Can get bedGrahp from STAR

[Nicolás Lemus]

Dear Community

I checked whether any of you have had this issue before, I want to generate a bedGraph from a Sorted.ByCoord.Out.Bam and it is not producing the bed file.

Any of you have encountered that issue:

Here is the input i used

nlemus@PC36420:~/12TB/Untitled Folder/GenomeHITSCLIP$ STAR --runMode=inputAligmentsFromBAM  \
> --genomeDir /home/nlemus/star/code/STAR-2.6.0a/DB/GrcH38/ \
> --inputBAMfile SRR6048658_clipped_qf.fastqAligned.sortedByCoord.out.bam \
> --outFileNamePrefix ola.bed  \
> --outWigType bedGraph    \
> --outWigStrand Stranded  \
> --outWigNorm RPM
Jun 07 18:24:50 ..... started STAR run
nlemus@PC36420:~/12TB/Untitled Folder/GenomeHITSCLIP$

Here is the bedlog.out File 

## Final effective command line:
STAR   --runMode inputAligmentsFromBAM   --inputBAMfile SRR6048658_clipped_qf.fastqAligned.sortedByCoord.out.bam   --outFileNamePrefix ola.bed   --outWigType bedGraph      --outWigStrand Unstranded      --outWigNorm RPM  

##### Final parameters after user input--------------------------------:
versionSTAR                       20201
versionGenome                     20101   20200  
parametersFiles                   -  
sysShell                          -
runMode                           inputAligmentsFromBAM
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                      SRR6048658_clipped_qf.fastqAligned.sortedByCoord.out.bam
bamRemoveDuplicatesType           -
bamRemoveDuplicatesMate2basesN    0
limitGenomeGenerateRAM            31000000000
limitIObufferSize                 150000000
limitOutSAMoneReadBytes           100000
limitOutSJcollapsed               1000000
limitOutSJoneRead                 1000
limitBAMsortRAM                   0
limitSjdbInsertNsj                1000000
outFileNamePrefix                 ola.bed
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                        bedGraph  
outWigStrand                      Unstranded  
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
----------------------------------------

Finished loading and checking parameters
EXITING because of INPUT ERROR: unknown value of input parameter runMode=inputAligmentsFromBAM

Thank you in advance

Nicolas

[Alexander Dobin]

Hi Nicolás,

per the error message, the parameter value is not spelled right:

EXITING because of INPUT ERROR: unknown value of input parameter runMode=inputAligmentsFromBAM

It should be inputAlignmentsFromBAM

Cheers

Alex