STAR version=2.7.10b STAR compilation time,server,dir=2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source STAR git: On branch master ; commit c6f8efc2c7043ef83bf8b0d9bed36bbb6b9b1133 ; diff files: CHANGES.md ##### Command Line: STAR --outTmpDir ./out/starsolo_tmp2 --soloType SmartSeq --genomeDir ./data/genome_overhang100 --readFilesIn ./data/fastq/S509_01_Cs_01_S1_R1_001.fastq ./data/fastq/S509_01_Cs_01_S1_R2_001.fastq --soloUMIdedup Exact --soloOutFileNames . genes.tsv barcodes.tsv matrix.mtx matrixSJ.mtx ##### Initial USER parameters from Command Line: outTmpDir ./out/starsolo_tmp2 ###### All USER parameters from Command Line: outTmpDir ./out/starsolo_tmp2 ~RE-DEFINED soloType SmartSeq ~RE-DEFINED genomeDir ./data/genome_overhang100 ~RE-DEFINED readFilesIn ./data/fastq/S509_01_Cs_01_S1_R1_001.fastq ./data/fastq/S509_01_Cs_01_S1_R2_001.fastq ~RE-DEFINED soloUMIdedup Exact ~RE-DEFINED soloOutFileNames . genes.tsv barcodes.tsv matrix.mtx matrixSJ.mtx ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: genomeDir ./data/genome_overhang100 readFilesIn ./data/fastq/S509_01_Cs_01_S1_R1_001.fastq ./data/fastq/S509_01_Cs_01_S1_R2_001.fastq outTmpDir ./out/starsolo_tmp2 soloType SmartSeq soloOutFileNames . genes.tsv barcodes.tsv matrix.mtx matrixSJ.mtx soloUMIdedup Exact ------------------------------- ##### Final effective command line: STAR --genomeDir ./data/genome_overhang100 --readFilesIn ./data/fastq/S509_01_Cs_01_S1_R1_001.fastq ./data/fastq/S509_01_Cs_01_S1_R2_001.fastq --outTmpDir ./out/starsolo_tmp2 --soloType SmartSeq --soloOutFileNames . genes.tsv barcodes.tsv matrix.mtx matrixSJ.mtx --soloUMIdedup Exact ---------------------------------------- Number of fastq files for each mate = 1 ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10 Mar 02 10:29:03 ... Finished reading, sorting and deduplicating CB whitelist sequences. Finished loading and checking parameters Reading genome generation parameters: ### STAR --runMode genomeGenerate --runThreadN 12 --genomeDir ./data/genome_overhang100 --genomeFastaFiles ./data/genome/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa --sjdbGTFfile ./data/genome/Macaca_fascicularis.Macaca_fascicularis_6.0.107.gtf --sjdbOverhang 100 ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles ./data/genome/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.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 ./data/genome/Macaca_fascicularis.Macaca_fascicularis_6.0.107.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3147841429 24053234109 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 937 1 1 223606306 0 2 2 194592313 223608832 3 3 186444865 418381824 4 4 171057148 605028352 5 5 186553353 776208384 6 6 179102756 962854912 7 7 171798370 1142161408 8 8 144116383 1314127872 9 9 131032084 1458307072 10 10 96731059 1589379072 11 11 132457180 1686110208 12 12 130596009 1818755072 13 13 108762655 1949564928 14 14 125104124 2058354688 15 15 111111006 2183659520 16 16 79120393 2294808576 17 17 95081867 2373976064 18 18 73713002 2469134336 19 19 58824109 2543058944 20 20 75859114 2602041344 21 X 150377965 2678063104 22 MU018701.1 11874780 2828533760 23 MU018684.1 1642214 2840592384 24 MU018688.1 1633698 2842427392 25 MU018689.1 1234068 2844262400 26 MU018687.1 1075538 2845573120 27 MU018682.1 961949 2846883840 28 MU018686.1 928488 2847932416 29 MU018693.1 893705 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JAANEP010001311.1 1959 3084386304 878 JAANEP010001239.1 1954 3084648448 879 JAANEP010000779.1 1953 3084910592 880 JAANEP010000968.1 1945 3085172736 881 JAANEP010000794.1 1933 3085434880 882 JAANEP010001399.1 1927 3085697024 883 JAANEP010001312.1 1924 3085959168 884 JAANEP010001049.1 1918 3086221312 885 JAANEP010001064.1 1918 3086483456 886 JAANEP010001340.1 1918 3086745600 887 JAANEP010000784.1 1896 3087007744 888 JAANEP010001240.1 1888 3087269888 889 JAANEP010000841.1 1885 3087532032 890 JAANEP010001052.1 1856 3087794176 891 JAANEP010000742.1 1854 3088056320 892 JAANEP010000729.1 1840 3088318464 893 JAANEP010001011.1 1837 3088580608 894 JAANEP010000987.1 1772 3088842752 895 JAANEP010000836.1 1771 3089104896 896 JAANEP010001401.1 1753 3089367040 897 JAANEP010001015.1 1723 3089629184 898 JAANEP010000883.1 1707 3089891328 899 JAANEP010001378.1 1700 3090153472 900 JAANEP010001455.1 1698 3090415616 901 JAANEP010001086.1 1697 3090677760 902 JAANEP010001398.1 1673 3090939904 903 JAANEP010000887.1 1642 3091202048 904 JAANEP010001347.1 1637 3091464192 905 JAANEP010000796.1 1634 3091726336 906 JAANEP010001042.1 1632 3091988480 907 JAANEP010001047.1 1626 3092250624 908 JAANEP010000967.1 1592 3092512768 909 JAANEP010000838.1 1585 3092774912 910 JAANEP010000993.1 1581 3093037056 911 JAANEP010000785.1 1577 3093299200 912 JAANEP010001313.1 1533 3093561344 913 JAANEP010000985.1 1520 3093823488 914 JAANEP010001037.1 1518 3094085632 915 JAANEP010000929.1 1505 3094347776 916 JAANEP010001372.1 1474 3094609920 917 JAANEP010001050.1 1463 3094872064 918 JAANEP010001315.1 1460 3095134208 919 JAANEP010001368.1 1439 3095396352 920 JAANEP010000982.1 1424 3095658496 921 JAANEP010000984.1 1369 3095920640 922 JAANEP010000902.1 1347 3096182784 923 JAANEP010001476.1 1346 3096444928 924 JAANEP010001241.1 1319 3096707072 925 JAANEP010000943.1 1284 3096969216 926 JAANEP010001000.1 1263 3097231360 927 JAANEP010001439.1 1255 3097493504 928 JAANEP010000947.1 1240 3097755648 929 JAANEP010001314.1 1236 3098017792 930 JAANEP010001400.1 1235 3098279936 931 JAANEP010000777.1 1203 3098542080 932 JAANEP010001316.1 1171 3098804224 933 JAANEP010000965.1 1158 3099066368 934 JAANEP010001440.1 1096 3099328512 935 JAANEP010001369.1 1050 3099590656 936 JAANEP010001370.1 1046 3099852800 937 JAANEP010001441.1 1033 3100114944 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Thu Mar 2 10:29:03 2023 Genome: size given as a parameter = 3147841429 SA: size given as a parameter = 24053234109 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3147841429; nSAbyte=24053234109 GstrandBit=32 SA number of indices=5831087056 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3147841429 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3147841429 bytes SA file size: 24053234109 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24053234109 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Thu Mar 2 10:38:51 2023 Processing splice junctions database sjdbN=236141, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Loaded transcript database, nTr=66619 Loaded exon database, nEx=592762 Thread #0 end of input stream, nextChar=-1