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Strange Error while running STAR.

While I am running the STAR command like this, 

STAR  --runMode alignReads 
--genomeDir /home/joshij/Desktop/STAR_Index 
--genomeLoad NoSharedMemory 
--readFilesIn $in_file 
--readFilesCommand "zcat -fc" 
--outStd SAM 
--runThreadN 18 
--outFilterMultimapNmax 10 
--outSAMmode Full 
--outSAMattributes Standard 
--outSAMstrandField intronMotif 
--outFileNamePrefix /home/joshij/Desktop/Result_files/STAR_Out_files/$prefix 
--outReadsUnmapped Fastx 
--outFilterScoreMinOverLread 0.9 
--outFilterMismatchNoverLmax 0.05 
--outFilterMismatchNmax 4 
--sjdbGTFfile /home/joshij/Desktop/STAR_Index/Rattus_norvegicus.Rnor_6.0.94.gtf 
--sjdbOverhang 100 
--outSAMtype BAM SortedByCoordinate

While some time produces this error:

terminate called after throwing an instance of 'std::ios_base::failure'
  what():  basic_filebuf::underflow error reading the file

And when once the above error occurs programme won't work without error until the next system bootup. Please help.

Thanks

rna-seq alignment next-gen
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written by jaidev53ster • jaidev53ster

This might be related to your zcat options, they look funny, in particular zcat doesn't have -c switch, -c is used with gunzip to cause equal behavior as zcat. Try:

--readFilesCommand "zcat"

or

--readFilesCommand "zcat -f"

or 

--readFilesCommand "zcat -f --stdout"
• 0 views • link
written by Michael Dondrup Michael Dondrup

I am not sure what OS you are running this on but a post on Stackoverflow seems to indicate that this may be a bug in one of the libraries.

• 0 views • link
written by GenoMax GenoMax

1 answer

A silly typo was causing this error and the issue is resolved. The path I was providing for GTF file was incomplete

It should be like this 

--sjdbGTFfile /home/joshij/Desktop/STAR_Index/Rattus_norvegicus.Rnor_6.0.94.gtf/Rattus_norvegicus.Rnor_6.0.94.gtf

Rather this 

 --sjdbGTFfile /home/joshij/Desktop/STAR_Index/Rattus_norvegicus.Rnor_6.0.94.gtf
• 0 views • link
written by jaidev53ster • jaidev53ster

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