A couple things I can think of: * You're not specifying a shell (-S /path/to/shell). Which shell is the queue set to use?
* Is there anything in the output or error logs for the job? On Mon, Jul 09, 2018 at 01:23:00PM -0400, VG 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 > GCANAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > > adrenal_4a_ERR315452_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > 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 > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > > appendix_4a_ERR315437_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > GGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGA > > appendix_4a_ERR315465_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > > appendix_4b_ERR315345_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > adrenal_4a_ERR315452_1.fastq.gz > GCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGGAACTATGTAGCATAGTGTCTTAACACCTCAGTAAAGAGATCGGAAGAGCACA > CAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAGGTAACATGTTTTAAGAAACTATGTAGCATAGTGTCTT > > What is it that I am doing wrong here. > > Thanks > > Regards > Varun > _______________________________________________ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users -- -- Skylar Thompson (skyl...@u.washington.edu) -- Genome Sciences Department, System Administrator -- Foege Building S046, (206)-685-7354 -- University of Washington School of Medicine _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
