STAR version=2.7.3a STAR compilation time,server,dir= ##### Command Line: /usr/bin/STAR --runThreadN 8 --genomeDir /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/genome_directory/ --genomeLoad NoSharedMemory --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS nM NM MD jM jI rB MC --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 1 --readFilesCommand gunzip -c --readFilesIn /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: runThreadN 8 ~RE-DEFINED genomeDir /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/genome_directory/ ~RE-DEFINED genomeLoad NoSharedMemory ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED outSAMattributes NH HI AS nM NM MD jM jI rB MC ~RE-DEFINED alignEndsType EndToEnd ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED outFilterMultimapNmax 1 ~RE-DEFINED readFilesCommand gunzip -c ~RE-DEFINED readFilesIn /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 8 genomeDir /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/genome_directory/ genomeLoad NoSharedMemory readFilesIn /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz readFilesCommand gunzip -c outSAMtype BAM SortedByCoordinate outSAMattributes NH HI AS nM NM MD jM jI rB MC outSAMunmapped Within outFilterMultimapNmax 1 alignEndsType EndToEnd ------------------------------- ##### Final effective command line: /usr/bin/STAR --runThreadN 8 --genomeDir /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/genome_directory/ --genomeLoad NoSharedMemory --readFilesIn /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS nM NM MD jM jI rB MC --outSAMunmapped Within --outFilterMultimapNmax 1 --alignEndsType EndToEnd ---------------------------------------- Input read files for mate 1, from input string /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz -rw-r--r-- 1 asiimwe asiimwe 2985172186 Feb 18 11:40 /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz readsCommandsFile: exec > "./_STARtmp/tmp.fifo.read1" echo FILE 0 gunzip -c "/scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz" Input read files for mate 2, from input string /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz -rw-r--r-- 1 asiimwe asiimwe 3048695446 Feb 18 11:40 /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz readsCommandsFile: exec > "./_STARtmp/tmp.fifo.read2" echo FILE 0 gunzip -c "/scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz" 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 /home/asiimwe/projects/run_env/alpha_star_wasp_comparison/n_threads_32/genome_directory --genomeFastaFiles /home/asiimwe/projects/star_wasp/fasta_and_gtf/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /home/asiimwe/projects/star_wasp/fasta_and_gtf/gencode.v39.primary_assembly.annotation.gtf --sjdbOverhang 100 ### GstrandBit=32 versionGenome 2.7.1a ~RE-DEFINED genomeFastaFiles /home/asiimwe/projects/star_wasp/fasta_and_gtf/GRCh38.primary_assembly.genome.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /home/asiimwe/projects/star_wasp/fasta_and_gtf/gencode.v39.primary_assembly.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 3217832615 24978336532 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 194 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 KI270302.1 2274 3095658496 43 KI270303.1 1942 3095920640 44 KI270304.1 2165 3096182784 45 KI270305.1 1472 3096444928 46 KI270310.1 1201 3096707072 47 KI270311.1 12399 3096969216 48 KI270312.1 998 3097231360 49 KI270315.1 2276 3097493504 50 KI270316.1 1444 3097755648 51 KI270317.1 37690 3098017792 52 KI270320.1 4416 3098279936 53 KI270322.1 21476 3098542080 54 KI270329.1 1040 3098804224 55 KI270330.1 1652 3099066368 56 KI270333.1 2699 3099328512 57 KI270334.1 1368 3099590656 58 KI270335.1 1048 3099852800 59 KI270336.1 1026 3100114944 60 KI270337.1 1121 3100377088 61 KI270338.1 1428 3100639232 62 KI270340.1 1428 3100901376 63 KI270362.1 3530 3101163520 64 KI270363.1 1803 3101425664 65 KI270364.1 2855 3101687808 66 KI270366.1 8320 3101949952 67 KI270371.1 2805 3102212096 68 KI270372.1 1650 3102474240 69 KI270373.1 1451 3102736384 70 KI270374.1 2656 3102998528 71 KI270375.1 2378 3103260672 72 KI270376.1 1136 3103522816 73 KI270378.1 1048 3103784960 74 KI270379.1 1045 3104047104 75 KI270381.1 1930 3104309248 76 KI270382.1 4215 3104571392 77 KI270383.1 1750 3104833536 78 KI270384.1 1658 3105095680 79 KI270385.1 990 3105357824 80 KI270386.1 1788 3105619968 81 KI270387.1 1537 3105882112 82 KI270388.1 1216 3106144256 83 KI270389.1 1298 3106406400 84 KI270390.1 2387 3106668544 85 KI270391.1 1484 3106930688 86 KI270392.1 971 3107192832 87 KI270393.1 1308 3107454976 88 KI270394.1 970 3107717120 89 KI270395.1 1143 3107979264 90 KI270396.1 1880 3108241408 91 KI270411.1 2646 3108503552 92 KI270412.1 1179 3108765696 93 KI270414.1 2489 3109027840 94 KI270417.1 2043 3109289984 95 KI270418.1 2145 3109552128 96 KI270419.1 1029 3109814272 97 KI270420.1 2321 3110076416 98 KI270422.1 1445 3110338560 99 KI270423.1 981 3110600704 100 KI270424.1 2140 3110862848 101 KI270425.1 1884 3111124992 102 KI270429.1 1361 3111387136 103 KI270435.1 92983 3111649280 104 KI270438.1 112505 3111911424 105 KI270442.1 392061 3112173568 106 KI270448.1 7992 3112697856 107 KI270465.1 1774 3112960000 108 KI270466.1 1233 3113222144 109 KI270467.1 3920 3113484288 110 KI270468.1 4055 3113746432 111 KI270507.1 5353 3114008576 112 KI270508.1 1951 3114270720 113 KI270509.1 2318 3114532864 114 KI270510.1 2415 3114795008 115 KI270511.1 8127 3115057152 116 KI270512.1 22689 3115319296 117 KI270515.1 6361 3115581440 118 KI270516.1 1300 3115843584 119 KI270517.1 3253 3116105728 120 KI270518.1 2186 3116367872 121 KI270519.1 138126 3116630016 122 KI270521.1 7642 3116892160 123 KI270522.1 5674 3117154304 124 KI270528.1 2983 3117416448 125 KI270529.1 1899 3117678592 126 KI270530.1 2168 3117940736 127 KI270538.1 91309 3118202880 128 KI270539.1 993 3118465024 129 KI270544.1 1202 3118727168 130 KI270548.1 1599 3118989312 131 KI270579.1 31033 3119251456 132 KI270580.1 1553 3119513600 133 KI270581.1 7046 3119775744 134 KI270582.1 6504 3120037888 135 KI270583.1 1400 3120300032 136 KI270584.1 4513 3120562176 137 KI270587.1 2969 3120824320 138 KI270588.1 6158 3121086464 139 KI270589.1 44474 3121348608 140 KI270590.1 4685 3121610752 141 KI270591.1 5796 3121872896 142 KI270593.1 3041 3122135040 143 KI270706.1 175055 3122397184 144 KI270707.1 32032 3122659328 145 KI270708.1 127682 3122921472 146 KI270709.1 66860 3123183616 147 KI270710.1 40176 3123445760 148 KI270711.1 42210 3123707904 149 KI270712.1 176043 3123970048 150 KI270713.1 40745 3124232192 151 KI270714.1 41717 3124494336 152 KI270715.1 161471 3124756480 153 KI270716.1 153799 3125018624 154 KI270717.1 40062 3125280768 155 KI270718.1 38054 3125542912 156 KI270719.1 176845 3125805056 157 KI270720.1 39050 3126067200 158 KI270721.1 100316 3126329344 159 KI270722.1 194050 3126591488 160 KI270723.1 38115 3126853632 161 KI270724.1 39555 3127115776 162 KI270725.1 172810 3127377920 163 KI270726.1 43739 3127640064 164 KI270727.1 448248 3127902208 165 KI270728.1 1872759 3128426496 166 KI270729.1 280839 3130523648 167 KI270730.1 112551 3131047936 168 KI270731.1 150754 3131310080 169 KI270732.1 41543 3131572224 170 KI270733.1 179772 3131834368 171 KI270734.1 165050 3132096512 172 KI270735.1 42811 3132358656 173 KI270736.1 181920 3132620800 174 KI270737.1 103838 3132882944 175 KI270738.1 99375 3133145088 176 KI270739.1 73985 3133407232 177 KI270740.1 37240 3133669376 178 KI270741.1 157432 3133931520 179 KI270742.1 186739 3134193664 180 KI270743.1 210658 3134455808 181 KI270744.1 168472 3134717952 182 KI270745.1 41891 3134980096 183 KI270746.1 66486 3135242240 184 KI270747.1 198735 3135504384 185 KI270748.1 93321 3135766528 186 KI270749.1 158759 3136028672 187 KI270750.1 148850 3136290816 188 KI270751.1 150742 3136552960 189 KI270752.1 27745 3136815104 190 KI270753.1 62944 3137077248 191 KI270754.1 40191 3137339392 192 KI270755.1 36723 3137601536 193 KI270756.1 79590 3137863680 194 KI270757.1 71251 3138125824 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Tue May 3 01:30:52 2022 Genome: size given as a parameter = 3217832615 SA: size given as a parameter = 24978336532 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3217832615; nSAbyte=24978336532 GstrandBit=32 SA number of indices=6055354310 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3217832615 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3217832615 bytes SA file size: 24978336532 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24978336532 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Tue May 3 01:31:00 2022 Processing splice junctions database sjdbN=395247, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Created thread # 1 Created thread # 2 Created thread # 3 Starting to map file # 0 mate 1: /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R1.fastq.gz mate 2: /scratch/asiimwe/STAR-WASP_FASTQs_VCFs/FASTQ/HG00512/R2.fastq.gz Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 BAM sorting: 265016 mapped reads BAM sorting bins genomic start loci: 1 0 28282358 2 0 65230770 3 0 153940199 4 0 201955514 5 1 38298219 6 1 88947738 7 1 201164799 8 2 15256286 9 2 100744915 10 2 187051323 11 3 102567083 12 4 82275582 13 4 150446846 14 5 26413324 15 5 32950570 16 5 73518112 17 5 138091031 18 6 54757547 19 7 6643570 20 7 102843667 21 8 83972017 22 8 133351048 23 9 87966091 24 10 10775525 25 10 63758336 26 10 119015913 27 11 21641962 28 11 62592588 29 11 120574605 30 12 97467341 31 13 74902874 32 14 42745198 33 14 75209564 34 15 18789561 35 15 84095709 36 16 18539575 37 16 45024465 38 16 81569036 39 18 3981408 40 18 34399732 41 18 49492235 42 19 38541133 43 21 20950165 44 21 45193505 45 22 107065162 46 24 3120 47 24 7607 48 24 10812 Thread #6 end of input stream, nextChar=-1 Completed: thread #6 Completed: thread #4 Completed: thread #5 Completed: thread #2 Completed: thread #3 Completed: thread #1 Completed: thread #7 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 May 03 01:36:07 ..... started sorting BAM Max memory needed for sorting = 643428111 ALL DONE!