Hi Daniel, I used a named script and it is working as I expected it to work. I am just trying to understand what is wrong here on the command line when I submit it to qsub. I know double quotes can be a real pain. I have one set of double quotes around the seq I want to grep and the other double quotes are the submission quotes to the qsub command.
Regards Varun On Mon, Jul 9, 2018 at 1:30 PM, Daniel Povey <dpo...@gmail.com> wrote: > 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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