STAR version=2.7.10a_alpha_220601 STAR compilation time,server,dir=2022-06-01T14:07:16-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source STAR git: On branch master ; commit c2f3c6589ffab7c69fc46684b5be0990584b7542 ; diff files: ##### Command Line: ../../../star/STAR-2.7.10a_alpha_220601/STAR --readFilesIn ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R1_001_cutadapt.fastq.gz ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R2_001_cutadapt.fastq.gz --runThreadN 24 --soloBarcodeMate 1 --clip5pNbases 65 0 --outSAMattributes GX GN CY UY CR UR CB UB --soloCBwhitelist ../../../downloaded_data/star/3M-february-2018.txt --quantMode TranscriptomeSAM --quantTranscriptomeBan Singleend --genomeDir ../../../downloaded_data/star/ --outSAMtype BAM SortedByCoordinate --readFilesCommand gunzip -c --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloCellFilter EmptyDrops_CR --soloStrand Unstranded --soloFeatures Gene GeneFull SJ Velocyto --soloMultiMappers Uniform PropUnique EM --soloOutFileNames output/ RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_genes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_barcodes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_matrix.mtx ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: readFilesIn ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R1_001_cutadapt.fastq.gz ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R2_001_cutadapt.fastq.gz ~RE-DEFINED runThreadN 24 ~RE-DEFINED soloBarcodeMate 1 ~RE-DEFINED clip5pNbases 65 0 ~RE-DEFINED outSAMattributes GX GN CY UY CR UR CB UB ~RE-DEFINED soloCBwhitelist ../../../downloaded_data/star/3M-february-2018.txt ~RE-DEFINED quantMode TranscriptomeSAM ~RE-DEFINED quantTranscriptomeBan Singleend ~RE-DEFINED genomeDir ../../../downloaded_data/star/ ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED readFilesCommand gunzip -c ~RE-DEFINED soloType CB_UMI_Simple ~RE-DEFINED soloCBstart 1 ~RE-DEFINED soloCBlen 16 ~RE-DEFINED soloUMIstart 17 ~RE-DEFINED soloUMIlen 12 ~RE-DEFINED soloCellFilter EmptyDrops_CR ~RE-DEFINED soloStrand Unstranded ~RE-DEFINED soloFeatures Gene GeneFull SJ Velocyto ~RE-DEFINED soloMultiMappers Uniform PropUnique EM ~RE-DEFINED soloOutFileNames output/ RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_genes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_barcodes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_matrix.mtx ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 24 genomeDir ../../../downloaded_data/star/ readFilesIn ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R1_001_cutadapt.fastq.gz ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R2_001_cutadapt.fastq.gz readFilesCommand gunzip -c outSAMtype BAM SortedByCoordinate outSAMattributes GX GN CY UY CR UR CB UB clip5pNbases 65 0 quantMode TranscriptomeSAM quantTranscriptomeBan Singleend soloType CB_UMI_Simple soloCBstart 1 soloUMIstart 17 soloCBlen 16 soloUMIlen 12 soloBarcodeMate 1 soloCBwhitelist ../../../downloaded_data/star/3M-february-2018.txt soloStrand Unstranded soloOutFileNames output/ RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_genes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_barcodes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_matrix.mtx soloFeatures Gene GeneFull SJ Velocyto soloCellFilter EmptyDrops_CR soloMultiMappers Uniform PropUnique EM ------------------------------- ##### Final effective command line: ../../../star/STAR-2.7.10a_alpha_220601/STAR --runThreadN 24 --genomeDir ../../../downloaded_data/star/ --readFilesIn ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R1_001_cutadapt.fastq.gz ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R2_001_cutadapt.fastq.gz --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate --outSAMattributes GX GN CY UY CR UR CB UB --clip5pNbases 65 0 --quantMode TranscriptomeSAM --quantTranscriptomeBan Singleend --soloType CB_UMI_Simple --soloCBstart 1 --soloUMIstart 17 --soloCBlen 16 --soloUMIlen 12 --soloBarcodeMate 1 --soloCBwhitelist ../../../downloaded_data/star/3M-february-2018.txt --soloStrand Unstranded --soloOutFileNames output/ RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_genes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_barcodes.tsv RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_matrix.mtx --soloFeatures Gene GeneFull SJ Velocyto --soloCellFilter EmptyDrops_CR --soloMultiMappers Uniform PropUnique EM ---------------------------------------- Number of fastq files for each mate = 1 Input read files for mate 1 : -rw-r--r-- 1 medgnt mec 14957706523 Jul 5 23:03 ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R1_001_cutadapt.fastq.gz readsCommandsFile: exec > "./_STARtmp/tmp.fifo.read1" echo FILE 0 gunzip -c "../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R1_001_cutadapt.fastq.gz" Input read files for mate 2 : -rw-r--r-- 1 medgnt mec 12366320668 Jul 5 23:03 ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R2_001_cutadapt.fastq.gz readsCommandsFile: exec > "./_STARtmp/tmp.fifo.read2" echo FILE 0 gunzip -c "../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R2_001_cutadapt.fastq.gz" ParametersSolo: using hardcoded filtering parameters for --soloCellFilterType EmptyDrops_CR ParametersSolo: --soloCellFilterType EmptyDrops_CR filtering parameters: 3000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 Number of CBs in the whitelist = 6794880 Jul 07 14:39:25 ... Finished reading, sorting and deduplicating CB whitelist sequences. WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters: ### star/STAR-2.7.10a/bin/Linux_x86_64_static/STAR --runMode genomeGenerate --runThreadN 24 --genomeDir downloaded_data/star/ --genomeFastaFiles /home/home02/medgnt/res/GBM_SC/downloaded_data/gencode/GRCh38.p10.genome.fa --sjdbGTFfile /home/home02/medgnt/res/GBM_TF_analysis/downloaded_data/gencode.v27.chr_patch_hapl_scaff.annotation.gtf ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles /home/home02/medgnt/res/GBM_SC/downloaded_data/gencode/GRCh38.p10.genome.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED genomeTransformType None ~RE-DEFINED genomeTransformVCF - ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /home/home02/medgnt/res/GBM_TF_analysis/downloaded_data/gencode.v27.chr_patch_hapl_scaff.annotation.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3398169073 26009673743 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 555 1 chr1 248956422 0 2 chr2 242193529 249036800 3 chr3 198295559 491257856 4 chr4 190214555 689700864 5 chr5 181538259 880017408 6 chr6 170805979 1061683200 7 chr7 159345973 1232601088 8 chr8 145138636 1391984640 9 chr9 138394717 1537212416 10 chr10 133797422 1675624448 11 chr11 135086622 1809580032 12 chr12 133275309 1944846336 13 chr13 114364328 2078277632 14 chr14 107043718 2192834560 15 chr15 101991189 2300051456 16 chr16 90338345 2402287616 17 chr17 83257441 2492727296 18 chr18 80373285 2576089088 19 chr19 58617616 2656567296 20 chr20 64444167 2715287552 21 chr21 46709983 2779774976 22 chr22 50818468 2826698752 23 chrX 156040895 2877554688 24 chrY 57227415 3033792512 25 chrM 16569 3091202048 26 GL000008.2 209709 3091464192 27 GL000009.2 201709 3091726336 28 GL000194.1 191469 3091988480 29 GL000195.1 182896 3092250624 30 GL000205.2 185591 3092512768 31 GL000208.1 92689 3092774912 32 GL000213.1 164239 3093037056 33 GL000214.1 137718 3093299200 34 GL000216.2 176608 3093561344 35 GL000218.1 161147 3093823488 36 GL000219.1 179198 3094085632 37 GL000220.1 161802 3094347776 38 GL000221.1 155397 3094609920 39 GL000224.1 179693 3094872064 40 GL000225.1 211173 3095134208 41 GL000226.1 15008 3095396352 42 KQ759759.1 196940 3095658496 43 KN538364.1 415308 3095920640 44 KQ759762.1 101037 3096444928 45 KQ031383.1 467143 3096707072 46 KN538369.1 541038 3097231360 47 JH159136.1 200998 3098017792 48 JH159137.1 191409 3098279936 49 KQ031387.1 320750 3098542080 50 KV766195.1 140877 3099066368 51 KN538360.1 460100 3099328512 52 KN196484.1 370917 3099852800 53 KN196476.1 305979 3100377088 54 KQ983257.1 230434 3100901376 55 KN196479.1 330164 3101163520 56 KV575245.1 154723 3101687808 57 KN196473.1 166200 3101949952 58 KN196487.1 101150 3102212096 59 KQ759760.1 315610 3102474240 60 KN196475.1 451168 3102998528 61 KV880766.1 156998 3103522816 62 KV880767.1 265876 3103784960 63 KQ090016.1 245716 3104309248 64 KV880764.1 142129 3104571392 65 KN538361.1 305542 3104833536 66 KN196474.1 122022 3105357824 67 KQ090022.1 181958 3105619968 68 KN196478.1 268330 3105882112 69 KN196480.1 277797 3106406400 70 KQ090028.1 407387 3106930688 71 KN196483.1 35455 3107454976 72 KN196481.1 108875 3107717120 73 KN538363.1 365499 3107979264 74 KN538362.1 208149 3108503552 75 KQ031385.1 373699 3108765696 76 KV766192.1 411654 3109289984 77 KQ031386.1 165718 3109814272 78 KQ031388.1 179932 3110076416 79 KN538365.1 14347 3110338560 80 KN538366.1 85284 3110600704 81 KN538367.1 420164 3110862848 82 KN538370.1 86533 3111387136 83 KN538373.1 148762 3111649280 84 KV880765.1 468267 3111911424 85 KV766196.1 281919 3112435712 86 KN538371.1 206320 3112960000 87 KQ031384.1 481245 3113222144 88 KN538372.1 356766 3113746432 89 KQ090021.1 264545 3114270720 90 KN196482.1 211377 3114795008 91 KQ458386.1 405389 3115057152 92 KV575244.1 673059 3115581440 93 KV880768.1 1927115 3116367872 94 KN196472.1 186494 3118465024 95 GL383545.1 179254 3118727168 96 GL383546.1 309802 3118989312 97 KI270824.1 181496 3119513600 98 KI270825.1 188315 3119775744 99 KQ090020.1 185507 3120037888 100 GL383547.1 154407 3120300032 101 KN538368.1 203552 3120562176 102 KI270826.1 186169 3120824320 103 KI270827.1 67707 3121086464 104 KI270829.1 204059 3121348608 105 KI270830.1 177092 3121610752 106 KI270831.1 296895 3121872896 107 KI270832.1 210133 3122397184 108 KI270902.1 106711 3122659328 109 KI270903.1 214625 3122921472 110 KI270927.1 218612 3123183616 111 GL877875.1 167313 3123445760 112 GL383549.1 120804 3123707904 113 GL383550.2 169178 3123970048 114 KQ090023.1 109323 3124232192 115 GL877876.1 408271 3124494336 116 GL383552.1 138655 3125018624 117 KI270904.1 572349 3125280768 118 GL383553.2 152874 3126067200 119 KI270835.1 238139 3126329344 120 GL383551.1 184319 3126591488 121 KI270837.1 40090 3126853632 122 KI270833.1 76061 3127115776 123 KI270834.1 119498 3127377920 124 KI270836.1 56134 3127640064 125 KI270838.1 306913 3127902208 126 KI270839.1 180306 3128426496 127 KI270840.1 191684 3128688640 128 KI270841.1 169134 3128950784 129 KI270842.1 37287 3129212928 130 KI270843.1 103832 3129475072 131 KQ090024.1 168146 3129737216 132 KQ090025.1 123480 3129999360 133 KI270844.1 322166 3130261504 134 KI270845.1 180703 3130785792 135 KI270846.1 1351393 3131047936 136 KI270847.1 1511111 3132620800 137 KI270852.1 478999 3134193664 138 KI270848.1 327382 3134717952 139 GL383554.1 296527 3135242240 140 KI270906.1 196384 3135766528 141 GL383555.2 388773 3136028672 142 KI270851.1 263054 3136552960 143 KI270849.1 244917 3137077248 144 KI270905.1 5161414 3137339392 145 KI270850.1 430880 3142582272 146 KQ031389.1 2365364 3143106560 147 KI270853.1 2659700 3145728000 148 GL383556.1 192462 3148611584 149 GL383557.1 89672 3148873728 150 KI270855.1 232857 3149135872 151 KQ031390.1 169136 3149398016 152 KI270856.1 63982 3149660160 153 KQ090027.1 267463 3149922304 154 KQ090026.1 59016 3150446592 155 KI270854.1 134193 3150708736 156 KI270909.1 325800 3150970880 157 KV766197.1 246895 3151495168 158 GL383563.3 375691 3151757312 159 KI270861.1 196688 3152281600 160 GL383564.2 133151 3152543744 161 GL000258.2 1821992 3152805888 162 KI270860.1 178921 3154640896 163 KI270907.1 137721 3154903040 164 KI270862.1 391357 3155165184 165 GL383565.1 223995 3155689472 166 KI270908.1 1423190 3155951616 167 KV766198.1 276292 3157524480 168 KI270910.1 157099 3158048768 169 GL383566.1 90219 3158310912 170 JH159146.1 278131 3158573056 171 JH159147.1 70345 3159097344 172 JH159148.1 88070 3159359488 173 KI270857.1 2877074 3159621632 174 KI270858.1 235827 3162505216 175 KI270859.1 108763 3162767360 176 GL383567.1 289831 3163029504 177 GL383568.1 104552 3163553792 178 GL383569.1 167950 3163815936 179 GL383570.1 164789 3164078080 180 GL383571.1 198278 3164340224 181 GL383572.1 159547 3164602368 182 KI270863.1 167999 3164864512 183 KI270864.1 111737 3165126656 184 KQ458385.1 205101 3165388800 185 KI270912.1 174061 3165650944 186 KI270911.1 157710 3165913088 187 KV575254.1 99845 3166175232 188 KV575246.1 163926 3166437376 189 KV575256.1 223118 3166699520 190 KV575253.1 166713 3166961664 191 KV575252.1 178197 3167223808 192 KV575255.1 161095 3167485952 193 KV575259.1 171263 3167748096 194 KI270917.1 190932 3168010240 195 KI270918.1 123111 3168272384 196 KI270919.1 170701 3168534528 197 KV575247.1 170206 3168796672 198 KV575248.1 168131 3169058816 199 KV575250.1 241058 3169320960 200 KV575249.1 293522 3169583104 201 KV575257.1 100553 3170107392 202 KI270920.1 198005 3170369536 203 KI270921.1 282224 3170631680 204 KI270922.1 187935 3171155968 205 KI270923.1 189352 3171418112 206 KI270929.1 186203 3171680256 207 KI270930.1 200773 3171942400 208 KI270931.1 170148 3172204544 209 KI270932.1 215732 3172466688 210 KI270933.1 170537 3172728832 211 KI270882.1 248807 3172990976 212 KI270883.1 170399 3173253120 213 KI270884.1 157053 3173515264 214 KI270885.1 171027 3173777408 215 KI270886.1 204239 3174039552 216 KI270887.1 209512 3174301696 217 KI270888.1 155532 3174563840 218 KV575258.1 156965 3174825984 219 KV575251.1 159285 3175088128 220 KV575260.1 145691 3175350272 221 KI270889.1 170698 3175612416 222 KI270890.1 184499 3175874560 223 GL000209.2 177381 3176136704 224 KI270891.1 170680 3176398848 225 KI270914.1 205194 3176660992 226 KI270915.1 170665 3176923136 227 KI270916.1 184516 3177185280 228 GL949746.1 987716 3177447424 229 GL949747.2 729520 3178496000 230 GL949748.2 1064304 3179282432 231 GL949749.2 1091841 3180593152 232 GL949750.2 1066390 3181903872 233 GL949751.2 1002683 3183214592 234 GL949752.1 987100 3184263168 235 GL949753.2 796479 3185311744 236 GL383573.1 385657 3186360320 237 GL383574.1 155864 3186884608 238 GL383575.2 170222 3187146752 239 KI270866.1 43156 3187408896 240 GL383576.1 188024 3187671040 241 KI270867.1 233762 3187933184 242 KI270865.1 52969 3188195328 243 KI270938.1 1066800 3188457472 244 KI270868.1 61734 3189768192 245 KI270760.1 109528 3190030336 246 KI270762.1 354444 3190292480 247 GL383518.1 182439 3190816768 248 KI270759.1 425601 3191078912 249 KI270766.1 256271 3191603200 250 GL383519.1 110268 3191865344 251 KI270761.1 165834 3192127488 252 KQ458382.1 141019 3192389632 253 GL383520.2 366580 3192651776 254 KI270763.1 911658 3193176064 255 KQ458383.1 349938 3194224640 256 KI270765.1 185285 3194748928 257 KI270764.1 50258 3195011072 258 KQ983255.1 278659 3195273216 259 KQ458384.1 212205 3195797504 260 KV880763.1 551020 3196059648 261 KI270892.1 162212 3196846080 262 GL383577.2 128386 3197108224 263 KI270869.1 118774 3197370368 264 KI270870.1 183433 3197632512 265 KI270871.1 58661 3197894656 266 GL383578.2 63917 3198156800 267 GL383579.2 201197 3198418944 268 GL383580.2 74653 3198681088 269 GL383581.2 116689 3198943232 270 KI270872.1 82692 3199205376 271 KI270873.1 143900 3199467520 272 KI270874.1 166743 3199729664 273 GL383582.2 162811 3199991808 274 GL383583.2 96924 3200253952 275 KI270875.1 259914 3200516096 276 KI270876.1 263666 3200778240 277 KI270877.1 101331 3201302528 278 KI270878.1 186262 3201564672 279 KI270879.1 304135 3201826816 280 KB663609.1 74013 3202351104 281 KI270928.1 176103 3202613248 282 KN196485.1 156562 3202875392 283 KN196486.1 153027 3203137536 284 KQ458387.1 155930 3203399680 285 KQ458388.1 174749 3203661824 286 KQ759761.1 145162 3203923968 287 KI270769.1 120616 3204186112 288 KI270767.1 161578 3204448256 289 GL383521.1 143390 3204710400 290 KI270772.1 133041 3204972544 291 GL383522.1 123821 3205234688 292 KI270770.1 136240 3205496832 293 KI270893.1 161218 3205758976 294 KI270894.1 214158 3206021120 295 GL582966.2 96131 3206283264 296 KI270773.1 70887 3206545408 297 KI270776.1 174166 3206807552 298 KI270768.1 110099 3207069696 299 KI270774.1 223625 3207331840 300 KI270771.1 110395 3207593984 301 KI270775.1 138019 3207856128 302 KQ983256.1 535088 3208118272 303 JH636055.2 173151 3208904704 304 GL383526.1 180671 3209166848 305 KI270779.1 205312 3209428992 306 KI270777.1 173649 3209691136 307 KI270782.1 162429 3209953280 308 KI270783.1 109187 3210215424 309 KI270778.1 248252 3210477568 310 KI270895.1 162896 3210739712 311 KI270780.1 224108 3211001856 312 KI270924.1 166540 3211264000 313 KI270781.1 113034 3211526144 314 KI270934.1 163458 3211788288 315 KI270935.1 197351 3212050432 316 KI270936.1 164170 3212312576 317 KI270937.1 165607 3212574720 318 KI270784.1 184404 3212836864 319 KQ983258.1 205407 3213099008 320 KV766193.1 420675 3213361152 321 GL383527.1 164536 3213885440 322 KI270790.1 220246 3214147584 323 GL383528.1 376187 3214409728 324 KI270787.1 111943 3214934016 325 GL000257.2 586476 3215196160 326 KI270785.1 119912 3215982592 327 KQ090013.1 90922 3216244736 328 KI270786.1 244096 3216506880 329 KI270788.1 158965 3216769024 330 KI270789.1 205944 3217031168 331 KI270896.1 378547 3217293312 332 KI270925.1 555799 3217817600 333 KQ090014.1 163749 3218604032 334 KQ090015.1 236512 3218866176 335 GL383532.1 82728 3219128320 336 KI270897.1 1144418 3219390464 337 GL383531.1 173459 3220701184 338 GL949742.1 226852 3220963328 339 GL339449.2 1612928 3221225472 340 KI270795.1 131892 3223060480 341 KI270791.1 195710 3223322624 342 GL383530.1 101241 3223584768 343 KI270898.1 130957 3223846912 344 KI270792.1 179043 3224109056 345 KI270796.1 172708 3224371200 346 KI270793.1 126136 3224633344 347 KI270794.1 164558 3224895488 348 KN196477.1 139087 3225157632 349 KV575243.1 362221 3225419776 350 KQ090017.1 82315 3225944064 351 GL383533.1 124736 3226206208 352 KB021644.2 185823 3226468352 353 KI270797.1 197536 3226730496 354 KI270798.1 271782 3226992640 355 KI270799.1 152148 3227516928 356 KI270800.1 175808 3227779072 357 KI270801.1 870480 3228041216 358 KI270802.1 75005 3229089792 359 KI270758.1 76752 3229351936 360 GL000250.2 4672374 3229614080 361 GL000251.2 4795265 3234332672 362 GL000252.2 4604811 3239313408 363 GL000253.2 4677643 3244032000 364 GL000254.2 4827813 3248750592 365 GL000255.2 4606388 3253731328 366 GL000256.2 4929269 3258449920 367 KI270804.1 157952 3263430656 368 KI270806.1 158166 3263692800 369 GL383534.2 119183 3263954944 370 KI270805.1 209988 3264217088 371 KI270899.1 190869 3264479232 372 KI270809.1 209586 3264741376 373 KI270803.1 1111570 3265003520 374 KI270807.1 126434 3266314240 375 KI270808.1 271455 3266576384 376 KI270811.1 292436 3267100672 377 KI270814.1 141812 3267624960 378 KI270810.1 374415 3267887104 379 KI270812.1 282736 3268411392 380 KI270815.1 132244 3268935680 381 KI270813.1 300230 3269197824 382 KI270816.1 305841 3269722112 383 KI270818.1 145606 3270246400 384 KI270817.1 158983 3270508544 385 KI270900.1 318687 3270770688 386 KI270819.1 133535 3271294976 387 KI270901.1 136959 3271557120 388 KI270820.1 36640 3271819264 389 KI270926.1 229282 3272081408 390 KI270821.1 985506 3272343552 391 KI270822.1 624492 3273392128 392 GL383539.1 162988 3274178560 393 GL383540.1 71551 3274440704 394 GL383541.1 171286 3274702848 395 GL383542.1 60032 3274964992 396 KI270823.1 439082 3275227136 397 KQ090018.1 163882 3275751424 398 KQ090019.1 134099 3276013568 399 KI270880.1 284869 3276275712 400 KI270881.1 144206 3276800000 401 KI270913.1 274009 3277062144 402 KV766199.1 188004 3277586432 403 KI270302.1 2274 3277848576 404 KI270303.1 1942 3278110720 405 KI270304.1 2165 3278372864 406 KI270305.1 1472 3278635008 407 KI270310.1 1201 3278897152 408 KI270311.1 12399 3279159296 409 KI270312.1 998 3279421440 410 KI270315.1 2276 3279683584 411 KI270316.1 1444 3279945728 412 KI270317.1 37690 3280207872 413 KI270320.1 4416 3280470016 414 KI270322.1 21476 3280732160 415 KI270329.1 1040 3280994304 416 KI270330.1 1652 3281256448 417 KI270333.1 2699 3281518592 418 KI270334.1 1368 3281780736 419 KI270335.1 1048 3282042880 420 KI270336.1 1026 3282305024 421 KI270337.1 1121 3282567168 422 KI270338.1 1428 3282829312 423 KI270340.1 1428 3283091456 424 KI270362.1 3530 3283353600 425 KI270363.1 1803 3283615744 426 KI270364.1 2855 3283877888 427 KI270366.1 8320 3284140032 428 KI270371.1 2805 3284402176 429 KI270372.1 1650 3284664320 430 KI270373.1 1451 3284926464 431 KI270374.1 2656 3285188608 432 KI270375.1 2378 3285450752 433 KI270376.1 1136 3285712896 434 KI270378.1 1048 3285975040 435 KI270379.1 1045 3286237184 436 KI270381.1 1930 3286499328 437 KI270382.1 4215 3286761472 438 KI270383.1 1750 3287023616 439 KI270384.1 1658 3287285760 440 KI270385.1 990 3287547904 441 KI270386.1 1788 3287810048 442 KI270387.1 1537 3288072192 443 KI270388.1 1216 3288334336 444 KI270389.1 1298 3288596480 445 KI270390.1 2387 3288858624 446 KI270391.1 1484 3289120768 447 KI270392.1 971 3289382912 448 KI270393.1 1308 3289645056 449 KI270394.1 970 3289907200 450 KI270395.1 1143 3290169344 451 KI270396.1 1880 3290431488 452 KI270411.1 2646 3290693632 453 KI270412.1 1179 3290955776 454 KI270414.1 2489 3291217920 455 KI270417.1 2043 3291480064 456 KI270418.1 2145 3291742208 457 KI270419.1 1029 3292004352 458 KI270420.1 2321 3292266496 459 KI270422.1 1445 3292528640 460 KI270423.1 981 3292790784 461 KI270424.1 2140 3293052928 462 KI270425.1 1884 3293315072 463 KI270429.1 1361 3293577216 464 KI270435.1 92983 3293839360 465 KI270438.1 112505 3294101504 466 KI270442.1 392061 3294363648 467 KI270448.1 7992 3294887936 468 KI270465.1 1774 3295150080 469 KI270466.1 1233 3295412224 470 KI270467.1 3920 3295674368 471 KI270468.1 4055 3295936512 472 KI270507.1 5353 3296198656 473 KI270508.1 1951 3296460800 474 KI270509.1 2318 3296722944 475 KI270510.1 2415 3296985088 476 KI270511.1 8127 3297247232 477 KI270512.1 22689 3297509376 478 KI270515.1 6361 3297771520 479 KI270516.1 1300 3298033664 480 KI270517.1 3253 3298295808 481 KI270518.1 2186 3298557952 482 KI270519.1 138126 3298820096 483 KI270521.1 7642 3299082240 484 KI270522.1 5674 3299344384 485 KI270528.1 2983 3299606528 486 KI270529.1 1899 3299868672 487 KI270530.1 2168 3300130816 488 KI270538.1 91309 3300392960 489 KI270539.1 993 3300655104 490 KI270544.1 1202 3300917248 491 KI270548.1 1599 3301179392 492 KI270579.1 31033 3301441536 493 KI270580.1 1553 3301703680 494 KI270581.1 7046 3301965824 495 KI270582.1 6504 3302227968 496 KI270583.1 1400 3302490112 497 KI270584.1 4513 3302752256 498 KI270587.1 2969 3303014400 499 KI270588.1 6158 3303276544 500 KI270589.1 44474 3303538688 501 KI270590.1 4685 3303800832 502 KI270591.1 5796 3304062976 503 KI270593.1 3041 3304325120 504 KI270706.1 175055 3304587264 505 KI270707.1 32032 3304849408 506 KI270708.1 127682 3305111552 507 KI270709.1 66860 3305373696 508 KI270710.1 40176 3305635840 509 KI270711.1 42210 3305897984 510 KI270712.1 176043 3306160128 511 KI270713.1 40745 3306422272 512 KI270714.1 41717 3306684416 513 KI270715.1 161471 3306946560 514 KI270716.1 153799 3307208704 515 KI270717.1 40062 3307470848 516 KI270718.1 38054 3307732992 517 KI270719.1 176845 3307995136 518 KI270720.1 39050 3308257280 519 KI270721.1 100316 3308519424 520 KI270722.1 194050 3308781568 521 KI270723.1 38115 3309043712 522 KI270724.1 39555 3309305856 523 KI270725.1 172810 3309568000 524 KI270726.1 43739 3309830144 525 KI270727.1 448248 3310092288 526 KI270728.1 1872759 3310616576 527 KI270729.1 280839 3312713728 528 KI270730.1 112551 3313238016 529 KI270731.1 150754 3313500160 530 KI270732.1 41543 3313762304 531 KI270733.1 179772 3314024448 532 KI270734.1 165050 3314286592 533 KI270735.1 42811 3314548736 534 KI270736.1 181920 3314810880 535 KI270737.1 103838 3315073024 536 KI270738.1 99375 3315335168 537 KI270739.1 73985 3315597312 538 KI270740.1 37240 3315859456 539 KI270741.1 157432 3316121600 540 KI270742.1 186739 3316383744 541 KI270743.1 210658 3316645888 542 KI270744.1 168472 3316908032 543 KI270745.1 41891 3317170176 544 KI270746.1 66486 3317432320 545 KI270747.1 198735 3317694464 546 KI270748.1 93321 3317956608 547 KI270749.1 158759 3318218752 548 KI270750.1 148850 3318480896 549 KI270751.1 150742 3318743040 550 KI270752.1 27745 3319005184 551 KI270753.1 62944 3319267328 552 KI270754.1 40191 3319529472 553 KI270755.1 36723 3319791616 554 KI270756.1 79590 3320053760 555 KI270757.1 71251 3320315904 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Thu Jul 7 14:39:25 2022 Genome: size given as a parameter = 3398169073 SA: size given as a parameter = 26009673743 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3398169073; nSAbyte=26009673743 GstrandBit=32 SA number of indices=6305375452 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3398169073 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3398169073 bytes SA file size: 26009673743 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 26009673743 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Thu Jul 7 14:41:39 2022 Processing splice junctions database sjdbN=386025, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Loaded transcript database, nTr=218862 Loaded exon database, nEx=1305599 Created thread # 1 Created thread # 2 Starting to map file # 0 mate 1: ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R1_001_cutadapt.fastq.gz mate 2: ../../../data/X204SC21021123-Z01-F001/raw_data/RNA_16_1037/RNA_16_1037-SCI7T027-SCI5T027_HHN5HDSX3_S1_L004_R2_001_cutadapt.fastq.gz 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 Created thread # 16 Created thread # 17 Created thread # 18 Created thread # 19 Created thread # 20 Created thread # 21 Created thread # 22 Created thread # 23