different results on terminal vs qsub submission
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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
Last activity: Jul 9, 2018, 06:16 PM