc0001355 3576 414973952 Started loading the genome: Tue May 6 09:23:04 2025 Genome: size given as a parameter = 468067901 SA: size given as a parameter = 3541187796 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=13 nSAi=89478484 nGenome=468067901; nSAbyte=3541187796 GstrandBit=32 SA number of indices=858469768 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 468067901 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 468067901 bytes SA file size: 3541187796 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3541187796 bytes Loading SAindex ... done: 391468491 bytes Finished loading the genome: Tue May 6 09:24:49 2025 Processing splice junctions database sjdbN=176695, pGe.sjdbOverhang=149 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 May 06 09:24:49 Loaded database junctions from the generated genome star//sjdbList.out.tab: 176695 total junctions May 06 09:24:49 ..... processing annotations GTF Processing pGe.sjdbGTFfile=Pocillopora_meandrina_HIv1.genes-validated.gtf, found: 31840 transcripts 208535 exons (non-collapsed) 176695 collapsed junctions Total junctions: 353390 May 06 09:24:53 ..... finished GTF processing WARNING: long repeat for junction # 78516 : Pocillopora_meandrina_HIv1___Sc0000009 4677582 4677980; left shift = 25; right shift = 255 WARNING: long repeat for junction # 255211 : Pocillopora_meandrina_HIv1___Sc0000009 4677582 4677980; left shift = 25; right shift = 255 May 06 09:24:53 Finished preparing junctions May 06 09:24:53 ..... inserting junctions into the genome indices May 06 09:24:54 Finished SA search: number of new junctions=0, old junctions=176695 May 06 09:24:54 Finished sorting SA indicesL nInd=0 Genome size with junctions=468067901 415236096 52831805 GstrandBit1=32 GstrandBit=32 May 06 09:25:02 Finished inserting junction indices May 06 09:25:03 Finished SAi May 06 09:25:03 ..... finished inserting junctions into genome Created thread # 1 Starting to map file # 0 mate 1: input1/POC-201-TP1_1.merged.fastq.gz mate 2: input2/POC-201-TP1_2.merged.fastq.gz Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Created thread # 8 Created thread # 9 Created thread # 10 Created thread # 11 Created thread # 12 Created thread # 13 Created thread # 14 Created thread # 15 Thread #15 end of input stream, nextChar=-1 Completed: thread #15 Completed: thread #1 Completed: thread #11 Completed: thread #7 Completed: thread #0 Joined thread # 1 Completed: thread #9 Completed: thread #6 Completed: thread #12 Completed: thread #4 Completed: thread #10 Completed: thread #2 Joined thread # 2 Completed: thread #5 Completed: thread #8 Completed: thread #14 Completed: thread #13 Completed: thread #3 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Joined thread # 8 Joined thread # 9 Joined thread # 10 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 May 06 09:30:54 Loaded database junctions from the 1st pass file: POC-201-TP1._STARpass1//SJ.out.tab: 576562 total junctions WARNING: long repeat for junction # 78516 : Pocillopora_meandrina_HIv1___Sc0000009 4677582 4677980; left shift = 25; right shift = 255 WARNING: long repeat for junction # 255211 : Pocillopora_meandrina_HIv1___Sc0000009 4677582 4677980; left shift = 25; right shift = 255 May 06 09:30:54 Finished preparing junctions May 06 09:30:54 ..... inserting junctions into the genome indices May 06 09:31:02 Finished SA search: number of new junctions=89836, old junctions=176695 May 06 09:31:14 Finished sorting SA indicesL nInd=53542090 Genome size with junctions=494928865 415236096 79692769 GstrandBit1=32 GstrandBit=32 May 06 09:31:24 Finished inserting junction indices May 06 09:31:28 Finished SAi May 06 09:31:28 ..... finished inserting junctions into genome Input read files for mate 1 : -rw-r--r-- 1 strigg all 1090686876 May 6 09:13 input1/POC-201-TP1_1.merged.fastq.gz readsCommandsFile: exec > "POC-201-TP1._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "input1/POC-201-TP1_1.merged.fastq.gz" Input read files for mate 2 : -rw-r--r-- 1 strigg all 1103160128 May 6 09:13 input2/POC-201-TP1_2.merged.fastq.gz readsCommandsFile: exec > "POC-201-TP1._STARtmp/tmp.fifo.read2" echo FILE 0 zcat "input2/POC-201-TP1_2.merged.fastq.gz" Created thread # 1 Starting to map file # 0 mate 1: input1/POC-201-TP1_1.merged.fastq.gz mate 2: input2/POC-201-TP1_2.merged.fastq.gz Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Created thread # 8 Created thread # 9 Created thread # 10 Created thread # 11 Created thread # 12 Created thread # 13 Created thread # 14 Created thread # 15 BAM sorting: 149907 mapped reads BAM sorting bins genomic start loci: 1 0 5214640 2 0 12222635 3 0 20540048 4 1 2552179 5 1 10153385 6 1 18623661 7 2 1532368 8 2 8334761 9 2 15832227 10 3 5181988 11 3 7948707 12 3 18365427 13 4 7873771 14 5 4634697 15 5 11842004 16 6 6931896 17 7 158495 18 7 4576868 19 7 7795988 20 8 4541532 21 8 10861538 22 10 1980661 23 10 11275835 24 11 4843954 25 11 7832886 26 12 4889695 27 14 559311 28 14 7103253 29 15 4223068 30 16 849264 31 17 2342861 32 17 8340185 33 18 6878124 34 19 4365487 35 21 1039411 36 22 3313110 37 25 237726 38 26 1623219 39 27 1359100 40 28 512488 41 29 2922746 42 30 1036174 43 32 101176 44 33 287779 45 36 1428813 46 38 1721835 47 41 1965750 48 84 861756 Thread #4 end of input stream, nextChar=-1 Completed: thread #15 Completed: thread #4 Completed: thread #7 Completed: thread #6 Completed: thread #0 Completed: thread #1 Joined thread # 1 Completed: thread #5 Completed: thread #11 Completed: thread #2 Joined thread # 2 Completed: thread #14 Completed: thread #3 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Completed: thread #12 Completed: thread #13 Completed: thread #8 Joined thread # 8 Completed: thread #10 Completed: thread #9 Joined thread # 9 Joined thread # 10 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 May 06 09:40:58 ..... finished mapping RAM after mapping: VmPeak: 17416444 kB; VmSize: 16020968 kB; VmHWM: 13970684 kB; VmRSS: 13621096 kB; RAM after freeing genome index memory: VmPeak: 17416444 kB; VmSize: 6321524 kB; VmHWM: 13970684 kB; VmRSS: 4478100 kB; May 06 09:40:59 ..... started sorting BAM Max memory needed for sorting = 261497305 ALL DONE!