You should put that in a bash script and invoke it by name. It's really a miracle that it gave you anything even remotely close to what you intended when run like that, because of how bash interprets double-quotes and variables. Inside double quotes it will expand variables with their values at the time the contents of the double-quotes are evaluated.
Best to sidestep all those issues by running it as a named scripts. On Mon, Jul 9, 2018 at 1:23 PM, VG <gupta567va...@gmail.com> wrote: > Hi, > I am trying to run a command on the terminal and also submit it to the > cluster but I am getting different results. > > When I type on the terminal this : > > for i in *_1.fastq.gz; do echo $i >> t.txt; zcat $i | grep > "GCTGGCAAAAAGAAGGTAACATGTTTT" >> t.txt ; echo >> t.txt ; done > > I get the output like this > > adrenal_4a_ERR315335_1.fastq.gz > GCANAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > > adrenal_4a_ERR315452_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAA > GAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4c_ERR315392_1.fastq.gz > > adrenal_4c_ERR315450_1.fastq.gz > > and so on.. > > > This is what the output is expected. > > When I submit the same command to the hpc cluster via qsub I am getting a > completely different result > > *qsub -l h_vmem=4G -cwd -j y -b y -N n_tr -R y "for i in *_1.fastq.gz; do > echo $i >> t.txt; zcat $i | grep "GCTGGCAAAAAGAAGGTAACATGTTTT" >> t.txt ; > echo >> t.txt ; done"* > > adrenal_4a_ERR315452_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAA > GAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > > appendix_4a_ERR315437_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAA > GAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAA > GAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > GGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTAT > GTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGA > > appendix_4a_ERR315465_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAA > GAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > > appendix_4b_ERR315345_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAA > GAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGC > ATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAA > GAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > What is it that I am doing wrong here. > > Thanks > > Regards > Varun > > _______________________________________________ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users > >
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