use: command not found. #PLEASE fix my problem, thanks!

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Zihua Liu

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Nov 1, 2017, 4:32:46 AM11/1/17
to 3D Genomics

Hi, Dr. Aiden

I am naive student to bioinformatics and I want to use juicer.sh to create merged_nodups.txt file which is as one of two inputs for 3d-dna de novo assembly.
But I get into trouble when I run juicer.sh.

I make another three subdirectories beneath UGER (fastq, references and restriction_sites, separately)

My command line is: 
"
nohup /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/scripts/juicer.sh \
-d /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER \
-D /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER \
-S final -r -R 2 \
-z /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/references/pilon_p.fasta \
-s MboI \
-y /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/restriction_sites/pilon_p_mboi.bed \
-p /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/restriction_sites/pilon_p.fasta.sizes \
2> juicer_muscle_Lib1_log &
"
I am not sure whether I make the options '-d' and '-D' rightly.

To my surprise, the command line was completed immediately and I am aware of that I did something wrong.

The nohup.out file outputs that
"
(-: Looking for fastq files...fastq files exist
(-: Aligning files matching /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/fastq/*_R*.fastq*
 in queue short to genome hg19 with site file /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/restriction_sites/pilon_p_mboi.bed
(-: Created /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/splits and /home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/aligned.  Splitting fi
(-: Starting job to launch other jobs once splitting is complete...
(-: Finished adding all jobs... please wait while processing.
(-: Looking for fastq files...fastq files exist
(-: Finished adding all jobs... please wait while processing.
(-: Looking for fastq files...fastq files exist
(-: Finished adding all jobs... please wait while processing.
"
 and the juicer_muscle_Lib1_log told that
"
nohup: ignoring input and appending output to `nohup.out'
/home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/scripts/juicer.sh: line 349: /broad/software/scripts/useuse: No such file or directory
/home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/scripts/juicer.sh: line 350: use: command not found
/home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/scripts/juicer.sh: line 397: qsub: command not found
/home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/scripts/juicer.sh: line 840: qsub: command not found
/home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/scripts/juicer.sh: line 864: qsub: command not found
/home/zkzhou/lm/Hi-C/juicer/juicer-master/UGER/scripts/juicer.sh: line 871: qsub: command not found
"
So could you please tell me where I did wrong? 
Thank you very much in advance and looking forward to your generous replies.

Regards,

Zihua

Neva Durand

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Nov 1, 2017, 9:46:04 AM11/1/17
to 3D Genomics, Zihua Liu
Hello,

What cluster system are you on?

Neva

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Neva Cherniavsky Durand, Ph.D.
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Neva Durand

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Nov 1, 2017, 9:59:05 AM11/1/17
to 刘子华, 3D Genomics
Hello Zihua,

You should be using the CPU scripts, indeed.  Here is a link with directions.


Best
Neva

On Wed, Nov 1, 2017 at 9:53 AM, 刘子华 <zl2...@nyu.edu> wrote:
Hi,

Thanks for your generous replies!

That is one point I miss to mention! I am using one computing node with Linux system. I tried with UGER firstly (although it seems not right) and then I tried with CPU but there is no scripts subdirectory within the CPU directory. So I don’t know how to deal with that… Could you please offer another valuable suggestions?

Thank you very much and looking forward to your generous replies! : )

Regards,

Zihua



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Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab
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