Sample Header Ad - 728x90

different results on terminal vs qsub submission

1 vote
2 answers
529 views
I'm 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'm 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'm doing wrong here?
Asked by user3138373 (2589 rep)
Jul 9, 2018, 05:55 PM
Last activity: Jul 9, 2018, 06:16 PM