Body: <p>I successfully installed cellranger and performed a test run. Even, I installed bcl2fastq. Everything looked perfect. Thus, I ran <code>cellranger count</code>. I ran into an error during the <code>cellranger count</code> run. I put command as suggested in the tutorial as follows (I double-checked any typo that can cause error).</p>
  <p>tutorial (<a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct" rel="nofollow noreferrer">https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct</a>)</p>
  <pre><code>cellranger count --id=run_count_1kpbmcs \
  --fastqs=/mnt/home/user.name/yard/run_cellranger_count/pbmc_1k_v3_fastqs \
  --sample=pbmc_1k_v3 \
  --transcriptome=/mnt/home/user.name/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0
  </code></pre>
  <p>Initially, the process went smoothly, but it suddenly found error as follows. It's not likely due to memory issues.</p>
  <hr />
  <pre><code>[error] Pipestance failed. Error log at:
  run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ALIGN_READS/fork0/chnk00-u27879f31e3/_errors
  </code></pre>
  <p>Log message:</p>
  <pre><code>Traceback (most recent call last):
    File &quot;/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py&quot;, line 589, in _main
      stage.main()
    File &quot;/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py&quot;, line 554, in main
      self._run(lambda: self._module.main(args, outs))
    File &quot;/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py&quot;, line 523, in _run
      cmd()
    File &quot;/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py&quot;, line 554, in &lt;lambda&gt;
      self._run(lambda: self._module.main(args, outs))
    File &quot;/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/__init__.py&quot;, line 128, in main
      align_reads(args, outs)
    File &quot;/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/__init__.py&quot;, line 67, in align_reads
      read_group_tags=tk_bam.make_star_rg_header(args.read_group))
    File &quot;/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/reference.py&quot;, line 616, in align
      raise cr_io.CRCalledProcessError(e.msg + ' Check STAR logs for errors: %s .' % star_log)
  CRCalledProcessError: Process returned error code -9: STAR . Check STAR logs for errors: /ufrc/zhangw/my.kim/yard/run_cellranger_count/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ALIGN_READS/fork0/chnk00-u27879f31e3/files/Log.out .
  
  
  Waiting 6 seconds for UI to do final refresh.
  Pipestance failed. Use --noexit option to keep UI running after failure.
  
  2020-04-21 13:48:37 Shutting down.
  </code></pre>
  <hr />
  <h2 id="meanwhile-i-checked-star-logs-for-errors-according-to-haci-said-and-i-found-these">Meanwhile, I checked STAR logs for errors according to Haci said, and I found these,</h2>
  <pre><code>STAR version=                 STAR_2.5.1b
  STAR compilation time,server,dir=Wed May 8 16:13:25 PDT 2019 :/mnt/home/jenkins/workspace/module-STAR-5dda596---latest/sake/modules/STAR/5dda596/source
  ##### DEFAULT parameters:
  versionSTAR                       20201
  versionGenome                     20101   20200   
  parametersFiles                   -   
  sysShell                          -
  runMode                           alignReads
  runThreadN                        1
  runDirPerm                        User_RWX
  runRNGseed                        777
  genomeDir                         ./GenomeDir/
  genomeLoad                        NoSharedMemory
  genomeFastaFiles                  -   
  genomeSAindexNbases               14
  genomeChrBinNbits                 18
  genomeSAsparseD                   1
  genomeSuffixLengthMax             18446744073709551615
  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
  outFileNamePrefix                 ./
  outTmpDir                         -
  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
  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
  chimSegmentMin                    0
  chimScoreMin                      0
  chimScoreDropMax                  20
  chimScoreSeparation               10
  chimScoreJunctionNonGTAG          -1
  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:
  STAR --genomeDir /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within KeepPairs --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1 SM:run_count_1kpbmcs LB:0.1 PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1 PL:ILLUMINA --readFilesIn /dev/fd/63
  ##### Initial USER parameters from Command Line:
  outStd                            SAM
  ###### All USER parameters from Command Line:
  genomeDir                     /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star     ~RE-DEFINED
  outSAMmultNmax                18446744073709551615     ~RE-DEFINED
  runThreadN                    4     ~RE-DEFINED
  readNameSeparator             space        ~RE-DEFINED
  outSAMunmapped                Within   KeepPairs        ~RE-DEFINED
  outSAMtype                    SAM        ~RE-DEFINED
  outStd                        SAM     ~RE-DEFINED
  outSAMorder                   PairedKeepInputOrder     ~RE-DEFINED
  outSAMattrRGline              ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA        ~RE-DEFINED
  readFilesIn                   /dev/fd/63        ~RE-DEFINED
  ##### Finished reading parameters from all sources
  
  ##### Final user re-defined parameters-----------------:
  runThreadN                        4
  genomeDir                         /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star
  readFilesIn                       /dev/fd/63   
  readNameSeparator                 space   
  outStd                            SAM
  outSAMtype                        SAM   
  outSAMunmapped                    Within   KeepPairs   
  outSAMorder                       PairedKeepInputOrder
  outSAMattrRGline                  ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA   
  outSAMmultNmax                    18446744073709551615
  
  -------------------------------
  ##### Final effective command line:
  STAR   --runThreadN 4   --genomeDir /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star   --readFilesIn /dev/fd/63      --readNameSeparator space      --outStd SAM   --outSAMtype SAM      --outSAMunmapped Within   KeepPairs      --outSAMorder PairedKeepInputOrder   --outSAMattrRGline ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA      --outSAMmultNmax 18446744073709551615
  
  ##### Final parameters after user input--------------------------------:
  versionSTAR                       20201
  versionGenome                     20101   20200   
  parametersFiles                   -   
  sysShell                          -
  runMode                           alignReads
  runThreadN                        4
  runDirPerm                        User_RWX
  runRNGseed                        777
  genomeDir                         /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star
  genomeLoad                        NoSharedMemory
  genomeFastaFiles                  -   
  genomeSAindexNbases               14
  genomeChrBinNbits                 18
  genomeSAsparseD                   1
  genomeSuffixLengthMax             18446744073709551615
  readFilesIn                       /dev/fd/63   
  readFilesCommand                  -   
  readMatesLengthsIn                NotEqual
  readMapNumber                     18446744073709551615
  readNameSeparator                 space   
  inputBAMfile                      -
  bamRemoveDuplicatesType           -
  bamRemoveDuplicatesMate2basesN    0
  limitGenomeGenerateRAM            31000000000
  limitIObufferSize                 150000000
  limitOutSAMoneReadBytes           100000
  limitOutSJcollapsed               1000000
  limitOutSJoneRead                 1000
  limitBAMsortRAM                   0
  limitSjdbInsertNsj                1000000
  outFileNamePrefix                 ./
  outTmpDir                         -
  outStd                            SAM
  outReadsUnmapped                  None
  outQSconversionAdd                0
  outMultimapperOrder               Old_2.4
  outSAMtype                        SAM   
  outSAMmode                        Full
  outSAMstrandField                 None
  outSAMattributes                  Standard   
  outSAMunmapped                    Within   KeepPairs   
  outSAMorder                       PairedKeepInputOrder
  outSAMprimaryFlag                 OneBestScore
  outSAMreadID                      Standard
  outSAMmapqUnique                  255
  outSAMflagOR                      0
  outSAMflagAND                     65535
  outSAMattrRGline                  ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA   
  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
  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
  chimSegmentMin                    0
  chimScoreMin                      0
  chimScoreDropMax                  20
  chimScoreSeparation               10
  chimScoreJunctionNonGTAG          -1
  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
  ----------------------------------------
  
  WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
  Finished loading and checking parameters
  Reading genome generation parameters:
  versionGenome                 20201        ~RE-DEFINED
  genomeFastaFiles              /mnt/yard2/pat/cr/new-refs/reference_buildscripts2/GRCh38/fasta/genome.fa        ~RE-DEFINED
  genomeSAindexNbases           14     ~RE-DEFINED
  genomeChrBinNbits             18     ~RE-DEFINED
  genomeSAsparseD               3     ~RE-DEFINED
  sjdbOverhang                  100     ~RE-DEFINED
  sjdbFileChrStartEnd           -        ~RE-DEFINED
  sjdbGTFfile                   /mnt/yard2/pat/cr/new-refs/reference_buildscripts2/GRCh38/genes/genes.gtf     ~RE-DEFINED
  sjdbGTFchrPrefix              -     ~RE-DEFINED
  sjdbGTFfeatureExon            exon     ~RE-DEFINED
  sjdbGTFtagExonParentTranscripttranscript_id     ~RE-DEFINED
  sjdbGTFtagExonParentGene      gene_id     ~RE-DEFINED
  sjdbInsertSave                Basic     ~RE-DEFINED
  Genome version is compatible with current STAR version
  Number of real (reference) chromosmes= 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: Tue Apr 21 13:48:20 2020
  
  checking Genome sizefile size: 3205385489 bytes; state: good=1 eof=0 fail=0 bad=0
  checking SA sizefile size: 8651064546 bytes; state: good=1 eof=0 fail=0 bad=0
  checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0
  Read from SAindex: genomeSAindexNbases=14  nSAi=357913940
  nGenome=3205385489;  nSAbyte=8651064546
  GstrandBit=32   SA number of indices=2097227768
  Shared memory is not used for genomes. Allocated a private copy of the genome.
  Genome file size: 3205385489 bytes; state: good=1 eof=0 fail=0 bad=0
  Loading Genome ... cat: .: 디렉터리입니다
  -----------------
  </code></pre>
  <p>I googled it but it failed to solve the issue. What should I do next? Do you have any idea?</p>
  <p>Thank you for helping me, toddler.</p>
  <p>Additional information:</p>
  <ul>
  <li>the issue seemed to be related to annotation, but MD5 for both fastq and reference file is correct.</li>
  </ul>
  <p>Here are the errors related to my problem:</p>
  <pre><code> (1) WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
   Finished loading and checking parameters
   Shared memory is not used for genomes
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-03T16:58:46.577Z
Comments.Text: I'm having the same problem.
  How do you solve it?
  Thanks in advance
Comments.UserDisplayName: user9463
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-05T21:03:36.893Z
Comments.Text: Yes. It's a memory issue so that I increased the memory as suggested by 10X genomics.
Comments.UserDisplayName: raiora
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-14T10:41:29.107Z
Comments.Text: If you've answered your own question, please add this as an accepted answer, especially given that so a few other people have the same issue. This makes it easier for search engines to find the answer, and stops the bot from recycling the question to fish for more answers.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-15T12:27:56.720Z
Comments.Text: Sorry to bother you and thanks for the comment. How to complete this answer section then?
Comments.UserDisplayName: raiora
Tags: <cellranger>
Title: 10X cellranger error during count
ThreadText: # 10X cellranger error during count
  
  (Asked by: username_0 on 2020-04-21)
  
  I successfully installed cellranger and performed a test run. Even, I installed bcl2fastq. Everything looked perfect. Thus, I ran `cellranger count`. I ran into an error during the `cellranger count` run. I put command as suggested in the tutorial as follows (I double-checked any typo that can cause error).
  
  tutorial (<https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct>)
  
  ```
  cellranger count --id=run_count_1kpbmcs \
  --fastqs=/mnt/home/user.name/yard/run_cellranger_count/pbmc_1k_v3_fastqs \
  --sample=pbmc_1k_v3 \
  --transcriptome=/mnt/home/user.name/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0
  
  ```
  
  Initially, the process went smoothly, but it suddenly found error as follows. It's not likely due to memory issues.
  
  ---
  
  ```
  [error] Pipestance failed. Error log at:
  run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ALIGN_READS/fork0/chnk00-u27879f31e3/_errors
  
  ```
  
  Log message:
  
  ```
  Traceback (most recent call last):
    File "/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 589, in _main
      stage.main()
    File "/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 554, in main
      self._run(lambda: self._module.main(args, outs))
    File "/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 523, in _run
      cmd()
    File "/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 554, in <lambda>
      self._run(lambda: self._module.main(args, outs))
    File "/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/__init__.py", line 128, in main
      align_reads(args, outs)
    File "/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/cellranger-cs/3.1.0/mro/stages/counter/align_reads/__init__.py", line 67, in align_reads
      read_group_tags=tk_bam.make_star_rg_header(args.read_group))
    File "/ufrc/zhangw/my.kim/yard/apps/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/reference.py", line 616, in align
      raise cr_io.CRCalledProcessError(e.msg + ' Check STAR logs for errors: %s .' % star_log)
  CRCalledProcessError: Process returned error code -9: STAR . Check STAR logs for errors: /ufrc/zhangw/my.kim/yard/run_cellranger_count/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ALIGN_READS/fork0/chnk00-u27879f31e3/files/Log.out .
  
  Waiting 6 seconds for UI to do final refresh.
  Pipestance failed. Use --noexit option to keep UI running after failure.
  
  2020-04-21 13:48:37 Shutting down.
  
  ```
  
  ---
  
  ## Meanwhile, I checked STAR logs for errors according to Haci said, and I found these,
  
  ```
  STAR version=                 STAR_2.5.1b
  STAR compilation time,server,dir=Wed May 8 16:13:25 PDT 2019 :/mnt/home/jenkins/workspace/module-STAR-5dda596---latest/sake/modules/STAR/5dda596/source
  ##### DEFAULT parameters:
  versionSTAR                       20201
  versionGenome                     20101   20200   
  parametersFiles                   -   
  sysShell                          -
  runMode                           alignReads
  runThreadN                        1
  runDirPerm                        User_RWX
  runRNGseed                        777
  genomeDir                         ./GenomeDir/
  genomeLoad                        NoSharedMemory
  genomeFastaFiles                  -   
  genomeSAindexNbases               14
  genomeChrBinNbits                 18
  genomeSAsparseD                   1
  genomeSuffixLengthMax             18446744073709551615
  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
  outFileNamePrefix                 ./
  outTmpDir                         -
  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
  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
  chimSegmentMin                    0
  chimScoreMin                      0
  chimScoreDropMax                  20
  chimScoreSeparation               10
  chimScoreJunctionNonGTAG          -1
  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:
  STAR --genomeDir /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within KeepPairs --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1 SM:run_count_1kpbmcs LB:0.1 PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1 PL:ILLUMINA --readFilesIn /dev/fd/63
  ##### Initial USER parameters from Command Line:
  outStd                            SAM
  ###### All USER parameters from Command Line:
  genomeDir                     /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star     ~RE-DEFINED
  outSAMmultNmax                18446744073709551615     ~RE-DEFINED
  runThreadN                    4     ~RE-DEFINED
  readNameSeparator             space        ~RE-DEFINED
  outSAMunmapped                Within   KeepPairs        ~RE-DEFINED
  outSAMtype                    SAM        ~RE-DEFINED
  outStd                        SAM     ~RE-DEFINED
  outSAMorder                   PairedKeepInputOrder     ~RE-DEFINED
  outSAMattrRGline              ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA        ~RE-DEFINED
  readFilesIn                   /dev/fd/63        ~RE-DEFINED
  ##### Finished reading parameters from all sources
  
  ##### Final user re-defined parameters-----------------:
  runThreadN                        4
  genomeDir                         /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star
  readFilesIn                       /dev/fd/63   
  readNameSeparator                 space   
  outStd                            SAM
  outSAMtype                        SAM   
  outSAMunmapped                    Within   KeepPairs   
  outSAMorder                       PairedKeepInputOrder
  outSAMattrRGline                  ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA   
  outSAMmultNmax                    18446744073709551615
  
  -------------------------------
  ##### Final effective command line:
  STAR   --runThreadN 4   --genomeDir /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star   --readFilesIn /dev/fd/63      --readNameSeparator space      --outStd SAM   --outSAMtype SAM      --outSAMunmapped Within   KeepPairs      --outSAMorder PairedKeepInputOrder   --outSAMattrRGline ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA      --outSAMmultNmax 18446744073709551615
  
  ##### Final parameters after user input--------------------------------:
  versionSTAR                       20201
  versionGenome                     20101   20200   
  parametersFiles                   -   
  sysShell                          -
  runMode                           alignReads
  runThreadN                        4
  runDirPerm                        User_RWX
  runRNGseed                        777
  genomeDir                         /ufrc/zhangw/my.kim/yard/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0/star
  genomeLoad                        NoSharedMemory
  genomeFastaFiles                  -   
  genomeSAindexNbases               14
  genomeChrBinNbits                 18
  genomeSAsparseD                   1
  genomeSuffixLengthMax             18446744073709551615
  readFilesIn                       /dev/fd/63   
  readFilesCommand                  -   
  readMatesLengthsIn                NotEqual
  readMapNumber                     18446744073709551615
  readNameSeparator                 space   
  inputBAMfile                      -
  bamRemoveDuplicatesType           -
  bamRemoveDuplicatesMate2basesN    0
  limitGenomeGenerateRAM            31000000000
  limitIObufferSize                 150000000
  limitOutSAMoneReadBytes           100000
  limitOutSJcollapsed               1000000
  limitOutSJoneRead                 1000
  limitBAMsortRAM                   0
  limitSjdbInsertNsj                1000000
  outFileNamePrefix                 ./
  outTmpDir                         -
  outStd                            SAM
  outReadsUnmapped                  None
  outQSconversionAdd                0
  outMultimapperOrder               Old_2.4
  outSAMtype                        SAM   
  outSAMmode                        Full
  outSAMstrandField                 None
  outSAMattributes                  Standard   
  outSAMunmapped                    Within   KeepPairs   
  outSAMorder                       PairedKeepInputOrder
  outSAMprimaryFlag                 OneBestScore
  outSAMreadID                      Standard
  outSAMmapqUnique                  255
  outSAMflagOR                      0
  outSAMflagAND                     65535
  outSAMattrRGline                  ID:run_count_1kpbmcs:0:1:HFWFVDMXX:1   SM:run_count_1kpbmcs   LB:0.1   PU:run_count_1kpbmcs:0:1:HFWFVDMXX:1   PL:ILLUMINA   
  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
  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
  chimSegmentMin                    0
  chimScoreMin                      0
  chimScoreDropMax                  20
  chimScoreSeparation               10
  chimScoreJunctionNonGTAG          -1
  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
  ----------------------------------------
  
  WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
  Finished loading and checking parameters
  Reading genome generation parameters:
  versionGenome                 20201        ~RE-DEFINED
  genomeFastaFiles              /mnt/yard2/pat/cr/new-refs/reference_buildscripts2/GRCh38/fasta/genome.fa        ~RE-DEFINED
  genomeSAindexNbases           14     ~RE-DEFINED
  genomeChrBinNbits             18     ~RE-DEFINED
  genomeSAsparseD               3     ~RE-DEFINED
  sjdbOverhang                  100     ~RE-DEFINED
  sjdbFileChrStartEnd           -        ~RE-DEFINED
  sjdbGTFfile                   /mnt/yard2/pat/cr/new-refs/reference_buildscripts2/GRCh38/genes/genes.gtf     ~RE-DEFINED
  sjdbGTFchrPrefix              -     ~RE-DEFINED
  sjdbGTFfeatureExon            exon     ~RE-DEFINED
  sjdbGTFtagExonParentTranscripttranscript_id     ~RE-DEFINED
  sjdbGTFtagExonParentGene      gene_id     ~RE-DEFINED
  sjdbInsertSave                Basic     ~RE-DEFINED
  Genome version is compatible with current STAR version
  Number of real (reference) chromosmes= 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: Tue Apr 21 13:48:20 2020
  
  checking Genome sizefile size: 3205385489 bytes; state: good=1 eof=0 fail=0 bad=0
  checking SA sizefile size: 8651064546 bytes; state: good=1 eof=0 fail=0 bad=0
  checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0
  Read from SAindex: genomeSAindexNbases=14  nSAi=357913940
  nGenome=3205385489;  nSAbyte=8651064546
  GstrandBit=32   SA number of indices=2097227768
  Shared memory is not used for genomes. Allocated a private copy of the genome.
  Genome file size: 3205385489 bytes; state: good=1 eof=0 fail=0 bad=0
  Loading Genome ... cat: .: 디렉터리입니다
  -----------------
  
  ```
  
  I googled it but it failed to solve the issue. What should I do next? Do you have any idea?
  
  Thank you for helping me, toddler.
  
  Additional information:
  
  * the issue seemed to be related to annotation, but MD5 for both fastq and reference file is correct.
  
  Here are the errors related to my problem:
  
  ```
   (1) WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
   Finished loading and checking parameters
   Shared memory is not used for genomes
  
  ```
  
  **Tags:** cellranger
  
  > **Comments:**
  > **username_1**: I'm having the same problem. How do you solve it? Thanks in advance  
  > **username_0**: Yes. It's a memory issue so that I increased the memory as suggested by 10X genomics.  
  > **username_2**: If you've answered your own question, please add this as an accepted answer, especially given that so a few other people have the same issue. This makes it easier for search engines to find the answer, and stops the bot from recycling the question to fish for more answers.  
  > **username_0**: Sorry to bother you and thanks for the comment. How to complete this answer section then?  
  
  ---
  
  ## 0 answers
  
  