Bioinformatics Asked by raiora on May 9, 2021
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).
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.
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
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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.
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