STAR version=2.7.11a STAR compilation time,server,dir=2023-09-15T02:58:53+0000 :/opt/conda/conda-bld/star_1694746407721/work/source ##### Command Line: /scratch/work/malonzm1/.conda_envs/star_env/bin/STAR-avx2 --limitBAMsortRAM 250000000000 --outSAMattributes NH HI AS nM NM MD jM jI MC ch XS CR UR GX GN sM CB UB --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesCommand gunzip -c --runThreadN 12 --sjdbGTFfile /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/genes/genes.gtf --outReadsUnmapped Fastx --outMultimapperOrder Random --genomeDir /scratch/cs/pan-autoimmune/utilities/STAR/hg38 --readFilesIn /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz --outFileNamePrefix SRR13716262 --soloType CB_UMI_Simple --soloBarcodeReadLength 0 --soloCBwhitelist /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/whitelists/737K-august-2016.txt --soloUMIlen 10 --soloCBlen 16 --soloUMIstart 17 ##### Initial USER parameters from Command Line: outFileNamePrefix SRR13716262 ###### All USER parameters from Command Line: limitBAMsortRAM 250000000000 ~RE-DEFINED outSAMattributes NH HI AS nM NM MD jM jI MC ch XS CR UR GX GN sM CB UB ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED quantMode GeneCounts ~RE-DEFINED readFilesCommand gunzip -c ~RE-DEFINED runThreadN 12 ~RE-DEFINED sjdbGTFfile /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/genes/genes.gtf ~RE-DEFINED outReadsUnmapped Fastx ~RE-DEFINED outMultimapperOrder Random ~RE-DEFINED genomeDir /scratch/cs/pan-autoimmune/utilities/STAR/hg38 ~RE-DEFINED readFilesIn /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz ~RE-DEFINED outFileNamePrefix SRR13716262 ~RE-DEFINED soloType CB_UMI_Simple ~RE-DEFINED soloBarcodeReadLength 0 ~RE-DEFINED soloCBwhitelist /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/whitelists/737K-august-2016.txt ~RE-DEFINED soloUMIlen 10 ~RE-DEFINED soloCBlen 16 ~RE-DEFINED soloUMIstart 17 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 12 genomeDir /scratch/cs/pan-autoimmune/utilities/STAR/hg38 readFilesIn /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz readFilesCommand gunzip -c limitBAMsortRAM 250000000000 outFileNamePrefix SRR13716262 outReadsUnmapped Fastx outMultimapperOrder Random outSAMtype BAM SortedByCoordinate outSAMattributes NH HI AS nM NM MD jM jI MC ch XS CR UR GX GN sM CB UB sjdbGTFfile /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/genes/genes.gtf quantMode GeneCounts soloType CB_UMI_Simple soloUMIstart 17 soloCBlen 16 soloUMIlen 10 soloBarcodeReadLength 0 soloCBwhitelist /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/whitelists/737K-august-2016.txt ------------------------------- ##### Final effective command line: /scratch/work/malonzm1/.conda_envs/star_env/bin/STAR-avx2 --runThreadN 12 --genomeDir /scratch/cs/pan-autoimmune/utilities/STAR/hg38 --readFilesIn /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz --readFilesCommand gunzip -c --limitBAMsortRAM 250000000000 --outFileNamePrefix SRR13716262 --outReadsUnmapped Fastx --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS nM NM MD jM jI MC ch XS CR UR GX GN sM CB UB --sjdbGTFfile /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/genes/genes.gtf --quantMode GeneCounts --soloType CB_UMI_Simple --soloUMIstart 17 --soloCBlen 16 --soloUMIlen 10 --soloBarcodeReadLength 0 --soloCBwhitelist /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/whitelists/737K-august-2016.txt ---------------------------------------- Number of fastq files for each mate = 1 Input read files for mate 1 : -rw-rw-r-- 1 malonzm1 pan-autoimmune 5922580389 May 16 2023 /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz readsCommandsFile: exec > "SRR13716262_STARtmp/tmp.fifo.read1" echo FILE 0 gunzip -c "/scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz" Input read files for mate 2 : -rw-rw-r-- 1 malonzm1 pan-autoimmune 1442965829 May 16 2023 /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz readsCommandsFile: exec > "SRR13716262_STARtmp/tmp.fifo.read2" echo FILE 0 gunzip -c "/scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz" WARNING --outSAMattributes contains XS, therefore STAR will use --outSAMstrandField intronMotif ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10 Number of CBs in the whitelist = 737280 Nov 24 11:17:57 ... Finished reading, sorting and deduplicating CB whitelist sequences. Finished loading and checking parameters Reading genome generation parameters: ### STAR --runMode genomeGenerate --runThreadN 4 --genomeDir hg38 --genomeFastaFiles /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/fasta/genome.fa --sjdbGTFfile /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/genes/genes.gtf --sjdbOverhang 99 ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/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 99 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/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 3210449251 24894772926 ~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 = 99 taken from the generated genome Started loading the genome: Fri Nov 24 11:17:57 2023 Genome: size given as a parameter = 3210449251 SA: size given as a parameter = 24894772926 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3210449251; nSAbyte=24894772926 GstrandBit=32 SA number of indices=6035096466 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3210449251 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3210449251 bytes SA file size: 24894772926 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24894772926 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Fri Nov 24 11:18:09 2023 Processing splice junctions database sjdbN=362117, pGe.sjdbOverhang=99 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Nov 24 11:18:10 Loaded database junctions from the generated genome /scratch/cs/pan-autoimmune/utilities/STAR/hg38//sjdbList.out.tab: 362117 total junctions Nov 24 11:18:10 ..... processing annotations GTF Processing pGe.sjdbGTFfile=/scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/genes/genes.gtf, found: 199138 transcripts 1305354 exons (non-collapsed) 362172 collapsed junctions Total junctions: 724289 Nov 24 11:18:24 ..... finished GTF processing WARNING: long repeat for junction # 119547 : chr15 88855522 88855578; left shift = 14; right shift = 255 WARNING: long repeat for junction # 481684 : chr15 88855522 88855578; left shift = 14; right shift = 255 Nov 24 11:18:24 Finished preparing junctions Nov 24 11:18:24 ..... inserting junctions into the genome indices Nov 24 11:18:25 Finished SA search: number of new junctions=0, old junctions=362117 Nov 24 11:18:26 Finished sorting SA indicesL nInd=0 Genome size with junctions=3210449251 3138387968 72061283 GstrandBit1=32 GstrandBit=32 Nov 24 11:19:43 Finished inserting junction indices Nov 24 11:19:47 Finished SAi Nov 24 11:19:47 ..... finished inserting junctions into genome Loaded transcript database, nTr=199138 Loaded exon database, nEx=1305354 Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread0 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread0 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread1 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread1 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread2 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread2 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread3 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread3 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread4 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread4 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread5 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread5 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread6 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread6 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread7 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread7 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread8 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread8 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread9 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread9 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread10 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread10 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate0.thread11 ... ok Opening the file: SRR13716262_STARtmp//Unmapped.out.mate1.thread11 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz mate 2: /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz Created thread # 6 Created thread # 7 Created thread # 8 Created thread # 9 Created thread # 10 Created thread # 11 BAM sorting: 160631 mapped reads BAM sorting bins genomic start loci: 1 0 42500060 2 0 155017587 3 1 79354312 4 2 61967368 5 3 6225469 6 3 93083391 7 5 33950898 8 6 69452983 9 7 89561268 10 8 49411359 11 10 12748026 12 10 48965470 13 11 84906104 14 12 29299548 15 13 8210199 16 13 8210870 17 13 8254197 18 13 8254978 19 13 8393146 20 13 8393722 21 13 8437117 22 13 8437639 23 13 8442982 24 14 31083192 25 15 96617915 26 16 151100525 27 17 150407233 28 18 33272676 29 18 159682512 30 20 29333444 31 21 124858028 32 22 939 33 22 1822 34 22 1967 35 22 2727 36 22 7071 37 22 9263 38 22 13843 39 23 129409146 40 40 126494 41 40 127158 42 40 171350 43 40 171902 44 40 179370 45 51 109709 46 51 110482 47 51 153468 48 51 154009 Thread #2 end of input stream, nextChar=-1 Completed: thread #7 Completed: thread #11 Completed: thread #2 Completed: thread #10 Completed: thread #8 Completed: thread #5 Completed: thread #6 Completed: thread #1 Completed: thread #9 Completed: thread #4 Completed: thread #0 Joined thread # 1 Joined thread # 2 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 Nov 24 11:26:58 ..... finished mapping RAM after mapping: VmPeak: 34873768 kB; VmSize: 34804492 kB; VmHWM: 33492292 kB; VmRSS: 33322336 kB; RAM after freeing genome index memory: VmPeak: 34873768 kB; VmSize: 4031196 kB; VmHWM: 33492292 kB; VmRSS: 2743376 kB; Nov 24 11:27:01 ..... started Solo counting Nov 24 11:27:01 ... Starting Solo post-map for Gene Nov 24 11:27:02 ... Allocated and initialized readInfo array, nReadsInput = 121267797 Nov 24 11:27:02 ... Finished allocating arrays for Solo 0 GiB Nov 24 11:27:02 ... Finished reading reads from Solo files nCB=0, nReadPerCBmax=0, yesWLmatch=0 RAM for solo feature Gene VmPeak: 34873768 kB; VmSize: 5926008 kB; VmHWM: 33492292 kB; VmRSS: 4638204 kB; Nov 24 11:27:02 ... Finished collapsing UMIs Nov 24 11:27:02 ... Solo: writing raw matrix Solo output directory directory created: SRR13716262Solo.out/Gene//raw/ Nov 24 11:27:02 ... Solo: cell filtering RAM after completing solo: VmPeak: 34873768 kB; VmSize: 5926008 kB; VmHWM: 33492292 kB; VmRSS: 4638224 kB; Nov 24 11:27:02 ..... finished Solo counting Nov 24 11:27:02 ..... started sorting BAM Max memory needed for sorting = 1393580264 ALL DONE!