readFilesCommand not working

Question

[vinishavvenugopal]

Hi,

I tried using zcat and gunzip in STAR to unzip the input files. The program runs fine but the output(aligned bam file is 0kb) has nothing in it. There was no mapping done(mapping is 0%), the same code runs fine if I use the fastq file instead of fastq.gz

Has anyone experienced the same?

Code is:

STAR \ --genomeDir /home/***/STAR-2.5.2b/source \ --sjdbGTFfile /home/***/STAR-2.5.2b/source/Homo_sapiens.GRCh37.75_new.gtf \ --readFilesCommand zcat \ --readFilesIn /home/***/globus/TGEN_STAR/Success_hg38run/read1.fastq.gz /home/***/globus/TGEN_STAR/Success_hg38run/read2.fastq.gz --runThreadN 9\ --limitBAMsortRAM 9600000000 \ --outFileNamePrefix /home/***/globus/TGEN_STAR/0604/out_ \ --runMode alignReads \ --outSAMtype BAM Unsorted\ --genomeLoad NoSharedMemory

Thanks, Vinisha

[GenoMax]

Is zcat not available on the computer you are using (unlikely but still)? What does which zcat produce?

[vinishavvenugopal]

Yes it's available but it doesn't map at all