Entering edit mode
5.3 years ago
jaidev53ster
•
0
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
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:
or
or
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.