zhouyiqi91
commented
4 days ago seems the fastq file is truncated. please check the md5sum
----------Reply to Message---------- On Fri, Sep 27, 2024 20:14 PM @.***> wrote:
Hi, I am trying to get the matrix file from paired single cell rna seq files that i obtained from singleron. However, I encountered this error, and am unsure how to proceed.
This is the log.out file output.
STAR version=2.7.11a STAR compilation time,server,dir=2023-09-15T02:58:53+0000 :/opt/conda/conda-bld/star_1694746407721/work/source
Command Line:
/home/jimmy/anaconda3/envs/celescope/bin/STAR-avx2 --genomeDir /media/jimmy/Ext/hs_ensembl_99/ --readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART_1.fq.gz --readFilesCommand zcat --soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 --soloCellFilter EmptyDropsCR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 --outFileNamePrefix .//Non/01.starsolo/Non --runThreadN 8 --clip3pAdapterSeq AAAAAAAAAAAA --outFilterMatchNmin 50 --soloFeatures Gene GeneFull_Ex50pAS --outSAMattributes NH HI nM AS CR UR CB UB GX GN --soloType CB_UMI_Complex --soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 --soloUMIposition 0_60_0_71 --soloUMIlen 12 --soloCBmatchWLtype 1MM --outSAMtype BAM SortedByCoordinate --soloCellReadStats Standard --soloBarcodeReadLength 0
Initial USER parameters from Command Line:
outFileNamePrefix .//Non/01.starsolo/Non_
All USER parameters from Command Line:
genomeDir /media/jimmy/Ext/hs_ensembl_99/ ~RE-DEFINED readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART_1.fq.gz ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 ~RE-DEFINED soloCellFilter EmptyDropsCR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 ~RE-DEFINED outFileNamePrefix .//Non/01.starsolo/Non ~RE-DEFINED runThreadN 8 ~RE-DEFINED clip3pAdapterSeq AAAAAAAAAAAA ~RE-DEFINED outFilterMatchNmin 50 ~RE-DEFINED soloFeatures Gene GeneFull_Ex50pAS ~RE-DEFINED outSAMattributes NH HI nM AS CR UR CB UB GX GN ~RE-DEFINED soloType CB_UMI_Complex ~RE-DEFINED soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 ~RE-DEFINED soloUMIposition 0_60_0_71 ~RE-DEFINED soloUMIlen 12 ~RE-DEFINED soloCBmatchWLtype 1MM ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED soloCellReadStats Standard ~RE-DEFINED soloBarcodeReadLength 0 ~RE-DEFINED
Finished reading parameters from all sources
Final user re-defined parameters-----------------:
runThreadN 8 genomeDir /media/jimmy/Ext/hs_ensembl_99/ readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART1.fq.gz readFilesCommand zcat outFileNamePrefix .//Non/01.starsolo/Non outSAMtype BAM SortedByCoordinate outSAMattributes NH HI nM AS CR UR CB UB GX GN outFilterMatchNmin 50 clip3pAdapterSeq AAAAAAAAAAAA soloType CB_UMI_Complex soloUMIlen 12 soloBarcodeReadLength 0 soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 soloFeatures Gene GeneFull_Ex50pAS soloCBmatchWLtype 1MM soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 soloUMIposition 0_60_0_71 soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 soloCellReadStats Standard
Final effective command line:
/home/jimmy/anaconda3/envs/celescope/bin/STAR-avx2 --runThreadN 8 --genomeDir /media/jimmy/Ext/hs_ensembl_99/ --readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART1.fq.gz --readFilesCommand zcat --outFileNamePrefix .//Non/01.starsolo/Non --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI nM AS CR UR CB UB GX GN --outFilterMatchNmin 50 --clip3pAdapterSeq AAAAAAAAAAAA --soloType CB_UMI_Complex --soloUMIlen 12 --soloBarcodeReadLength 0 --soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 --soloFeatures Gene GeneFull_Ex50pAS --soloCBmatchWLtype 1MM --soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 --soloUMIposition 0_60_0_71 --soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 --soloCellReadStats Standard
Number of fastq files for each mate = 1
Input read files for mate 1 : -rwxrwxrwx 1 jimmy jimmy 68155574216 Sep 17 16:39 ./Non-CART-R/Non-CART_2.fq.gz
readsCommandsFile: exec > ".//Non/01.starsolo/Non__STARtmp/tmp.fifo.read1" echo FILE 0 zcat "./Non-CART-R/Non-CART_2.fq.gz"
Input read files for mate 2 : -rwxrwxrwx 1 jimmy jimmy 67439953618 Sep 22 03:42 ./Non-CART-R/Non-CART_1.fq.gz
readsCommandsFile: exec > ".//Non/01.starsolo/Non__STARtmp/tmp.fifo.read2" echo FILE 0 zcat "./Non-CART-R/Non-CART_1.fq.gz"
ParametersSolo: --soloCellFilterType EmptyDrops_CR filtering parameters: 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 Sep 27 12:39:58 ... Finished reading, sorting and deduplicating CB whitelist sequences. WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters:
/home/jim/anaconda3/envs/celescope/bin/STAR-avx2 --runMode genomeGenerate --runThreadN 6 --genomeDir ./ --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa --genomeSAindexNbases 14 --sjdbGTFfile Homo_sapiens.GRCh38.99.filtered.gtf --sjdbOverhang 100
GstrandBit=32
versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.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 Homo_sapiens.GRCh38.99.filtered.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3211751963 24905496556 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 194 112489564220 210133797422249036800 311135086622382992384 412133275309518258688 513114364328651689984 614107043718766246912 715101991189873463808 81690338345975699968 917832574411066139648 1018803732851149501440 1119586176161229979648 1222421935291288699904 1320644441671530920960 1421467099831595408384 1522508184681642332160 1631982955591693188096 1741902145551891631104 1851815382592081947648 1961708059792263613440 2071593459732434531328 2181451386362593914880 2291383947172739142656 23MT165692877554688 24X1560408952877816832 25Y572274153034054656 26KI270728.118727593091464192 27KI270727.14482483093561344 28KI270442.13920613094085632 29KI270729.12808393094609920 30GL000225.12111733095134208 31KI270743.12106583095396352 32GL000008.22097093095658496 33GL000009.22017093095920640 34KI270747.11987353096182784 35KI270722.11940503096444928 36GL000194.11914693096707072 37KI270742.11867393096969216 38GL000205.21855913097231360 39GL000195.11828963097493504 40KI270736.11819203097755648 41KI270733.11797723098017792 42GL000224.11796933098279936 43GL000219.11791983098542080 44KI270719.11768453098804224 45GL000216.21766083099066368 46KI270712.11760433099328512 47KI270706.11750553099590656 48KI270725.11728103099852800 49KI270744.11684723100114944 50KI270734.11650503100377088 51GL000213.11642393100639232 52GL000220.11618023100901376 53KI270715.11614713101163520 54GL000218.11611473101425664 55KI270749.11587593101687808 56KI270741.11574323101949952 57GL000221.11553973102212096 58KI270716.11537993102474240 59KI270731.11507543102736384 60KI270751.11507423102998528 61KI270750.11488503103260672 62KI270519.11381263103522816 63GL000214.11377183103784960 64KI270708.11276823104047104 65KI270730.11125513104309248 66KI270438.11125053104571392 67KI270737.11038383104833536 68KI270721.11003163105095680 69KI270738.1993753105357824 70KI270748.1933213105619968 71KI270435.1929833105882112 72GL000208.1926893106144256 73KI270538.1913093106406400 74KI270756.1795903106668544 75KI270739.1739853106930688 76KI270757.1712513107192832 77KI270709.1668603107454976 78KI270746.1664863107717120 79KI270753.1629443107979264 80KI270589.1444743108241408 81KI270726.1437393108503552 82KI270735.1428113108765696 83KI270711.1422103109027840 84KI270745.1418913109289984 85KI270714.1417173109552128 86KI270732.1415433109814272 87KI270713.1407453110076416 88KI270754.1401913110338560 89KI270710.1401763110600704 90KI270717.1400623110862848 91KI270724.1395553111124992 92KI270720.1390503111387136 93KI270723.1381153111649280 94KI270718.1380543111911424 95KI270317.1376903112173568 96KI270740.1372403112435712 97KI270755.1367233112697856 98KI270707.1320323112960000 99KI270579.1310333113222144 100KI270752.1277453113484288 101KI270512.1226893113746432 102KI270322.1214763114008576 103GL000226.1150083114270720 104KI270311.1123993114532864 105KI270366.183203114795008 106KI270511.181273115057152 107KI270448.179923115319296 108KI270521.176423115581440 109KI270581.170463115843584 110KI270582.165043116105728 111KI270515.163613116367872 112KI270588.161583116630016 113KI270591.157963116892160 114KI270522.156743117154304 115KI270507.153533117416448 116KI270590.146853117678592 117KI270584.145133117940736 118KI270320.144163118202880 119KI270382.142153118465024 120KI270468.140553118727168 121KI270467.139203118989312 122KI270362.135303119251456 123KI270517.132533119513600 124KI270593.130413119775744 125KI270528.129833120037888 126KI270587.129693120300032 127KI270364.128553120562176 128KI270371.128053120824320 129KI270333.126993121086464 130KI270374.126563121348608 131KI270411.126463121610752 132KI270414.124893121872896 133KI270510.124153122135040 134KI270390.123873122397184 135KI270375.123783122659328 136KI270420.123213122921472 137KI270509.123183123183616 138KI270315.122763123445760 139KI270302.122743123707904 140KI270518.121863123970048 141KI270530.121683124232192 142KI270304.121653124494336 143KI270418.121453124756480 144KI270424.121403125018624 145KI270417.120433125280768 146KI270508.119513125542912 147KI270303.119423125805056 148KI270381.119303126067200 149KI270529.118993126329344 150KI270425.118843126591488 151KI270396.118803126853632 152KI270363.118033127115776 153KI270386.117883127377920 154KI270465.117743127640064 155KI270383.117503127902208 156KI270384.116583128164352 157KI270330.116523128426496 158KI270372.116503128688640 159KI270548.115993128950784 160KI270580.115533129212928 161KI270387.115373129475072 162KI270391.114843129737216 163KI270305.114723129999360 164KI270373.114513130261504 165KI270422.114453130523648 166KI270316.114443130785792 167KI270340.114283131047936 168KI270338.114283131310080 169KI270583.114003131572224 170KI270334.113683131834368 171KI270429.113613132096512 172KI270393.113083132358656 173KI270516.113003132620800 174KI270389.112983132882944 175KI270466.112333133145088 176KI270388.112163133407232 177KI270544.112023133669376 178KI270310.112013133931520 179KI270412.111793134193664 180KI270395.111433134455808 181KI270376.111363134717952 182KI270337.111213134980096 183KI270335.110483135242240 184KI270378.110483135504384 185KI270379.110453135766528 186KI270329.110403136028672 187KI270419.110293136290816 188KI270336.110263136552960 189KI270312.19983136815104 190KI270539.19933137077248 191KI270385.19903137339392 192KI270423.19813137601536 193KI270392.19713137863680 194KI270394.19703138125824 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Fri Sep 27 12:39:58 2024
Genome: size given as a parameter = 3211751963 SA: size given as a parameter = 24905496556 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3211751963; nSAbyte=24905496556 GstrandBit=32 SA number of indices=6037696134 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3211751963 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3211751963 bytes SA file size: 24905496556 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24905496556 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Fri Sep 27 12:44:31 2024
Processing splice junctions database sjdbN=364995, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Loaded transcript database, nTr=200956 Loaded exon database, nEx=1321486 Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Starting to map file # 0 mate 1: ./Non-CART-R/Non-CART_2.fq.gz mate 2: ./Non-CART-R/Non-CART_1.fq.gz BAM sorting: 120922 mapped reads BAM sorting bins genomic start loci: 1027534282 2093877009 30173986575 4173783177 528685786 6265538817 736538132 8356161418 93120498171 10521211844 115105842006 12669452975 1372772006 14787302949 15828723582 16859585122 17974521029 181017861453 191048327592 201110791814 211188857552 2211216499384 231249113918 24138210401 25138392860 26138437123 27138988543 281422922967 291522382120 3015116645388 311670820660 321740832461 3317141527664 341826104033 351841941503 3618155269339 371976066458 382073290674 392137357460 4022648 41225368 42228207 432210319 442312976952 4523154400598 4640127439 4740172741 4851114773
EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length @A00151:1193:HCTLLDSXC:4:1414:15411:2065 + @A00151:1193:HCTLLDSXC:4:1414:1565TTTTTTTTTTATTTGTAGTATCACTCTGTCACCTAGGCTGTAGTGCAGTGACACGAGCTTGACTCACTG SOLUTION: fix your fastq file
Sep 27 14:00:53 ...... FATAL ERROR, exiting
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Hi, I am trying to get the matrix file from paired single cell rna seq files that i obtained from singleron. However, I encountered this error, and am unsure how to proceed.
This is the log.out file output.
STAR version=2.7.11a STAR compilation time,server,dir=2023-09-15T02:58:53+0000 :/opt/conda/conda-bld/star_1694746407721/work/source
Command Line:
/home/jimmy/anaconda3/envs/celescope/bin/STAR-avx2 --genomeDir /media/jimmy/Ext/hs_ensembl_99/ --readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART_1.fq.gz --readFilesCommand zcat --soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 --soloCellFilter EmptyDropsCR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 --outFileNamePrefix .//Non/01.starsolo/Non --runThreadN 8 --clip3pAdapterSeq AAAAAAAAAAAA --outFilterMatchNmin 50 --soloFeatures Gene GeneFull_Ex50pAS --outSAMattributes NH HI nM AS CR UR CB UB GX GN --soloType CB_UMI_Complex --soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 --soloUMIposition 0_60_0_71 --soloUMIlen 12 --soloCBmatchWLtype 1MM --outSAMtype BAM SortedByCoordinate --soloCellReadStats Standard --soloBarcodeReadLength 0
Initial USER parameters from Command Line:
outFileNamePrefix .//Non/01.starsolo/Non_
All USER parameters from Command Line:
genomeDir /media/jimmy/Ext/hs_ensembl_99/ ~RE-DEFINED readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART_1.fq.gz ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 ~RE-DEFINED soloCellFilter EmptyDropsCR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 ~RE-DEFINED outFileNamePrefix .//Non/01.starsolo/Non ~RE-DEFINED runThreadN 8 ~RE-DEFINED clip3pAdapterSeq AAAAAAAAAAAA ~RE-DEFINED outFilterMatchNmin 50 ~RE-DEFINED soloFeatures Gene GeneFull_Ex50pAS ~RE-DEFINED outSAMattributes NH HI nM AS CR UR CB UB GX GN ~RE-DEFINED soloType CB_UMI_Complex ~RE-DEFINED soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 ~RE-DEFINED soloUMIposition 0_60_0_71 ~RE-DEFINED soloUMIlen 12 ~RE-DEFINED soloCBmatchWLtype 1MM ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED soloCellReadStats Standard ~RE-DEFINED soloBarcodeReadLength 0 ~RE-DEFINED
Finished reading parameters from all sources
Final user re-defined parameters-----------------:
runThreadN 8 genomeDir /media/jimmy/Ext/hs_ensembl_99/ readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART1.fq.gz
readFilesCommand zcat
outFileNamePrefix .//Non/01.starsolo/Non outSAMtype BAM SortedByCoordinate
outSAMattributes NH HI nM AS CR UR CB UB GX GN
outFilterMatchNmin 50 clip3pAdapterSeq AAAAAAAAAAAA
soloType CB_UMI_Complex soloUMIlen 12 soloBarcodeReadLength 0 soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3
soloFeatures Gene GeneFull_Ex50pAS
soloCBmatchWLtype 1MM soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58
soloUMIposition 0_60_0_71 soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000
soloCellReadStats Standard
Final effective command line:
/home/jimmy/anaconda3/envs/celescope/bin/STAR-avx2 --runThreadN 8 --genomeDir /media/jimmy/Ext/hs_ensembl_99/ --readFilesIn ./Non-CART-R/Non-CART_2.fq.gz ./Non-CART-R/Non-CART1.fq.gz --readFilesCommand zcat --outFileNamePrefix .//Non/01.starsolo/Non --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI nM AS CR UR CB UB GX GN --outFilterMatchNmin 50 --clip3pAdapterSeq AAAAAAAAAAAA --soloType CB_UMI_Complex --soloUMIlen 12 --soloBarcodeReadLength 0 --soloCBwhitelist /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /home/jimmy/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 --soloFeatures Gene GeneFull_Ex50pAS --soloCBmatchWLtype 1MM --soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 --soloUMIposition 0_60_0_71 --soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 --soloCellReadStats Standard
Number of fastq files for each mate = 1
Input read files for mate 1 : -rwxrwxrwx 1 jimmy jimmy 68155574216 Sep 17 16:39 ./Non-CART-R/Non-CART_2.fq.gz
readsCommandsFile: exec > ".//Non/01.starsolo/Non__STARtmp/tmp.fifo.read1" echo FILE 0 zcat "./Non-CART-R/Non-CART_2.fq.gz"
Input read files for mate 2 : -rwxrwxrwx 1 jimmy jimmy 67439953618 Sep 22 03:42 ./Non-CART-R/Non-CART_1.fq.gz
readsCommandsFile: exec > ".//Non/01.starsolo/Non__STARtmp/tmp.fifo.read2" echo FILE 0 zcat "./Non-CART-R/Non-CART_1.fq.gz"
ParametersSolo: --soloCellFilterType EmptyDrops_CR filtering parameters: 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 Sep 27 12:39:58 ... Finished reading, sorting and deduplicating CB whitelist sequences. WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters:
/home/jim/anaconda3/envs/celescope/bin/STAR-avx2 --runMode genomeGenerate --runThreadN 6 --genomeDir ./ --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa --genomeSAindexNbases 14 --sjdbGTFfile Homo_sapiens.GRCh38.99.filtered.gtf --sjdbOverhang 100
GstrandBit=32
versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.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 Homo_sapiens.GRCh38.99.filtered.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3211751963 24905496556 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 194 1 1 248956422 0 2 10 133797422 249036800 3 11 135086622 382992384 4 12 133275309 518258688 5 13 114364328 651689984 6 14 107043718 766246912 7 15 101991189 873463808 8 16 90338345 975699968 9 17 83257441 1066139648 10 18 80373285 1149501440 11 19 58617616 1229979648 12 2 242193529 1288699904 13 20 64444167 1530920960 14 21 46709983 1595408384 15 22 50818468 1642332160 16 3 198295559 1693188096 17 4 190214555 1891631104 18 5 181538259 2081947648 19 6 170805979 2263613440 20 7 159345973 2434531328 21 8 145138636 2593914880 22 9 138394717 2739142656 23 MT 16569 2877554688 24 X 156040895 2877816832 25 Y 57227415 3034054656 26 KI270728.1 1872759 3091464192 27 KI270727.1 448248 3093561344 28 KI270442.1 392061 3094085632 29 KI270729.1 280839 3094609920 30 GL000225.1 211173 3095134208 31 KI270743.1 210658 3095396352 32 GL000008.2 209709 3095658496 33 GL000009.2 201709 3095920640 34 KI270747.1 198735 3096182784 35 KI270722.1 194050 3096444928 36 GL000194.1 191469 3096707072 37 KI270742.1 186739 3096969216 38 GL000205.2 185591 3097231360 39 GL000195.1 182896 3097493504 40 KI270736.1 181920 3097755648 41 KI270733.1 179772 3098017792 42 GL000224.1 179693 3098279936 43 GL000219.1 179198 3098542080 44 KI270719.1 176845 3098804224 45 GL000216.2 176608 3099066368 46 KI270712.1 176043 3099328512 47 KI270706.1 175055 3099590656 48 KI270725.1 172810 3099852800 49 KI270744.1 168472 3100114944 50 KI270734.1 165050 3100377088 51 GL000213.1 164239 3100639232 52 GL000220.1 161802 3100901376 53 KI270715.1 161471 3101163520 54 GL000218.1 161147 3101425664 55 KI270749.1 158759 3101687808 56 KI270741.1 157432 3101949952 57 GL000221.1 155397 3102212096 58 KI270716.1 153799 3102474240 59 KI270731.1 150754 3102736384 60 KI270751.1 150742 3102998528 61 KI270750.1 148850 3103260672 62 KI270519.1 138126 3103522816 63 GL000214.1 137718 3103784960 64 KI270708.1 127682 3104047104 65 KI270730.1 112551 3104309248 66 KI270438.1 112505 3104571392 67 KI270737.1 103838 3104833536 68 KI270721.1 100316 3105095680 69 KI270738.1 99375 3105357824 70 KI270748.1 93321 3105619968 71 KI270435.1 92983 3105882112 72 GL000208.1 92689 3106144256 73 KI270538.1 91309 3106406400 74 KI270756.1 79590 3106668544 75 KI270739.1 73985 3106930688 76 KI270757.1 71251 3107192832 77 KI270709.1 66860 3107454976 78 KI270746.1 66486 3107717120 79 KI270753.1 62944 3107979264 80 KI270589.1 44474 3108241408 81 KI270726.1 43739 3108503552 82 KI270735.1 42811 3108765696 83 KI270711.1 42210 3109027840 84 KI270745.1 41891 3109289984 85 KI270714.1 41717 3109552128 86 KI270732.1 41543 3109814272 87 KI270713.1 40745 3110076416 88 KI270754.1 40191 3110338560 89 KI270710.1 40176 3110600704 90 KI270717.1 40062 3110862848 91 KI270724.1 39555 3111124992 92 KI270720.1 39050 3111387136 93 KI270723.1 38115 3111649280 94 KI270718.1 38054 3111911424 95 KI270317.1 37690 3112173568 96 KI270740.1 37240 3112435712 97 KI270755.1 36723 3112697856 98 KI270707.1 32032 3112960000 99 KI270579.1 31033 3113222144 100 KI270752.1 27745 3113484288 101 KI270512.1 22689 3113746432 102 KI270322.1 21476 3114008576 103 GL000226.1 15008 3114270720 104 KI270311.1 12399 3114532864 105 KI270366.1 8320 3114795008 106 KI270511.1 8127 3115057152 107 KI270448.1 7992 3115319296 108 KI270521.1 7642 3115581440 109 KI270581.1 7046 3115843584 110 KI270582.1 6504 3116105728 111 KI270515.1 6361 3116367872 112 KI270588.1 6158 3116630016 113 KI270591.1 5796 3116892160 114 KI270522.1 5674 3117154304 115 KI270507.1 5353 3117416448 116 KI270590.1 4685 3117678592 117 KI270584.1 4513 3117940736 118 KI270320.1 4416 3118202880 119 KI270382.1 4215 3118465024 120 KI270468.1 4055 3118727168 121 KI270467.1 3920 3118989312 122 KI270362.1 3530 3119251456 123 KI270517.1 3253 3119513600 124 KI270593.1 3041 3119775744 125 KI270528.1 2983 3120037888 126 KI270587.1 2969 3120300032 127 KI270364.1 2855 3120562176 128 KI270371.1 2805 3120824320 129 KI270333.1 2699 3121086464 130 KI270374.1 2656 3121348608 131 KI270411.1 2646 3121610752 132 KI270414.1 2489 3121872896 133 KI270510.1 2415 3122135040 134 KI270390.1 2387 3122397184 135 KI270375.1 2378 3122659328 136 KI270420.1 2321 3122921472 137 KI270509.1 2318 3123183616 138 KI270315.1 2276 3123445760 139 KI270302.1 2274 3123707904 140 KI270518.1 2186 3123970048 141 KI270530.1 2168 3124232192 142 KI270304.1 2165 3124494336 143 KI270418.1 2145 3124756480 144 KI270424.1 2140 3125018624 145 KI270417.1 2043 3125280768 146 KI270508.1 1951 3125542912 147 KI270303.1 1942 3125805056 148 KI270381.1 1930 3126067200 149 KI270529.1 1899 3126329344 150 KI270425.1 1884 3126591488 151 KI270396.1 1880 3126853632 152 KI270363.1 1803 3127115776 153 KI270386.1 1788 3127377920 154 KI270465.1 1774 3127640064 155 KI270383.1 1750 3127902208 156 KI270384.1 1658 3128164352 157 KI270330.1 1652 3128426496 158 KI270372.1 1650 3128688640 159 KI270548.1 1599 3128950784 160 KI270580.1 1553 3129212928 161 KI270387.1 1537 3129475072 162 KI270391.1 1484 3129737216 163 KI270305.1 1472 3129999360 164 KI270373.1 1451 3130261504 165 KI270422.1 1445 3130523648 166 KI270316.1 1444 3130785792 167 KI270340.1 1428 3131047936 168 KI270338.1 1428 3131310080 169 KI270583.1 1400 3131572224 170 KI270334.1 1368 3131834368 171 KI270429.1 1361 3132096512 172 KI270393.1 1308 3132358656 173 KI270516.1 1300 3132620800 174 KI270389.1 1298 3132882944 175 KI270466.1 1233 3133145088 176 KI270388.1 1216 3133407232 177 KI270544.1 1202 3133669376 178 KI270310.1 1201 3133931520 179 KI270412.1 1179 3134193664 180 KI270395.1 1143 3134455808 181 KI270376.1 1136 3134717952 182 KI270337.1 1121 3134980096 183 KI270335.1 1048 3135242240 184 KI270378.1 1048 3135504384 185 KI270379.1 1045 3135766528 186 KI270329.1 1040 3136028672 187 KI270419.1 1029 3136290816 188 KI270336.1 1026 3136552960 189 KI270312.1 998 3136815104 190 KI270539.1 993 3137077248 191 KI270385.1 990 3137339392 192 KI270423.1 981 3137601536 193 KI270392.1 971 3137863680 194 KI270394.1 970 3138125824 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Fri Sep 27 12:39:58 2024
Genome: size given as a parameter = 3211751963 SA: size given as a parameter = 24905496556 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3211751963; nSAbyte=24905496556 GstrandBit=32 SA number of indices=6037696134 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3211751963 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3211751963 bytes SA file size: 24905496556 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24905496556 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Fri Sep 27 12:44:31 2024
Processing splice junctions database sjdbN=364995, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Loaded transcript database, nTr=200956 Loaded exon database, nEx=1321486 Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Starting to map file # 0 mate 1: ./Non-CART-R/Non-CART_2.fq.gz mate 2: ./Non-CART-R/Non-CART_1.fq.gz BAM sorting: 120922 mapped reads BAM sorting bins genomic start loci: 1 0 27534282 2 0 93877009 3 0 173986575 4 1 73783177 5 2 8685786 6 2 65538817 7 3 6538132 8 3 56161418 9 3 120498171 10 5 21211844 11 5 105842006 12 6 69452975 13 7 2772006 14 7 87302949 15 8 28723582 16 8 59585122 17 9 74521029 18 10 17861453 19 10 48327592 20 11 10791814 21 11 88857552 22 11 216499384 23 12 49113918 24 13 8210401 25 13 8392860 26 13 8437123 27 13 8988543 28 14 22922967 29 15 22382120 30 15 116645388 31 16 70820660 32 17 40832461 33 17 141527664 34 18 26104033 35 18 41941503 36 18 155269339 37 19 76066458 38 20 73290674 39 21 37357460 40 22 648 41 22 5368 42 22 8207 43 22 10319 44 23 12976952 45 23 154400598 46 40 127439 47 40 172741 48 51 114773
EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length @A00151:1193:HCTLLDSXC:4:1414:15411:2065 + @A00151:1193:HCTLLDSXC:4:1414:1565TTTTTTTTTTATTTGTAGTATCACTCTGTCACCTAGGCTGTAGTGCAGTGACACGAGCTTGACTCACTG SOLUTION: fix your fastq file
Sep 27 14:00:53 ...... FATAL ERROR, exiting