STAR version=STAR_2.5.3a STAR compilation time,server,dir=Fri Mar 17 11:35:46 EDT 2017 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source ##### DEFAULT parameters: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype SAM outSAMmode Full outSAMstrandField None outSAMattributes Standard outSAMunmapped None outSAMorder Paired outSAMprimaryFlag OneBestScore outSAMreadID Standard outSAMmapqUnique 255 outSAMflagOR 0 outSAMflagAND 65535 outSAMattrRGline - outSAMheaderHD - outSAMheaderPG - outSAMheaderCommentFile - outBAMcompression 1 outBAMsortingThreadN 0 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 1 outSJfilterReads All outSJfilterCountUniqueMin 3 1 1 1 outSJfilterCountTotalMin 3 1 1 1 outSJfilterOverhangMin 30 12 12 12 outSJfilterDistToOtherSJmin 10 0 5 10 outSJfilterIntronMaxVsReadN 50000 100000 200000 outWigType None outWigStrand Stranded outWigReferencesPrefix - outWigNorm RPM outFilterType Normal outFilterMultimapNmax 10 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.3 outFilterMismatchNoverReadLmax 1 outFilterIntronMotifs None clip5pNbases 0 clip3pNbases 0 clip3pAfterAdapterNbases 0 clip3pAdapterSeq - clip3pAdapterMMp 0.1 winBinNbits 16 winAnchorDistNbins 9 winFlankNbins 4 winAnchorMultimapNmax 50 winReadCoverageRelativeMin 0.5 winReadCoverageBasesMin 0 scoreGap 0 scoreGapNoncan -8 scoreGapGCAG -4 scoreGapATAC -8 scoreStitchSJshift 1 scoreGenomicLengthLog2scale -0.25 scoreDelBase -2 scoreDelOpen -2 scoreInsOpen -2 scoreInsBase -2 seedSearchLmax 0 seedSearchStartLmax 50 seedSearchStartLmaxOverLread 1 seedPerReadNmax 1000 seedPerWindowNmax 50 seedNoneLociPerWindow 10 seedMultimapNmax 10000 alignIntronMin 21 alignIntronMax 0 alignMatesGapMax 0 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 5 alignSJDBoverhangMin 3 alignSJstitchMismatchNmax 0 -1 0 0 alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes alignEndsProtrude 0 ConcordantPair chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimMainSegmentMultNmax 10 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ##### Command Line: /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --outFileNamePrefix L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz --runThreadN 8 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 250000000000 ##### Initial USER parameters from Command Line: outFileNamePrefix L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a- ###### All USER parameters from Command Line: limitSjdbInsertNsj 10000000 ~RE-DEFINED genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR ~RE-DEFINED outFileNamePrefix L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a- ~RE-DEFINED readFilesIn L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz ~RE-DEFINED runThreadN 8 ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED outFilterType BySJout ~RE-DEFINED outSAMattributes NH HI AS NM MD ~RE-DEFINED outFilterMultimapNmax 50 ~RE-DEFINED outSAMstrandField intronMotif ~RE-DEFINED outFilterMismatchNmax 999 ~RE-DEFINED outFilterMismatchNoverReadLmax0.04 ~RE-DEFINED alignIntronMin 10 ~RE-DEFINED alignIntronMax 1000000 ~RE-DEFINED alignMatesGapMax 1000000 ~RE-DEFINED alignSJoverhangMin 8 ~RE-DEFINED alignSJDBoverhangMin 1 ~RE-DEFINED sjdbScore 1 ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED quantMode TranscriptomeSAM ~RE-DEFINED outWigStrand Stranded ~RE-DEFINED twopassMode Basic ~RE-DEFINED twopass1readsN 18446744073709551615 ~RE-DEFINED limitBAMsortRAM 250000000000 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 8 genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR readFilesIn L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz readFilesCommand zcat limitBAMsortRAM 250000000000 limitSjdbInsertNsj 10000000 outFileNamePrefix L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a- outSAMtype BAM SortedByCoordinate outSAMstrandField intronMotif outSAMattributes NH HI AS NM MD outSAMunmapped Within outWigStrand Stranded outFilterType BySJout outFilterMultimapNmax 50 outFilterMismatchNmax 999 outFilterMismatchNoverReadLmax 0.04 alignIntronMin 10 alignIntronMax 1000000 alignMatesGapMax 1000000 alignSJoverhangMin 8 alignSJDBoverhangMin 1 sjdbScore 1 quantMode TranscriptomeSAM twopass1readsN 18446744073709551615 twopassMode Basic ------------------------------- ##### Final effective command line: /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --runThreadN 8 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR --readFilesIn L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz --readFilesCommand zcat --limitBAMsortRAM 250000000000 --limitSjdbInsertNsj 10000000 --outFileNamePrefix L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a- --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD --outSAMunmapped Within --outWigStrand Stranded --outFilterType BySJout --outFilterMultimapNmax 50 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM --twopass1readsN 18446744073709551615 --twopassMode Basic ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 8 runDirPerm User_RWX runRNGseed 777 genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz readFilesCommand zcat readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 250000000000 limitSjdbInsertNsj 10000000 outFileNamePrefix L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a- outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM SortedByCoordinate outSAMmode Full outSAMstrandField intronMotif outSAMattributes NH HI AS NM MD outSAMunmapped Within outSAMorder Paired outSAMprimaryFlag OneBestScore outSAMreadID Standard outSAMmapqUnique 255 outSAMflagOR 0 outSAMflagAND 65535 outSAMattrRGline - outSAMheaderHD - outSAMheaderPG - outSAMheaderCommentFile - outBAMcompression 1 outBAMsortingThreadN 0 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 1 outSJfilterReads All outSJfilterCountUniqueMin 3 1 1 1 outSJfilterCountTotalMin 3 1 1 1 outSJfilterOverhangMin 30 12 12 12 outSJfilterDistToOtherSJmin 10 0 5 10 outSJfilterIntronMaxVsReadN 50000 100000 200000 outWigType None outWigStrand Stranded outWigReferencesPrefix - outWigNorm RPM outFilterType BySJout outFilterMultimapNmax 50 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 999 outFilterMismatchNoverLmax 0.3 outFilterMismatchNoverReadLmax 0.04 outFilterIntronMotifs None clip5pNbases 0 clip3pNbases 0 clip3pAfterAdapterNbases 0 clip3pAdapterSeq - clip3pAdapterMMp 0.1 winBinNbits 16 winAnchorDistNbins 9 winFlankNbins 4 winAnchorMultimapNmax 50 winReadCoverageRelativeMin 0.5 winReadCoverageBasesMin 0 scoreGap 0 scoreGapNoncan -8 scoreGapGCAG -4 scoreGapATAC -8 scoreStitchSJshift 1 scoreGenomicLengthLog2scale -0.25 scoreDelBase -2 scoreDelOpen -2 scoreInsOpen -2 scoreInsBase -2 seedSearchLmax 0 seedSearchStartLmax 50 seedSearchStartLmaxOverLread 1 seedPerReadNmax 1000 seedPerWindowNmax 50 seedNoneLociPerWindow 10 seedMultimapNmax 10000 alignIntronMin 10 alignIntronMax 1000000 alignMatesGapMax 1000000 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 8 alignSJDBoverhangMin 1 alignSJstitchMismatchNmax 0 -1 0 0 alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes alignEndsProtrude 0 ConcordantPair chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimMainSegmentMultNmax 10 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 1 sjdbInsertSave Basic quantMode TranscriptomeSAM quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode Basic ---------------------------------------- Input read files for mate 1, from input string L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz -rw-r--r--+ 1 marinovg akundaje 215428 Sep 27 06:15 L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz readsCommandsFile: exec > "L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz" Input read files for mate 2, from input string L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz -rw-r--r--+ 1 marinovg akundaje 252461 Sep 27 06:16 L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz readsCommandsFile: exec > "L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read2" echo FILE 0 zcat "L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz" WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/sequence/symbB.v1.0.genome.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 16 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/symbB.v1.2.augustus.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 1963467900 6286772971 ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 21899 1 scaffold5.1 591268 0 2 scaffold12.1 696765 655360 3 scaffold2.1 810747 1376256 4 scaffold14.1 490050 2228224 5 scaffold13.1 649746 2752512 6 scaffold15.1 524375 3407872 7 scaffold16.1 462966 3997696 8 scaffold9.1 548078 4521984 9 scaffold21.1 436736 5111808 10 scaffold4.1 632614 5570560 11 scaffold18.1 443654 6225920 12 scaffold20.1 573419 6684672 13 scaffold23.1 448910 7274496 14 scaffold24.1 426843 7733248 15 scaffold6.1 569784 8192000 16 scaffold22.1 431927 8781824 17 scaffold10.1 532363 9240576 18 scaffold17.1 449295 9830400 19 scaffold30.1 408469 10289152 20 scaffold32.1 404110 10747904 21 scaffold11.1 528316 11206656 22 scaffold31.1 417612 11796480 23 scaffold19.1 442511 12255232 24 scaffold3.1 668332 12713984 25 scaffold26.1 421074 13434880 26 scaffold7.1 571691 13893632 27 scaffold28.1 412500 14483456 28 scaffold35.1 398631 14942208 29 scaffold41.1 391747 15400960 30 scaffold40.1 394752 15794176 31 scaffold29.1 409034 16252928 32 scaffold36.1 400010 16711680 33 scaffold25.1 426618 17170432 34 scaffold8.1 548667 17629184 35 scaffold42.1 391451 18219008 36 scaffold44.1 390484 18612224 37 scaffold49.1 383012 19005440 38 scaffold37.1 396772 19398656 39 scaffold38.1 396437 19857408 40 scaffold51.1 380501 20316160 41 scaffold27.1 413907 20709376 42 scaffold54.1 375458 21168128 43 scaffold45.1 391142 21561344 44 scaffold39.1 395540 21954560 45 scaffold43.1 390779 22413312 46 scaffold52.1 380536 22806528 47 scaffold56.1 371791 23199744 48 scaffold33.1 515728 23592960 49 scaffold59.1 365403 24117248 50 scaffold46.1 429861 24510464 51 scaffold62.1 502766 24969216 52 scaffold47.1 387964 25493504 53 scaffold60.1 580612 25886720 54 scaffold50.1 382847 26476544 55 scaffold66.1 356486 26869760 56 scaffold63.1 477125 27262976 57 scaffold65.1 364933 27787264 58 scaffold64.1 358915 28180480 59 scaffold68.1 354401 28573696 60 scaffold57.1 371098 28966912 61 scaffold73.1 366342 29360128 62 scaffold69.1 352833 29753344 63 scaffold71.1 352360 30146560 64 scaffold67.1 356375 30539776 65 scaffold75.1 348875 30932992 66 scaffold74.1 351324 31326208 67 scaffold34.1 401838 31719424 68 scaffold58.1 370801 32178176 69 scaffold81.1 342878 32571392 70 scaffold48.1 387749 32964608 71 scaffold82.1 400617 33357824 72 scaffold83.1 344947 33816576 73 scaffold72.1 349888 34209792 74 scaffold85.1 340753 34603008 75 scaffold70.1 352470 34996224 76 scaffold88.1 340489 35389440 77 scaffold89.1 472099 35782656 78 scaffold80.1 342192 36306944 79 scaffold90.1 339750 36700160 80 scaffold86.1 363860 37093376 81 scaffold93.1 335976 37486592 82 scaffold61.1 363008 37879808 83 scaffold94.1 333627 38273024 84 scaffold95.1 601332 38666240 85 scaffold97.1 332292 39321600 86 scaffold77.1 346586 39714816 87 scaffold98.1 414015 40108032 88 scaffold79.1 343859 40566784 89 scaffold101.1 361610 40960000 90 scaffold102.1 329125 41353216 91 scaffold55.1 376020 41746432 92 scaffold84.1 341103 42139648 93 scaffold78.1 345549 42532864 94 scaffold53.1 378577 42926080 95 scaffold87.1 341030 43319296 96 scaffold104.1 474317 43712512 97 scaffold105.1 329178 44236800 98 scaffold108.1 327786 44630016 99 scaffold76.1 345916 45023232 100 scaffold111.1 322964 45416448 101 scaffold109.1 324260 45744128 102 scaffold114.1 324259 46071808 103 scaffold106.1 365475 46399488 104 scaffold116.1 323891 46792704 105 scaffold112.1 324010 47120384 106 scaffold96.1 336118 47448064 107 scaffold119.1 317328 47841280 108 scaffold118.1 318037 48168960 109 scaffold92.1 544772 48496640 110 scaffold122.1 316262 49086464 111 scaffold100.1 331095 49414144 112 scaffold107.1 326882 49807360 113 scaffold123.1 314665 50135040 114 scaffold121.1 316986 50462720 115 scaffold110.1 323740 50790400 116 scaffold125.1 311545 51118080 117 scaffold129.1 311530 51445760 118 scaffold126.1 313092 51773440 119 scaffold99.1 345889 52101120 120 scaffold131.1 311446 52494336 121 scaffold132.1 311261 52822016 122 scaffold134.1 305934 53149696 123 scaffold127.1 312888 53477376 124 scaffold103.1 328425 53805056 125 scaffold136.1 305123 54198272 126 scaffold137.1 303511 54525952 127 scaffold135.1 305990 54853632 128 scaffold139.1 300435 55181312 129 scaffold140.1 299172 55508992 130 scaffold142.1 299696 55836672 131 scaffold143.1 297422 56164352 132 scaffold138.1 303458 56492032 133 scaffold120.1 316736 56819712 134 scaffold133.1 307637 57147392 135 scaffold145.1 472179 57475072 136 scaffold148.1 298117 57999360 137 scaffold146.1 297444 58327040 138 scaffold141.1 299152 58654720 139 scaffold150.1 294599 58982400 140 scaffold91.1 337822 59310080 141 scaffold152.1 294886 59703296 142 scaffold144.1 297976 60030976 143 scaffold130.1 334439 60358656 144 scaffold155.1 292319 60751872 145 scaffold153.1 295744 61079552 146 scaffold156.1 292129 61407232 147 scaffold115.1 320586 61734912 148 scaffold160.1 428337 62062592 149 scaffold147.1 298528 62521344 150 scaffold162.1 291107 62849024 151 scaffold163.1 290233 63176704 152 scaffold164.1 289556 63504384 153 scaffold154.1 328577 63832064 154 scaffold165.1 289892 64225280 155 scaffold159.1 291873 64552960 156 scaffold113.1 326497 64880640 157 scaffold168.1 289405 65208320 158 scaffold167.1 289001 65536000 159 scaffold161.1 290306 65863680 160 scaffold124.1 444859 66191360 161 scaffold169.1 288394 66650112 162 scaffold174.1 396295 66977792 163 scaffold151.1 297330 67436544 164 scaffold128.1 312604 67764224 165 scaffold177.1 287804 68091904 166 scaffold173.1 339667 68419584 167 scaffold158.1 291898 68812800 168 scaffold166.1 288739 69140480 169 scaffold181.1 282537 69468160 170 scaffold179.1 284344 69795840 171 scaffold180.1 283672 70123520 172 scaffold157.1 292391 70451200 173 scaffold117.1 318956 70778880 174 scaffold184.1 280689 71106560 175 scaffold182.1 413946 71434240 176 scaffold187.1 279452 71892992 177 scaffold171.1 347290 72220672 178 scaffold172.1 291242 72613888 179 scaffold186.1 278711 72941568 180 scaffold189.1 277141 73269248 181 scaffold190.1 276531 73596928 182 scaffold185.1 279344 73924608 183 scaffold183.1 281477 74252288 184 scaffold195.1 274551 74579968 185 scaffold194.1 273414 74907648 186 scaffold149.1 459750 75235328 187 scaffold178.1 285993 75759616 188 scaffold198.1 278520 76087296 189 scaffold197.1 273805 76414976 190 scaffold201.1 271809 76742656 191 scaffold196.1 274565 77070336 192 scaffold204.1 273655 77398016 193 scaffold202.1 271198 77725696 194 scaffold203.1 271948 78053376 195 scaffold175.1 369726 78381056 196 scaffold193.1 400917 78774272 197 scaffold206.1 269744 79233024 198 scaffold209.1 265839 79560704 199 scaffold176.1 288390 79888384 200 scaffold191.1 276886 80216064 201 scaffold207.1 267754 80543744 202 scaffold214.1 263623 80871424 203 scaffold192.1 616482 81199104 204 scaffold216.1 294022 81854464 205 scaffold213.1 262417 82182144 206 scaffold211.1 373343 82509824 207 scaffold217.1 263730 82903040 208 scaffold199.1 272469 83230720 209 scaffold210.1 302064 83558400 210 scaffold212.1 266275 83886080 211 scaffold170.1 288320 84213760 212 scaffold224.1 261091 84541440 213 scaffold208.1 267606 84803584 214 scaffold225.1 260654 85131264 215 scaffold227.1 259828 85393408 216 scaffold228.1 261222 85655552 217 scaffold229.1 261113 85917696 218 scaffold200.1 463366 86179840 219 scaffold231.1 296418 86704128 220 scaffold205.1 267914 87031808 221 scaffold232.1 260040 87359488 222 scaffold218.1 261953 87621632 223 scaffold235.1 320345 87883776 224 scaffold233.1 288484 88211456 225 scaffold236.1 256787 88539136 226 scaffold238.1 305305 88801280 227 scaffold215.1 329978 89128960 228 scaffold221.1 261001 89522176 229 scaffold241.1 254129 89784320 230 scaffold222.1 270430 90046464 231 scaffold220.1 263879 90374144 232 scaffold244.1 253306 90701824 233 scaffold188.1 279434 90963968 234 scaffold243.1 254542 91291648 235 scaffold240.1 263617 91553792 236 scaffold246.1 253147 91881472 237 scaffold223.1 262397 92143616 238 scaffold247.1 254238 92471296 239 scaffold237.1 256113 92733440 240 scaffold248.1 252607 92995584 241 scaffold251.1 319966 93257728 242 scaffold249.1 274165 93585408 243 scaffold254.1 250224 93913088 244 scaffold250.1 251301 94175232 245 scaffold252.1 381635 94437376 246 scaffold257.1 249331 94830592 247 scaffold256.1 249964 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scaffold62337.1 101 1804075008 21897 scaffold62702.1 100 1804140544 21898 scaffold59515.1 113 1804206080 21899 scaffold61685.1 99 1804271616 --sjdbOverhang = 99 taken from the generated genome Started loading the genome: Sun Sep 27 06:27:52 2020 Genome: size given as a parameter = 1963467900 SA: size given as a parameter = 6286772971 /SAindex: size given as a parameter = 1 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=1963467900; nSAbyte=6286772971 GstrandBit=32 SA number of indices=1524066174 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 1963467900 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 1963467900 bytes SA file size: 6286772971 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 6286772971 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Sun Sep 27 06:28:07 2020 Processing splice junctions database sjdbN=799652, sjdbOverhang=99 To accomodate alignIntronMax=1000000 redefined winBinNbits=18 winBinNbits=18 > genomeChrBinNbits=16 redefining: winBinNbits=16 To accomodate alignIntronMax=1000000 and alignMatesGapMax=1000000, redefined winFlankNbins=16 and winAnchorDistNbins=32 Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread0 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread1 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread2 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread3 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread4 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread5 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread6 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread7 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz mate 2: L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz Created thread # 6 Created thread # 7 Thread #1 end of input stream, nextChar=-1 Completed: thread #2 Completed: thread #4 Completed: thread #3 Completed: thread #5 Completed: thread #6 Completed: thread #7 Completed: thread #0 Completed: thread #1 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Sep 27 06:28:10 Loaded database junctions from the generated genome /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/STAR/sjdbList.out.tab: 799652 total junctions Sep 27 06:28:10 Loaded database junctions from the 1st pass file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARpass1//SJ.out.tab: 800301 total junctions Sep 27 06:28:11 Finished preparing junctions Sep 27 06:28:11 ..... inserting junctions into the genome indices Sep 27 06:28:15 Finished SA search: number of new junctions=14, old junctions=799652 Sep 27 06:28:15 Finished sorting SA indicesL nInd=5544 Sep 27 06:28:43 Finished inserting junction indices Sep 27 06:28:47 Finished SAi Sep 27 06:28:48 ..... finished inserting junctions into genome Input read files for mate 1, from input string L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz -rw-r--r--+ 1 marinovg akundaje 215428 Sep 27 06:15 L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz readsCommandsFile: exec > "L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz" Input read files for mate 2, from input string L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz -rw-r--r--+ 1 marinovg akundaje 252461 Sep 27 06:16 L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz readsCommandsFile: exec > "L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read2" echo FILE 0 zcat "L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz" Loaded transcript database, nTr=47014 Loaded exon database, nEx=985369 Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread0 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread1 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread2 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread3 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread4 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread5 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread6 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: L1798-SLAM_4SU_10mM-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate2.thread7 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Starting to map file # 0 mate 1: L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end1.fastq.gz mate 2: L1798-SLAM_4SU_10mM.200925_NB551514_0471_AHTTNJBGXG.end2.fastq.gz Created thread # 5 Created thread # 6 Created thread # 7 Thread #2 end of input stream, nextChar=-1 Completed: thread #1 Completed: thread #3 Completed: thread #4 Completed: thread #5 Completed: thread #6 Completed: thread #7 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 Completed stage 1 mapping of outFilterBySJout mapping Detected 0 novel junctions that passed filtering, will proceed to filter reads that contained unannotated junctions Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Completed: thread #0 Completed: thread #3 Completed: thread #5 Completed: thread #7 Completed: thread #1 Joined thread # 1 BAM sorting: 2620 mapped reads BAM sorting bins genomic start loci: 1 116 29327 2 278 18224 3 418 301045 4 632 250430 5 822 140050 6 1088 117246 7 1309 8120 8 1545 94252 9 1827 76940 10 2248 64501 11 2720 3277 12 3091 10151 13 3670 29659 14 4240 24981 15 5355 20414 16 6453 17249 Completed: thread #6 Completed: thread #4 Completed: thread #2 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Sep 27 06:28:53 ..... started sorting BAM Max memory needed for sorting = 30861 ALL DONE!