STAR version=2.7.10a STAR compilation time,server,dir=2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source STAR git: On branch master ; commit ae26add7ea1724f3281ec8abedb71bcff6a4ae73 ; diff files: CHANGES.md README.md RELEASEnotes.md doc/STARmanual.pdf extras/doc-latex/STARmanual.tex extras/doc-latex/convertParDefToLatexTable.awk extras/doc-latex/parametersDefault.tex extras/docker/Dockerfile source/VERSION ##### Command Line: STAR --runThreadN 16 --genomeDir /home/sharan/genome_indexes/mm39/star/STAR --readFilesIn data/PR2_R1.fastq.gz data/PR2_R2.fastq.gz --outFileNamePrefix analysis/PR2/star/NA_ --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --quantMode GeneCounts --readFilesCommand zcat ##### Initial USER parameters from Command Line: outFileNamePrefix analysis/PR2/star/NA_ ###### All USER parameters from Command Line: runThreadN 16 ~RE-DEFINED genomeDir /home/sharan/genome_indexes/mm39/star/STAR ~RE-DEFINED readFilesIn data/PR2_R1.fastq.gz data/PR2_R2.fastq.gz ~RE-DEFINED outFileNamePrefix analysis/PR2/star/NA_ ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED outSAMattributes Standard ~RE-DEFINED quantMode GeneCounts ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 16 genomeDir /home/sharan/genome_indexes/mm39/star/STAR readFilesIn data/PR2_R1.fastq.gz data/PR2_R2.fastq.gz readFilesCommand zcat outFileNamePrefix analysis/PR2/star/NA_ outSAMtype BAM SortedByCoordinate outSAMattributes Standard outSAMunmapped Within quantMode GeneCounts ------------------------------- ##### Final effective command line: STAR --runThreadN 16 --genomeDir /home/sharan/genome_indexes/mm39/star/STAR --readFilesIn data/PR2_R1.fastq.gz data/PR2_R2.fastq.gz --readFilesCommand zcat --outFileNamePrefix analysis/PR2/star/NA_ --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMunmapped Within --quantMode GeneCounts ---------------------------------------- Number of fastq files for each mate = 1 Input read files for mate 1 : -rw-rw-r-- 1 sharan sharan 1491362430 Nov 8 11:20 data/PR2_R1.fastq.gz readsCommandsFile: exec > "analysis/PR2/star/NA__STARtmp/tmp.fifo.read1" echo FILE 0 zcat "data/PR2_R1.fastq.gz" Input read files for mate 2 : -rw-rw-r-- 1 sharan sharan 1515430328 Nov 8 11:20 data/PR2_R2.fastq.gz readsCommandsFile: exec > "analysis/PR2/star/NA__STARtmp/tmp.fifo.read2" echo FILE 0 zcat "data/PR2_R2.fastq.gz" 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: ### STAR --runMode genomeGenerate --runThreadN 10 --genomeDir asangani2/genome/GRCm39/STAR --genomeFastaFiles asangani2/genome/GRCm39/GRCm39.primary_assembly.genome.fa --sjdbGTFfile /media/asangani2/genome/GRCm39/gencode.vM28.primary_assembly.annotation.gff3 ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles asangani2/genome/GRCm39/GRCm39.primary_assembly.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 /media/asangani2/genome/GRCm39/gencode.vM28.primary_assembly.annotation.gff3 ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 2795626953 22370762390 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 61 1 chr1 195154279 0 2 chr2 181755017 195297280 3 chr3 159745316 377225216 4 chr4 156860686 537133056 5 chr5 151758149 694157312 6 chr6 149588044 845938688 7 chr7 144995196 995622912 8 chr8 130127694 1140850688 9 chr9 124359700 1271136256 10 chr10 130530862 1395654656 11 chr11 121973369 1526202368 12 chr12 120092757 1648361472 13 chr13 120883175 1768685568 14 chr14 125139656 1889796096 15 chr15 104073951 2015100928 16 chr16 98008968 2119434240 17 chr17 95294699 2217476096 18 chr18 90720763 2312896512 19 chr19 61420004 2403860480 20 chrX 169476592 2465464320 21 chrY 91455967 2635071488 22 chrM 16299 2726559744 23 GL456210.1 169725 2726821888 24 GL456211.1 241735 2727084032 25 GL456212.1 153618 2727346176 26 GL456219.1 175968 2727608320 27 GL456221.1 206961 2727870464 28 GL456233.2 559103 2728132608 29 GL456239.1 40056 2728919040 30 GL456354.1 195993 2729181184 31 GL456359.1 22974 2729443328 32 GL456360.1 31704 2729705472 33 GL456366.1 47073 2729967616 34 GL456367.1 42057 2730229760 35 GL456368.1 20208 2730491904 36 GL456370.1 26764 2730754048 37 GL456372.1 28664 2731016192 38 GL456378.1 31602 2731278336 39 GL456379.1 72385 2731540480 40 GL456381.1 25871 2731802624 41 GL456382.1 23158 2732064768 42 GL456383.1 38659 2732326912 43 GL456385.1 35240 2732589056 44 GL456387.1 24685 2732851200 45 GL456389.1 28772 2733113344 46 GL456390.1 24668 2733375488 47 GL456392.1 23629 2733637632 48 GL456394.1 24323 2733899776 49 GL456396.1 21240 2734161920 50 JH584295.1 1976 2734424064 51 JH584296.1 199368 2734686208 52 JH584297.1 205776 2734948352 53 JH584298.1 184189 2735210496 54 JH584299.1 953012 2735472640 55 JH584300.1 182347 2736521216 56 JH584301.1 259875 2736783360 57 JH584302.1 155838 2737045504 58 JH584303.1 158099 2737307648 59 JH584304.1 114452 2737569792 60 MU069434.1 8412 2737831936 61 MU069435.1 31129 2738094080 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Fri Nov 18 16:48:48 2022 Genome: size given as a parameter = 2795626953 SA: size given as a parameter = 22370762390 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=2795626953; nSAbyte=22370762390 GstrandBit=32 SA number of indices=5423215124 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 2795626953 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2795626953 bytes SA file size: 22370762390 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 22370762390 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Fri Nov 18 16:49:18 2022 Processing splice junctions database sjdbN=284929, 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 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: data/PR2_R1.fastq.gz mate 2: data/PR2_R2.fastq.gz 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: 144108 mapped reads BAM sorting bins genomic start loci: 1 0 30982131 2 0 89770745 3 0 172028100 4 1 31894414 5 1 102642248 6 1 164303037 7 2 84423074 8 2 101489082 9 3 34809372 10 3 119135134 11 3 150332004 12 4 90416280 13 4 124708945 14 4 147482892 15 5 75273303 16 5 125139570 17 6 28050187 18 6 97165453 19 7 3633769 20 7 72076840 21 7 111781235 22 8 42938573 23 8 76042586 24 8 114552705 25 9 79546102 26 9 127429792 27 10 33106727 28 10 61045246 29 10 77732797 30 10 97920223 31 10 115823993 32 11 31870133 33 11 112872550 34 12 58547797 35 13 26367837 36 13 76084140 37 14 59213928 38 14 85322328 39 15 10961773 40 16 5489863 41 16 27853329 42 16 45878998 43 17 12344907 44 17 75135827 45 18 8992966 46 18 47723719 47 19 105168572 48 21 6395 Thread #15 end of input stream, nextChar=-1 Completed: thread #8 Completed: thread #13 Completed: thread #11 Completed: thread #10 Completed: thread #6 Completed: thread #4 Completed: thread #7 Completed: thread #1 Completed: thread #3 Completed: thread #15 Completed: thread #2 Completed: thread #14 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Completed: thread #9 Completed: thread #12 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 Nov 18 16:54:11 ..... started sorting BAM Max memory needed for sorting = 210668610 ALL DONE!