STAR version=2.7.9a_2021-06-17 STAR compilation time,server,dir=2021-06-23T12:32:55-07:00 :/home/chang/STAR/source ##### Command Line: STAR --genomeDir /media/chang/HDD-1/reference_cellranger/STAR_GRCh38-2020-A --runThreadN 32 --soloType CB_UMI_Simple --readFilesIn ../lane2_fastq/bamtofastq_S1_L001_R2_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R2_001.fastq.gz ../lane2_fastq/bamtofastq_S1_L001_R1_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R1_001.fastq.gz --soloUMIlen 12 --soloCBwhitelist ../737K-arc-v1.txt --readFilesCommand zcat --outSAMattributes CB CR CY GX GN UB UR UY --outSAMtype BAM SortedByCoordinate --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIdedup 1MM_CR --soloFeatures GeneFull --soloMultiMappers Uniform EM --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --soloUMIfiltering MultiGeneUMI_CR ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: genomeDir /media/chang/HDD-1/reference_cellranger/STAR_GRCh38-2020-A ~RE-DEFINED runThreadN 32 ~RE-DEFINED soloType CB_UMI_Simple ~RE-DEFINED readFilesIn ../lane2_fastq/bamtofastq_S1_L001_R2_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R2_001.fastq.gz ../lane2_fastq/bamtofastq_S1_L001_R1_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R1_001.fastq.gz ~RE-DEFINED soloUMIlen 12 ~RE-DEFINED soloCBwhitelist ../737K-arc-v1.txt ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED outSAMattributes CB CR CY GX GN UB UR UY ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts ~RE-DEFINED soloUMIdedup 1MM_CR ~RE-DEFINED soloFeatures GeneFull ~RE-DEFINED soloMultiMappers Uniform EM ~RE-DEFINED soloCellFilter EmptyDrops_CR ~RE-DEFINED clipAdapterType CellRanger4 ~RE-DEFINED soloUMIfiltering MultiGeneUMI_CR ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 32 genomeDir /media/chang/HDD-1/reference_cellranger/STAR_GRCh38-2020-A readFilesIn ../lane2_fastq/bamtofastq_S1_L001_R2_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R2_001.fastq.gz ../lane2_fastq/bamtofastq_S1_L001_R1_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R1_001.fastq.gz readFilesCommand zcat outSAMtype BAM SortedByCoordinate outSAMattributes CB CR CY GX GN UB UR UY clipAdapterType CellRanger4 soloType CB_UMI_Simple soloUMIlen 12 soloCBwhitelist ../737K-arc-v1.txt soloFeatures GeneFull soloUMIdedup 1MM_CR soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts soloCellFilter EmptyDrops_CR soloUMIfiltering MultiGeneUMI_CR soloMultiMappers Uniform EM ------------------------------- ##### Final effective command line: STAR --runThreadN 32 --genomeDir /media/chang/HDD-1/reference_cellranger/STAR_GRCh38-2020-A --readFilesIn ../lane2_fastq/bamtofastq_S1_L001_R2_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R2_001.fastq.gz ../lane2_fastq/bamtofastq_S1_L001_R1_001.fastq.gz,../lane2_fastq/bamtofastq_S1_L002_R1_001.fastq.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMattributes CB CR CY GX GN UB UR UY --clipAdapterType CellRanger4 --soloType CB_UMI_Simple --soloUMIlen 12 --soloCBwhitelist ../737K-arc-v1.txt --soloFeatures GeneFull --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloCellFilter EmptyDrops_CR --soloUMIfiltering MultiGeneUMI_CR --soloMultiMappers Uniform EM ---------------------------------------- Number of fastq files for each mate = 2 Input read files for mate 1 : -rw-rw-r-- 1 chang chang 11075234860 Jun 23 10:12 ../lane2_fastq/bamtofastq_S1_L001_R2_001.fastq.gz -rw-rw-r-- 1 chang chang 11291872878 Jun 23 10:12 ../lane2_fastq/bamtofastq_S1_L002_R2_001.fastq.gz readsCommandsFile: exec > "./_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "../lane2_fastq/bamtofastq_S1_L001_R2_001.fastq.gz" echo FILE 1 zcat "../lane2_fastq/bamtofastq_S1_L002_R2_001.fastq.gz" Input read files for mate 2 : -rw-rw-r-- 1 chang chang 8137808868 Jun 23 10:12 ../lane2_fastq/bamtofastq_S1_L001_R1_001.fastq.gz -rw-rw-r-- 1 chang chang 8200552125 Jun 23 10:12 ../lane2_fastq/bamtofastq_S1_L002_R1_001.fastq.gz readsCommandsFile: exec > "./_STARtmp/tmp.fifo.read2" echo FILE 0 zcat "../lane2_fastq/bamtofastq_S1_L001_R1_001.fastq.gz" echo FILE 1 zcat "../lane2_fastq/bamtofastq_S1_L002_R1_001.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 = 736320 Jun 23 15:34:33 ... 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 --runMode genomeGenerate --runThreadN 32 --genomeDir STAR_GRCh38-2020-A --genomeFastaFiles refdata-gex-GRCh38-2020-A/fasta/genome.fa --sjdbGTFfile refdata-gex-GRCh38-2020-A/genes/genes.gtf ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles refdata-gex-GRCh38-2020-A/fasta/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 refdata-gex-GRCh38-2020-A/genes/genes.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3211173485 24900747856 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 194 1 chr1 248956422 0 2 chr10 133797422 249036800 3 chr11 135086622 382992384 4 chr12 133275309 518258688 5 chr13 114364328 651689984 6 chr14 107043718 766246912 7 chr15 101991189 873463808 8 chr16 90338345 975699968 9 chr17 83257441 1066139648 10 chr18 80373285 1149501440 11 chr19 58617616 1229979648 12 chr2 242193529 1288699904 13 chr20 64444167 1530920960 14 chr21 46709983 1595408384 15 chr22 50818468 1642332160 16 chr3 198295559 1693188096 17 chr4 190214555 1891631104 18 chr5 181538259 2081947648 19 chr6 170805979 2263613440 20 chr7 159345973 2434531328 21 chr8 145138636 2593914880 22 chr9 138394717 2739142656 23 chrM 16569 2877554688 24 chrX 156040895 2877816832 25 chrY 57227415 3034054656 26 KI270728.1 1872759 3091464192 27 KI270727.1 448248 3093561344 28 KI270442.1 392061 3094085632 29 KI270729.1 280839 3094609920 30 GL000225.1 211173 3095134208 31 KI270743.1 210658 3095396352 32 GL000008.2 209709 3095658496 33 GL000009.2 201709 3095920640 34 KI270747.1 198735 3096182784 35 KI270722.1 194050 3096444928 36 GL000194.1 191469 3096707072 37 KI270742.1 186739 3096969216 38 GL000205.2 185591 3097231360 39 GL000195.1 182896 3097493504 40 KI270736.1 181920 3097755648 41 KI270733.1 179772 3098017792 42 GL000224.1 179693 3098279936 43 GL000219.1 179198 3098542080 44 KI270719.1 176845 3098804224 45 GL000216.2 176608 3099066368 46 KI270712.1 176043 3099328512 47 KI270706.1 175055 3099590656 48 KI270725.1 172810 3099852800 49 KI270744.1 168472 3100114944 50 KI270734.1 165050 3100377088 51 GL000213.1 164239 3100639232 52 GL000220.1 161802 3100901376 53 KI270715.1 161471 3101163520 54 GL000218.1 161147 3101425664 55 KI270749.1 158759 3101687808 56 KI270741.1 157432 3101949952 57 GL000221.1 155397 3102212096 58 KI270716.1 153799 3102474240 59 KI270731.1 150754 3102736384 60 KI270751.1 150742 3102998528 61 KI270750.1 148850 3103260672 62 KI270519.1 138126 3103522816 63 GL000214.1 137718 3103784960 64 KI270708.1 127682 3104047104 65 KI270730.1 112551 3104309248 66 KI270438.1 112505 3104571392 67 KI270737.1 103838 3104833536 68 KI270721.1 100316 3105095680 69 KI270738.1 99375 3105357824 70 KI270748.1 93321 3105619968 71 KI270435.1 92983 3105882112 72 GL000208.1 92689 3106144256 73 KI270538.1 91309 3106406400 74 KI270756.1 79590 3106668544 75 KI270739.1 73985 3106930688 76 KI270757.1 71251 3107192832 77 KI270709.1 66860 3107454976 78 KI270746.1 66486 3107717120 79 KI270753.1 62944 3107979264 80 KI270589.1 44474 3108241408 81 KI270726.1 43739 3108503552 82 KI270735.1 42811 3108765696 83 KI270711.1 42210 3109027840 84 KI270745.1 41891 3109289984 85 KI270714.1 41717 3109552128 86 KI270732.1 41543 3109814272 87 KI270713.1 40745 3110076416 88 KI270754.1 40191 3110338560 89 KI270710.1 40176 3110600704 90 KI270717.1 40062 3110862848 91 KI270724.1 39555 3111124992 92 KI270720.1 39050 3111387136 93 KI270723.1 38115 3111649280 94 KI270718.1 38054 3111911424 95 KI270317.1 37690 3112173568 96 KI270740.1 37240 3112435712 97 KI270755.1 36723 3112697856 98 KI270707.1 32032 3112960000 99 KI270579.1 31033 3113222144 100 KI270752.1 27745 3113484288 101 KI270512.1 22689 3113746432 102 KI270322.1 21476 3114008576 103 GL000226.1 15008 3114270720 104 KI270311.1 12399 3114532864 105 KI270366.1 8320 3114795008 106 KI270511.1 8127 3115057152 107 KI270448.1 7992 3115319296 108 KI270521.1 7642 3115581440 109 KI270581.1 7046 3115843584 110 KI270582.1 6504 3116105728 111 KI270515.1 6361 3116367872 112 KI270588.1 6158 3116630016 113 KI270591.1 5796 3116892160 114 KI270522.1 5674 3117154304 115 KI270507.1 5353 3117416448 116 KI270590.1 4685 3117678592 117 KI270584.1 4513 3117940736 118 KI270320.1 4416 3118202880 119 KI270382.1 4215 3118465024 120 KI270468.1 4055 3118727168 121 KI270467.1 3920 3118989312 122 KI270362.1 3530 3119251456 123 KI270517.1 3253 3119513600 124 KI270593.1 3041 3119775744 125 KI270528.1 2983 3120037888 126 KI270587.1 2969 3120300032 127 KI270364.1 2855 3120562176 128 KI270371.1 2805 3120824320 129 KI270333.1 2699 3121086464 130 KI270374.1 2656 3121348608 131 KI270411.1 2646 3121610752 132 KI270414.1 2489 3121872896 133 KI270510.1 2415 3122135040 134 KI270390.1 2387 3122397184 135 KI270375.1 2378 3122659328 136 KI270420.1 2321 3122921472 137 KI270509.1 2318 3123183616 138 KI270315.1 2276 3123445760 139 KI270302.1 2274 3123707904 140 KI270518.1 2186 3123970048 141 KI270530.1 2168 3124232192 142 KI270304.1 2165 3124494336 143 KI270418.1 2145 3124756480 144 KI270424.1 2140 3125018624 145 KI270417.1 2043 3125280768 146 KI270508.1 1951 3125542912 147 KI270303.1 1942 3125805056 148 KI270381.1 1930 3126067200 149 KI270529.1 1899 3126329344 150 KI270425.1 1884 3126591488 151 KI270396.1 1880 3126853632 152 KI270363.1 1803 3127115776 153 KI270386.1 1788 3127377920 154 KI270465.1 1774 3127640064 155 KI270383.1 1750 3127902208 156 KI270384.1 1658 3128164352 157 KI270330.1 1652 3128426496 158 KI270372.1 1650 3128688640 159 KI270548.1 1599 3128950784 160 KI270580.1 1553 3129212928 161 KI270387.1 1537 3129475072 162 KI270391.1 1484 3129737216 163 KI270305.1 1472 3129999360 164 KI270373.1 1451 3130261504 165 KI270422.1 1445 3130523648 166 KI270316.1 1444 3130785792 167 KI270340.1 1428 3131047936 168 KI270338.1 1428 3131310080 169 KI270583.1 1400 3131572224 170 KI270334.1 1368 3131834368 171 KI270429.1 1361 3132096512 172 KI270393.1 1308 3132358656 173 KI270516.1 1300 3132620800 174 KI270389.1 1298 3132882944 175 KI270466.1 1233 3133145088 176 KI270388.1 1216 3133407232 177 KI270544.1 1202 3133669376 178 KI270310.1 1201 3133931520 179 KI270412.1 1179 3134193664 180 KI270395.1 1143 3134455808 181 KI270376.1 1136 3134717952 182 KI270337.1 1121 3134980096 183 KI270335.1 1048 3135242240 184 KI270378.1 1048 3135504384 185 KI270379.1 1045 3135766528 186 KI270329.1 1040 3136028672 187 KI270419.1 1029 3136290816 188 KI270336.1 1026 3136552960 189 KI270312.1 998 3136815104 190 KI270539.1 993 3137077248 191 KI270385.1 990 3137339392 192 KI270423.1 981 3137601536 193 KI270392.1 971 3137863680 194 KI270394.1 970 3138125824 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Wed Jun 23 15:34:33 2021 Genome: size given as a parameter = 3211173485 SA: size given as a parameter = 24900747856 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3211173485; nSAbyte=24900747856 GstrandBit=32 SA number of indices=6036544934 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3211173485 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3211173485 bytes SA file size: 24900747856 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24900747856 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Wed Jun 23 15:35:04 2021 Processing splice junctions database sjdbN=362117, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Created thread # 1 Starting to map file # 0 mate 1: ../lane2_fastq/bamtofastq_S1_L001_R2_001.fastq.gz mate 2: ../lane2_fastq/bamtofastq_S1_L001_R1_001.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 Created thread # 16 Created thread # 17 Created thread # 18 Created thread # 19 Created thread # 20 Created thread # 21 Created thread # 22 Created thread # 23 Created thread # 24 Created thread # 25 Created thread # 26 Created thread # 27 Created thread # 28 Created thread # 29 Created thread # 30 Created thread # 31 BAM sorting: 170708 mapped reads BAM sorting bins genomic start loci: 1 0 23812 2 0 99205 3 0 141978 4 0 184959 5 0 197501 6 0 276657 7 0 441529 8 0 517092 9 0 695732 10 0 755464 11 0 783745 12 0 789770 13 0 795786 14 0 810126 15 0 835709 16 0 855939 17 0 916500 18 0 955966 19 0 999059 20 0 1013369 21 0 1030846 22 0 1055813 23 0 1055946 24 0 223919759 25 0 224011018 26 0 224031908 27 1 38481683 28 2 163109 29 3 29322 30 6 101962160 31 6 101976381 32 7 90123363 33 7 90183794 34 8 85901 35 10 69284 36 10 220452 37 11 113594181 38 11 242143112 39 15 198175387 40 16 118661403 41 17 181328047 42 18 72816 43 19 13358 44 20 127313 45 20 311033 46 21 27882 47 21 138274469 48 24 25349507 Starting to map file # 1 mate 1: ../lane2_fastq/bamtofastq_S1_L002_R2_001.fastq.gz mate 2: ../lane2_fastq/bamtofastq_S1_L002_R1_001.fastq.gz Thread #0 end of input stream, nextChar=-1 Completed: thread #10 Completed: thread #24 Completed: thread #9 Completed: thread #6 Completed: thread #7 Completed: thread #2 Completed: thread #22 Completed: thread #14 Completed: thread #0 Completed: thread #29 Completed: thread #30 Completed: thread #17 Completed: thread #12 Completed: thread #4 Completed: thread #21 Completed: thread #20 Completed: thread #27 Completed: thread #18 Completed: thread #15 Completed: thread #31 Completed: thread #13 Completed: thread #11 Completed: thread #23 Completed: thread #19 Completed: thread #28 Completed: thread #25 Completed: thread #1 Joined thread # 1 Joined thread # 2 Completed: thread #26 Completed: thread #8 Completed: thread #16 Completed: thread #3 Joined thread # 3 Joined thread # 4 Completed: thread #5 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 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Joined thread # 20 Joined thread # 21 Joined thread # 22 Joined thread # 23 Joined thread # 24 Joined thread # 25 Joined thread # 26 Joined thread # 27 Joined thread # 28 Joined thread # 29 Joined thread # 30 Joined thread # 31 Jun 23 16:16:49 ..... started Solo counting Jun 23 16:16:49 ... Starting Solo post-map for GeneFull Jun 23 16:16:57 ... Allocated and initialized readInfo array, nReadsInput = 715781411 Jun 23 16:16:57 ... Finished allocating arrays for Solo 7.45386 GB Jun 23 16:26:00 ... Finished reading reads from Solo files nCB=649523, nReadPerCBmax=8012714, nMatch=0