<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>

CC BY-SA 4.0
2020-09-03T16:58:46.577Z
I'm having the same problem.
How do you solve it?
Thanks in advance
user9463
CC BY-SA 4.0
2021-01-05T21:03:36.893Z
Yes. It's a memory issue so that I increased the memory as suggested by 10X genomics.
raiora
CC BY-SA 4.0
2021-07-14T10:41:29.107Z
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.
gringer
CC BY-SA 4.0
2021-07-15T12:27:56.720Z
Sorry to bother you and thanks for the comment. How to complete this answer section then?
raiora
<cellranger>
10X cellranger error during count
# 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 
    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?  

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## 0 answers

