[gridengine users] different results on terminal and on submission via qsub

VG gupta567varun at gmail.com
Mon Jul 9 17:42:56 UTC 2018


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 <dpovey at 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 <gupta567varun at 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
>>
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>> https://gridengine.org/mailman/listinfo/users
>>
>>
>
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