STAR version=2.7.9a STAR compilation time,server,dir=2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source ##### Command Line: STAR --readFilesIn /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_1.fastq /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_2.fastq --outFileNamePrefix /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.wasp. --runThreadN 16 --genomeDir /grid/gillis/home/hover/data/cross_mammal_xci/genomes/Canis_lupus_familiaris --twopassMode Basic --twopass1readsN -1 --outSAMtype BAM Unsorted --quantMode GeneCounts --waspOutputMode SAMtag --varVCFfile /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.3.snps_filtered.vcf ##### Initial USER parameters from Command Line: outFileNamePrefix /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.wasp. ###### All USER parameters from Command Line: readFilesIn /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_1.fastq /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_2.fastq ~RE-DEFINED outFileNamePrefix /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.wasp. ~RE-DEFINED runThreadN 16 ~RE-DEFINED genomeDir /grid/gillis/home/hover/data/cross_mammal_xci/genomes/Canis_lupus_familiaris ~RE-DEFINED twopassMode Basic ~RE-DEFINED twopass1readsN 18446744073709551615 ~RE-DEFINED outSAMtype BAM Unsorted ~RE-DEFINED quantMode GeneCounts ~RE-DEFINED waspOutputMode SAMtag ~RE-DEFINED varVCFfile /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.3.snps_filtered.vcf ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 16 genomeDir /grid/gillis/home/hover/data/cross_mammal_xci/genomes/Canis_lupus_familiaris readFilesIn /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_1.fastq /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_2.fastq outFileNamePrefix /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.wasp. outSAMtype BAM Unsorted varVCFfile /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.3.snps_filtered.vcf waspOutputMode SAMtag quantMode GeneCounts twopass1readsN 18446744073709551615 twopassMode Basic ------------------------------- ##### Final effective command line: STAR --runThreadN 16 --genomeDir /grid/gillis/home/hover/data/cross_mammal_xci/genomes/Canis_lupus_familiaris --readFilesIn /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_1.fastq /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782_2.fastq --outFileNamePrefix /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.wasp. --outSAMtype BAM Unsorted --varVCFfile /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.3.snps_filtered.vcf --waspOutputMode SAMtag --quantMode GeneCounts --twopass1readsN 18446744073709551615 --twopassMode Basic ---------------------------------------- Number of fastq files for each mate = 1 WARNING --waspOutputMode is set, therefore STAR will output vW attribute ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10 Finished loading and checking parameters Reading genome generation parameters: ### STAR --runMode genomeGenerate --runThreadN 6 --genomeDir ./ --genomeFastaFiles .//genome.fa --sjdbGTFfile .//annotation.gtf ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles .//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 .//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 2399445440 19534529193 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 147 1 NC_006583.4 122014068 0 2 NC_006584.4 82037489 122159104 3 NC_006585.4 94329250 204210176 4 NC_006586.4 87912527 298582016 5 NC_006587.4 88913986 386662400 6 NC_006588.4 80213190 475791360 7 NC_006589.4 80419774 556007424 8 NC_006590.4 73585679 636485632 9 NC_006591.4 60315500 710148096 10 NC_006592.4 69219345 770703360 11 NC_006593.4 72832428 840171520 12 NC_006594.4 72300020 913047552 13 NC_006595.4 62895387 985399296 14 NC_006596.4 60430354 1048313856 15 NC_006597.4 64389122 1108869120 16 NC_006598.4 54556944 1173356544 17 NC_006599.4 63738581 1228144640 18 NC_006600.4 54357284 1292107776 19 NC_006601.4 52989165 1346633728 20 NC_006602.4 57984708 1399848960 21 NC_006603.4 50232922 1458044928 22 NC_006604.4 61822301 1508376576 23 NC_006605.4 52413914 1570242560 24 NC_006606.4 46832179 1622671360 25 NC_006607.4 51908704 1669595136 26 NC_006608.4 38725074 1721761792 27 NC_006609.4 46280981 1760559104 28 NC_006610.4 41264955 1806958592 29 NC_006611.4 40893792 1848377344 30 NC_006612.4 40067686 1889271808 31 NC_006613.4 39086971 1929379840 32 NC_006614.4 41857359 1968701440 33 NC_006615.4 31422675 2010644480 34 NC_006616.4 51113282 2042101760 35 NC_006617.4 26040529 2093219840 36 NC_006618.4 30723464 2119434240 37 NC_006619.4 31754289 2150367232 38 NC_006620.4 23973277 2182348800 39 NC_006621.4 108808365 2206466048 40 NW_023329667.1 7753 2315517952 41 NW_023329668.1 93402 2315780096 42 NW_023329669.1 985 2316042240 43 NW_023329670.1 57590 2316304384 44 NW_023329671.1 22211 2316566528 45 NW_023329672.1 257600 2316828672 46 NW_023329673.1 1655 2317090816 47 NW_023329674.1 978 2317352960 48 NW_023329675.1 6273 2317615104 49 NW_023329676.1 4928 2317877248 50 NW_023329677.1 3309 2318139392 51 NW_023329678.1 702 2318401536 52 NW_023329679.1 954 2318663680 53 NW_023329680.1 784 2318925824 54 NW_023329681.1 1287 2319187968 55 NW_023329682.1 76816 2319450112 56 NW_023329683.1 119162 2319712256 57 NW_023329684.1 6348 2319974400 58 NW_023329685.1 962 2320236544 59 NW_023329686.1 956 2320498688 60 NW_023329687.1 6544 2320760832 61 NW_023329688.1 4275 2321022976 62 NW_023329689.1 977 2321285120 63 NW_023329690.1 5182 2321547264 64 NW_023329691.1 3195 2321809408 65 NW_023329692.1 811 2322071552 66 NW_023329693.1 4027 2322333696 67 NW_023329694.1 6885 2322595840 68 NW_023329695.1 5227 2322857984 69 NW_023329696.1 1090 2323120128 70 NW_023329697.1 583 2323382272 71 NW_023329698.1 975 2323644416 72 NW_023329699.1 58962 2323906560 73 NW_023329700.1 4712 2324168704 74 NW_023329701.1 324414 2324430848 75 NW_023329702.1 16658 2324955136 76 NW_023329703.1 52552 2325217280 77 NW_023329704.1 4211 2325479424 78 NW_023329705.1 10187 2325741568 79 NW_023329706.1 729 2326003712 80 NW_023329707.1 6860 2326265856 81 NW_023329708.1 7637 2326528000 82 NW_023329709.1 1317 2326790144 83 NW_023329710.1 5957 2327052288 84 NW_023329711.1 940 2327314432 85 NW_023329712.1 3235 2327576576 86 NW_023329713.1 1133 2327838720 87 NW_023329714.1 746 2328100864 88 NW_023329715.1 2851 2328363008 89 NW_023329716.1 669 2328625152 90 NW_023329717.1 1932 2328887296 91 NW_023329718.1 955 2329149440 92 NW_023329719.1 853 2329411584 93 NW_023329720.1 72059 2329673728 94 NW_023329721.1 968 2329935872 95 NW_023329722.1 7024 2330198016 96 NW_023329723.1 5203 2330460160 97 NW_023329724.1 558 2330722304 98 NW_023329725.1 5195 2330984448 99 NW_023329726.1 3889 2331246592 100 NW_023329727.1 11202 2331508736 101 NW_023329728.1 845 2331770880 102 NW_023329729.1 9760 2332033024 103 NW_023329730.1 6522 2332295168 104 NW_023329731.1 9306 2332557312 105 NW_023329732.1 1382 2332819456 106 NW_023329733.1 9943 2333081600 107 NW_023329734.1 14199 2333343744 108 NW_023329735.1 64905 2333605888 109 NW_023329736.1 45116 2333868032 110 NW_023329737.1 8889 2334130176 111 NW_023329738.1 997 2334392320 112 NW_023329739.1 74212 2334654464 113 NW_023329740.1 4456 2334916608 114 NW_023329741.1 5574 2335178752 115 NW_023329742.1 59583 2335440896 116 NW_023329743.1 3970 2335703040 117 NW_023329744.1 6022 2335965184 118 NW_023329745.1 7625 2336227328 119 NW_023329746.1 975 2336489472 120 NW_023329747.1 5521 2336751616 121 NW_023329748.1 761 2337013760 122 NW_023329749.1 700 2337275904 123 NW_023329750.1 671 2337538048 124 NW_023329751.1 732 2337800192 125 NW_023329752.1 551 2338062336 126 NW_023329753.1 610 2338324480 127 NW_023329754.1 3758 2338586624 128 NW_023329755.1 156523 2338848768 129 NW_023329756.1 596 2339110912 130 NW_023329757.1 879 2339373056 131 NW_023329758.1 6499 2339635200 132 NW_023329759.1 11993 2339897344 133 NW_023329760.1 34643 2340159488 134 NW_023329761.1 8153 2340421632 135 NW_023329762.1 1061 2340683776 136 NW_023329763.1 19377 2340945920 137 NW_023329764.1 4512 2341208064 138 NW_023329765.1 5698 2341470208 139 NW_023329766.1 57845 2341732352 140 NW_023329767.1 27427 2341994496 141 NW_023329768.1 2548 2342256640 142 NW_023329769.1 15679 2342518784 143 NW_023329770.1 9700 2342780928 144 NW_023329771.1 570 2343043072 145 NW_023329772.1 2751 2343305216 146 NW_023329773.1 95878 2343567360 147 NC_002008.4 16727 2343829504 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Fri May 19 10:46:03 2023 Genome: size given as a parameter = 2399445440 SA: size given as a parameter = 19534529193 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=2399445440; nSAbyte=19534529193 GstrandBit=32 SA number of indices=4735643440 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 2399445440 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2399445440 bytes SA file size: 19534529193 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 19534529193 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Fri May 19 10:53:10 2023 Processing splice junctions database sjdbN=275392, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 May 19 10:53:11 ..... loading variations VCF May 19 10:53:11 ..... Loaded VCF data, found 6919 SNPs May 19 10:53:11 ..... Finished sorting VCF data Created thread # 1 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 Thread #12 end of input stream, nextChar=-1 Completed: thread #10 Completed: thread #2 Completed: thread #9 Completed: thread #5 Completed: thread #7 Completed: thread #8 Completed: thread #1 Completed: thread #13 Completed: thread #6 Completed: thread #4 Completed: thread #3 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Joined thread # 8 Joined thread # 9 Joined thread # 10 Completed: thread #12 Completed: thread #14 Completed: thread #11 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Completed: thread #15 Joined thread # 15 May 19 10:57:18 Loaded database junctions from the generated genome /grid/gillis/home/hover/data/cross_mammal_xci/genomes/Canis_lupus_familiaris//sjdbList.out.tab: 275392 total junctions May 19 10:57:18 Loaded database junctions from the 1st pass file: /grid/gillis/home/hover/work/cmxci.paired/Canis_lupus_familiaris/SRR5025782.wasp._STARpass1//SJ.out.tab: 476970 total junctions WARNING: long repeat for junction # 18867 : NC_006584.4 33362235 33370971; left shift = 255; right shift = 16 WARNING: long repeat for junction # 18878 : NC_006584.4 33401981 33422330; left shift = 255; right shift = 16 WARNING: long repeat for junction # 215479 : NC_006608.4 9586368 9588181; left shift = 255; right shift = 16 May 19 10:57:19 Finished preparing junctions May 19 10:57:19 ..... inserting junctions into the genome indices May 19 10:57:25 Finished SA search: number of new junctions=67284, old junctions=275392 May 19 10:57:33 Finished sorting SA indicesL nInd=26913600 Genome size with junctions=2412969524 2344091648 68877876 GstrandBit1=32 GstrandBit=32 May 19 10:58:48 Finished inserting junction indices May 19 10:58:59 Finished SAi May 19 10:58:59 ..... finished inserting junctions into genome Created thread # 1 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 Thread #15 end of input stream, nextChar=-1 Completed: thread #4 Completed: thread #6 Completed: thread #14 Completed: thread #13 Completed: thread #10 Completed: thread #8 Completed: thread #5 Completed: thread #12 Completed: thread #7 Completed: thread #3 Completed: thread #9 Completed: thread #1 Completed: thread #11 Completed: thread #15 Completed: thread #0 Joined thread # 1 Completed: thread #2 Joined thread # 2 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 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 ALL DONE!