Problem during genome loading

[Stefano]

Hi,

I am trying to alling som fastq with STAR_2.6.0a6 but I keep getting this error:

runned cmd: STAR --runThreadN 4 --outSAMstrandField intronMotif --genomeDir STAR/ --readFilesCommand zless --readFilesIn ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz  ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz --outFileNamePrefix ~/Desktop/  --genomeLoad LoadAndKeep

Jan 25 16:30:21 ..... started STAR run
Jan 25 16:30:21 ..... loading genome
Abort trap: 6

Any idea?

here the log

STAR version=STAR_2.6.0a
STAR compilation time,server,dir=Mon Apr 23 17:28:43 GMT 2018 :/Users/travis/build/alexdobin/travis-tests/STARcompile/source
##### DEFAULT parameters:
versionSTAR                       20201
versionGenome                     20101   20200  
parametersFiles                   -  
sysShell                          -
runMode                           alignReads
runThreadN                        1
runDirPerm                        User_RWX
runRNGseed                        777
genomeDir                         ./GenomeDir/
genomeLoad                        NoSharedMemory
genomeFastaFiles                  -  
genomeChainFiles                  -  
genomeSAindexNbases               14
genomeChrBinNbits                 18
genomeSAsparseD                   1
genomeSuffixLengthMax             18446744073709551615
genomeFileSizes                   0  
genomeConsensusFile               -
readFilesType                     Fastx  
readFilesIn                       Read1   Read2  
readFilesPrefix                   -
readFilesCommand                  -  
readMatesLengthsIn                NotEqual
readMapNumber                     18446744073709551615
readNameSeparator                 /  
inputBAMfile                      -
bamRemoveDuplicatesType           -
bamRemoveDuplicatesMate2basesN    0
limitGenomeGenerateRAM            31000000000
limitIObufferSize                 150000000
limitOutSAMoneReadBytes           100000
limitOutSJcollapsed               1000000
limitOutSJoneRead                 1000
limitBAMsortRAM                   0
limitSjdbInsertNsj                1000000
outTmpDir                         -
outTmpKeep                        None
outStd                            Log
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
outBAMsortingBinsN                50
outSAMfilter                      None  
outSAMmultNmax                    18446744073709551615
outSAMattrIHstart                 1
outSAMtlen                        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
outFilterIntronStrands            RemoveInconsistentStrands
clip5pNbases                      0  
clip3pNbases                      0  
clip3pAfterAdapterNbases          0  
clip3pAdapterSeq                  -  
clip3pAdapterMMp                  0.1  
winBinNbits                       16
winAnchorDistNbins                9
winFlankNbins                     4
winAnchorMultimapNmax             50
winReadCoverageRelativeMin        0.5
winReadCoverageBasesMin           0
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
seedSplitMin                      12
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
alignEndsProtrude                 0   ConcordantPair  
alignInsertionFlush               None
peOverlapNbasesMin                0
peOverlapMMp                      0.1
chimSegmentMin                    0
chimScoreMin                      0
chimScoreDropMax                  20
chimScoreSeparation               10
chimScoreJunctionNonGTAG          -1
chimMainSegmentMultNmax           10
chimJunctionOverhangMin           20
chimOutType                       Junctions  
chimFilter                        banGenomicN  
chimSegmentReadGapMax             0
chimMultimapNmax                  0
chimMultimapScoreRange            1
chimNonchimScoreDropMin           20
sjdbFileChrStartEnd               -  
sjdbGTFfile                       -
sjdbGTFchrPrefix                  -
sjdbGTFfeatureExon                exon
sjdbGTFtagExonParentTranscript    transcript_id
sjdbGTFtagExonParentGene          gene_id
sjdbOverhang                      100
sjdbScore                         2
sjdbInsertSave                    Basic
varVCFfile                        -
waspOutputMode                    None
quantMode                         -  
quantTranscriptomeBAMcompression    1
quantTranscriptomeBan             IndelSoftclipSingleend
twopass1readsN                    18446744073709551615
twopassMode                       None
##### Command Line:
STAR --runThreadN 1 --outSAMstrandField intronMotif --genomeDir /Users/sgnan/alliners_compilers/STAR/ --readFilesCommand zless --readFilesIn /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz --outFileNamePrefix /Users/sgnan/Desktop/ --genomeLoad LoadAndKeep
##### Initial USER parameters from Command Line:
outFileNamePrefix                 /Users/sgnan/Desktop/
###### All USER parameters from Command Line:
runThreadN                    1     ~RE-DEFINED
outSAMstrandField             intronMotif     ~RE-DEFINED
genomeDir                     /Users/sgnan/alliners_compilers/STAR/     ~RE-DEFINED
readFilesCommand              zless        ~RE-DEFINED
readFilesIn                   /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz   /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz        ~RE-DEFINED
outFileNamePrefix             /Users/sgnan/Desktop/     ~RE-DEFINED
genomeLoad                    LoadAndKeep     ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runThreadN                        1
genomeDir                         /Users/sgnan/alliners_compilers/STAR/
genomeLoad                        LoadAndKeep
readFilesIn                       /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz   /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz  
readFilesCommand                  zless  
outFileNamePrefix                 /Users/sgnan/Desktop/
outSAMstrandField                 intronMotif

-------------------------------
##### Final effective command line:
STAR   --runThreadN 1   --genomeDir /Users/sgnan/alliners_compilers/STAR/   --genomeLoad LoadAndKeep   --readFilesIn /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz   /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz      --readFilesCommand zless      --outFileNamePrefix /Users/sgnan/Desktop/   --outSAMstrandField intronMotif

##### Final parameters after user input--------------------------------:
versionSTAR                       20201
versionGenome                     20101   20200  
parametersFiles                   -  
sysShell                          -
runMode                           alignReads
runThreadN                        1
runDirPerm                        User_RWX
runRNGseed                        777
genomeDir                         /Users/sgnan/alliners_compilers/STAR/
genomeLoad                        LoadAndKeep
genomeFastaFiles                  -  
genomeChainFiles                  -  
genomeSAindexNbases               14
genomeChrBinNbits                 18
genomeSAsparseD                   1
genomeSuffixLengthMax             18446744073709551615
genomeFileSizes                   0  
genomeConsensusFile               -
readFilesType                     Fastx  
readFilesIn                       /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz   /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz  
readFilesPrefix                   -
readFilesCommand                  zless  
readMatesLengthsIn                NotEqual
readMapNumber                     18446744073709551615
readNameSeparator                 /  
inputBAMfile                      -
bamRemoveDuplicatesType           -
bamRemoveDuplicatesMate2basesN    0
limitGenomeGenerateRAM            31000000000
limitIObufferSize                 150000000
limitOutSAMoneReadBytes           100000
limitOutSJcollapsed               1000000
limitOutSJoneRead                 1000
limitBAMsortRAM                   0
limitSjdbInsertNsj                1000000
outFileNamePrefix                 /Users/sgnan/Desktop/
outTmpDir                         -
outTmpKeep                        None
outStd                            Log
outReadsUnmapped                  None
outQSconversionAdd                0
outMultimapperOrder               Old_2.4
outSAMtype                        SAM  
outSAMmode                        Full
outSAMstrandField                 intronMotif
outSAMattributes                  Standard  
outSAMunmapped                    None  
outSAMorder                       Paired
outSAMprimaryFlag                 OneBestScore
outSAMreadID                      Standard
outSAMmapqUnique                  255
outSAMflagOR                      0
outSAMflagAND                     65535
outSAMattrRGline                  -  
outSAMheaderHD                    -  
outSAMheaderPG                    -  
outSAMheaderCommentFile           -
outBAMcompression                 1
outBAMsortingThreadN              0
outBAMsortingBinsN                50
outSAMfilter                      None  
outSAMmultNmax                    18446744073709551615
outSAMattrIHstart                 1
outSAMtlen                        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
outFilterIntronStrands            RemoveInconsistentStrands
clip5pNbases                      0  
clip3pNbases                      0  
clip3pAfterAdapterNbases          0  
clip3pAdapterSeq                  -  
clip3pAdapterMMp                  0.1  
winBinNbits                       16
winAnchorDistNbins                9
winFlankNbins                     4
winAnchorMultimapNmax             50
winReadCoverageRelativeMin        0.5
winReadCoverageBasesMin           0
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
seedSplitMin                      12
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
alignEndsProtrude                 0   ConcordantPair  
alignInsertionFlush               None
peOverlapNbasesMin                0
peOverlapMMp                      0.1
chimSegmentMin                    0
chimScoreMin                      0
chimScoreDropMax                  20
chimScoreSeparation               10
chimScoreJunctionNonGTAG          -1
chimMainSegmentMultNmax           10
chimJunctionOverhangMin           20
chimOutType                       Junctions  
chimFilter                        banGenomicN  
chimSegmentReadGapMax             0
chimMultimapNmax                  0
chimMultimapScoreRange            1
chimNonchimScoreDropMin           20
sjdbFileChrStartEnd               -  
sjdbGTFfile                       -
sjdbGTFchrPrefix                  -
sjdbGTFfeatureExon                exon
sjdbGTFtagExonParentTranscript    transcript_id
sjdbGTFtagExonParentGene          gene_id
sjdbOverhang                      100
sjdbScore                         2
sjdbInsertSave                    Basic
varVCFfile                        -
waspOutputMode                    None
quantMode                         -  
quantTranscriptomeBAMcompression    1
quantTranscriptomeBan             IndelSoftclipSingleend
twopass1readsN                    18446744073709551615
twopassMode                       None
----------------------------------------


   Input read files for mate 1, from input string /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz
-rw-r--r--  1 sgnan  staff  51313075 Jan 24 21:11 /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz

   readsCommandsFile:
exec > "/Users/sgnan/Desktop/_STARtmp/tmp.fifo.read1"
echo FILE 0
zless      "/Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R1_val_1.fq.gz"


   Input read files for mate 2, from input string /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz
ls: /Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz: No such file or directory

   readsCommandsFile:
exec > "/Users/sgnan/Desktop/_STARtmp/tmp.fifo.read2"
echo FILE 0
zless      "/Volumes/Storage/single_cell_download/ATAC-seq/output/trimmed_fastq/ACTATTCATT.GTTGACGGCC.R2_val_1.fq.gz"

WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute
Finished loading and checking parameters
Reading genome generation parameters:
### STAR   --runMode genomeGenerate   --runThreadN 6   --genomeDir ../STAR/   --genomeFastaFiles chr1.fa   chr10.fa   chr11.fa   chr12.fa   chr13.fa   chr14.fa   chr15.fa   chr16.fa   chr17.fa   chr18.fa   chr19.fa   chr2.fa   chr20.fa   chr21.fa   chr22.fa   chr3.fa   chr4.fa   chr5.fa   chr6.fa   chr7.fa   chr8.fa   chr9.fa   chrM.fa   chrX.fa   chrY.fa  
### GstrandBit=0
versionGenome                 20201        ~RE-DEFINED
genomeFastaFiles              chr1.fa   chr10.fa   chr11.fa   chr12.fa   chr13.fa   chr14.fa   chr15.fa   chr16.fa   chr17.fa   chr18.fa   chr19.fa   chr2.fa   chr20.fa   chr21.fa   chr22.fa   chr3.fa   chr4.fa   chr5.fa   chr6.fa   chr7.fa   chr8.fa   chr9.fa   chrM.fa   chrX.fa   chrY.fa        ~RE-DEFINED
genomeSAindexNbases           14     ~RE-DEFINED
genomeChrBinNbits             18     ~RE-DEFINED
genomeSAsparseD               1     ~RE-DEFINED
sjdbOverhang                  0     ~RE-DEFINED
sjdbFileChrStartEnd           -        ~RE-DEFINED
sjdbGTFfile                   -     ~RE-DEFINED
sjdbGTFchrPrefix              -     ~RE-DEFINED
sjdbGTFfeatureExon            exon     ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id     ~RE-DEFINED
sjdbGTFtagExonParentGene      gene_id     ~RE-DEFINED
sjdbInsertSave                Basic     ~RE-DEFINED
genomeFileSizes               3099328512   23606085545        ~RE-DEFINED
Genome version is compatible with current STAR version
Number of real (reference) chromosomes= 25
1    chr1    249250621    0
2    chr10    135534747    249298944
3    chr11    135006516    385089536
4    chr12    133851895    520355840
5    chr13    115169878    654311424
6    chr14    107349540    769654784
7    chr15    102531392    877133824
8    chr16    90354753    979894272
9    chr17    81195210    1070333952
10    chr18    78077248    1151598592
11    chr19    59128983    1229717504
12    chr2    243199373    1288962048
13    chr20    63025520    1532231680
14    chr21    48129895    1595408384
15    chr22    51304566    1643642880
16    chr3    198022430    1695023104
17    chr4    191154276    1893203968
18    chr5    180915260    2084569088
19    chr6    171115067    2265710592
20    chr7    159138663    2436890624
21    chr8    146364022    2596274176
22    chr9    141213431    2742812672
23    chrM    16571    2884108288
24    chrX    155270560    2884370432
25    chrY    59373566    3039821824
Started loading the genome: Fri Jan 25 16:30:21 2019

Genome: size given as a parameter = 3099328512
SA: size given as a parameter = 23606085545
SAindex: size given as a parameter = 1
Read from SAindex: pGe.gSAindexNbases=14  nSAi=357913940
nGenome=3099328512;  nSAbyte=23606085545
GstrandBit=32   SA number of indices=5722687404
Allocating shared memory for genome

[Alexander Dobin]

Hi Stefano,

how much RAM do you have? Also, please try to run it without the --genomeLoad option.

Cheers

Alex

[Alexander Dobin]

Also, 2.6.0a was a buggy release and it was superseded by 2.6.0c, even better try 2.6.1d or 2.7.0a.

On Friday, January 25, 2019 at 11:57:25 AM UTC-5, Stefano wrote:

[Stefano]

Hi, I updated the version to 2.7 and now it works.

thanks,

Stefano