STAR version=2.7.10a_alpha_220314 STAR compilation time,server,dir=2022-03-30T12:27:55+0200 ln1.leibniz:/data/antwerpen/205/vsc20587/software/STAR/source STAR git: On branch master ; commit f4d5de8344b5be1171c809c1c4590eba66594232 ; diff files: ##### Command Line: /user/antwerpen/205/vsc20587/data/software/STAR/source/STAR --readFilesCommand zcat --readFilesIn /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R2_001.fastq.gz /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R1_001.fastq.gz --runThreadN 28 --soloType CB_UMI_Simple --soloCBwhitelist /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/starsolo/3M-february-2018.txt --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloFeatures Gene --genomeDir /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/star_ncbi_3UTR_pLeXSY_debug/ --soloMultiMappers Uniform --outFileNamePrefix /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/results/starsolo_ncbi_3UTR_pLeXSY_debug//gex_sample02/ --alignIntronMax 1 --outSAMtype BAM Unsorted --soloCellFilter EmptyDrops_CR 16000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 ##### Initial USER parameters from Command Line: outFileNamePrefix /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/results/starsolo_ncbi_3UTR_pLeXSY_debug//gex_sample02/ ###### All USER parameters from Command Line: readFilesCommand zcat ~RE-DEFINED readFilesIn /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R2_001.fastq.gz /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R1_001.fastq.gz ~RE-DEFINED runThreadN 28 ~RE-DEFINED soloType CB_UMI_Simple ~RE-DEFINED soloCBwhitelist /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/starsolo/3M-february-2018.txt ~RE-DEFINED soloCBstart 1 ~RE-DEFINED soloCBlen 16 ~RE-DEFINED soloUMIstart 17 ~RE-DEFINED soloUMIlen 12 ~RE-DEFINED soloFeatures Gene ~RE-DEFINED genomeDir /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/star_ncbi_3UTR_pLeXSY_debug/ ~RE-DEFINED soloMultiMappers Uniform ~RE-DEFINED outFileNamePrefix /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/results/starsolo_ncbi_3UTR_pLeXSY_debug//gex_sample02/ ~RE-DEFINED alignIntronMax 1 ~RE-DEFINED outSAMtype BAM Unsorted ~RE-DEFINED soloCellFilter EmptyDrops_CR 16000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 28 genomeDir /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/star_ncbi_3UTR_pLeXSY_debug/ readFilesIn /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R2_001.fastq.gz /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R1_001.fastq.gz readFilesCommand zcat outFileNamePrefix /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/results/starsolo_ncbi_3UTR_pLeXSY_debug//gex_sample02/ outSAMtype BAM Unsorted alignIntronMax 1 soloType CB_UMI_Simple soloCBstart 1 soloUMIstart 17 soloCBlen 16 soloUMIlen 12 soloCBwhitelist /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/starsolo/3M-february-2018.txt soloFeatures Gene soloCellFilter EmptyDrops_CR 16000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 soloMultiMappers Uniform ------------------------------- ##### Final effective command line: /user/antwerpen/205/vsc20587/data/software/STAR/source/STAR --runThreadN 28 --genomeDir /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/star_ncbi_3UTR_pLeXSY_debug/ --readFilesIn /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R2_001.fastq.gz /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R1_001.fastq.gz --readFilesCommand zcat --outFileNamePrefix /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/results/starsolo_ncbi_3UTR_pLeXSY_debug//gex_sample02/ --outSAMtype BAM Unsorted --alignIntronMax 1 --soloType CB_UMI_Simple --soloCBstart 1 --soloUMIstart 17 --soloCBlen 16 --soloUMIlen 12 --soloCBwhitelist /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/starsolo/3M-february-2018.txt --soloFeatures Gene --soloCellFilter EmptyDrops_CR 16000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 --soloMultiMappers Uniform ---------------------------------------- Number of fastq files for each mate = 1 Input read files for mate 1 : -r--r--r-- 1 vsc20587 aitg 38344444317 Jan 3 12:18 /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R2_001.fastq.gz readsCommandsFile: exec > "/user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/results/starsolo_ncbi_3UTR_pLeXSY_debug//gex_sample02/_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R2_001.fastq.gz" Input read files for mate 2 : -r--r--r-- 1 vsc20587 aitg 11471244852 Jan 3 11:30 /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R1_001.fastq.gz readsCommandsFile: exec > "/user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/results/starsolo_ncbi_3UTR_pLeXSY_debug//gex_sample02/_STARtmp/tmp.fifo.read2" echo FILE 0 zcat "/user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R1_001.fastq.gz" ParametersSolo: --soloCellFilterType EmptyDrops_CR filtering parameters: 16000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 Number of CBs in the whitelist = 6794880 Apr 29 11:45:39 ... Finished reading, sorting and deduplicating CB whitelist sequences. Finished loading and checking parameters Reading genome generation parameters: ### /user/antwerpen/205/vsc20587/data/software/STAR-2.7.9a/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/star_ncbi_3UTR_pLeXSY_debug/ --genomeFastaFiles /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/GCF_000227135.1_ASM22713v2_genomic_pLeXSY.fna --genomeSAindexNbases 11 --sjdbGTFfile /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/GCF_000227135.1_ASM22713v2_genomic_3UTR_pLeXSY.debug.gtf --sjdbOverhang 100 ### GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/GCF_000227135.1_ASM22713v2_genomic_pLeXSY.fna ~RE-DEFINED genomeSAindexNbases 11 ~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 /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/refgenome/GCF_000227135.1_ASM22713v2_genomic_3UTR_pLeXSY.debug.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 37224448 257878685 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 37 1 NC_018228.1 283432 0 2 NC_018229.1 334314 524288 3 NC_018230.1 389946 1048576 4 NC_018231.1 479467 1572864 5 NC_018232.1 452426 2097152 6 NC_018233.1 529559 2621440 7 NC_018234.1 604754 3407872 8 NC_018235.1 505720 4194304 9 NC_018236.1 588727 4718592 10 NC_018237.1 558170 5505024 11 NC_018238.1 580223 6291456 12 NC_018239.1 569561 7077888 13 NC_018240.1 649814 7864320 14 NC_018241.1 645099 8650752 15 NC_018242.1 618357 9437184 16 NC_018243.1 698406 10223616 17 NC_018244.1 671483 11010048 18 NC_018245.1 735610 11796480 19 NC_018246.1 757180 12582912 20 NC_018247.1 752621 13369344 21 NC_018248.1 767234 14155776 22 NC_018249.1 704761 14942208 23 NC_018250.1 783272 15728640 24 NC_018251.1 877124 16515072 25 NC_018252.1 897883 17563648 26 NC_018253.1 1058259 18612224 27 NC_018254.1 1024085 19922944 28 NC_018255.1 1171725 20971520 29 NC_018256.1 1258350 22282240 30 NC_018257.1 1374157 23592960 31 NC_018258.1 1531288 25165824 32 NC_018259.1 1559911 26738688 33 NC_018260.1 1453978 28311552 34 NC_018261.1 1750858 29884416 35 NC_018262.1 2113966 31719424 36 NC_018263.1 2713248 34078720 37 pLeXSY-Hyg-eGFP 5887 36962304 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Fri Apr 29 11:45:39 2022 Genome: size given as a parameter = 37224448 SA: size given as a parameter = 257878685 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=11 nSAi=5592404 nGenome=37224448; nSAbyte=257878685 GstrandBit=32 SA number of indices=62516044 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 37224448 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 37224448 bytes SA file size: 257878685 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 257878685 bytes Loading SAindex ... done: 24466875 bytes Finished loading the genome: Fri Apr 29 11:45:45 2022 To accommodate alignIntronMax=1 redefined winBinNbits=10 To accommodate alignIntronMax=1 and alignMatesGapMax=0, redefined winFlankNbins=1 and winAnchorDistNbins=2 Loaded transcript database, nTr=8125 Loaded exon database, nEx=8126 Created thread # 1 Starting to map file # 0 mate 1: /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R2_001.fastq.gz mate 2: /user/antwerpen/205/vsc20587/scratch/leishmania_10X_Q/data/fastq/gex/gex_sample02_S1_L001_R1_001.fastq.gz 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 Created thread # 16 Created thread # 17 Created thread # 18 Created thread # 19 Created thread # 20 Created thread # 21 Created thread # 22 Created thread # 23 Created thread # 24 Created thread # 25 Created thread # 26 Created thread # 27 Thread #18 end of input stream, nextChar=-1 Completed: thread #17 Completed: thread #23 Completed: thread #22 Completed: thread #18 Completed: thread #9 Completed: thread #20 Completed: thread #21 Completed: thread #19 Completed: thread #25 Completed: thread #24 Completed: thread #27 Completed: thread #1 Completed: thread #26 Completed: thread #2 Completed: thread #3 Completed: thread #4 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Completed: thread #6 Completed: thread #7 Completed: thread #5 Joined thread # 5 Joined thread # 6 Joined thread # 7 Completed: thread #11 Completed: thread #8 Joined thread # 8 Joined thread # 9 Completed: thread #14 Completed: thread #13 Completed: thread #15 Completed: thread #12 Completed: thread #10 Joined thread # 10 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 Completed: thread #16 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Joined thread # 20 Joined thread # 21 Joined thread # 22 Joined thread # 23 Joined thread # 24 Joined thread # 25 Joined thread # 26 Joined thread # 27 Apr 29 12:35:50 ..... started Solo counting Apr 29 12:35:50 ... Starting Solo post-map for Gene Apr 29 12:35:51 ... Finished allocating arrays for Solo 1.97303 GiB Apr 29 12:40:02 ... Finished reading reads from Solo files nCB=1650761, nReadPerCBmax=397558, yesWLmatch=0