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

Daniel Povey dpovey at gmail.com
Mon Jul 9 17:46:08 UTC 2018


Using single quotes would fix it.
But fundamentally this is a bash question-- this list is for GridEngine
questions and more on this topic would bore the subscribers.  Best to look
for a bash tutorial online and learn more about it that way.


On Mon, Jul 9, 2018 at 1:42 PM, VG <gupta567varun at gmail.com> wrote:

> 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
>>>
>>> _______________________________________________
>>> users mailing list
>>> users at gridengine.org
>>> https://gridengine.org/mailman/listinfo/users
>>>
>>>
>>
>
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