Juicer CPU

[remi.mo...@gmail.com]

Hello,

I am trying to run the CPU version of Juicer on my local machine but the program failed after creating the sam file.

Here is my command;

bash scripts/CPU/juicer.sh -g scW -z references/Scerevisiae_W303/Scerevisiae_W303.fna -p references/Scerevisiae_W303/scW.chrom.sizes -y references/Scerevisiae_W303/scW_DpnII.txt

And here is the result:

awk: fatal: can't open source file `/opt/juicer/scripts/common/chimeric_blacklist.awk' for reading (No such file or directory)
***! Failure during chimera handling of /media/remi/Disk1/Juicer/splits/AT147.pcrfree.fastq

There is actually no opt/ folder in my root folder so my best guess is that I missed something during the installation, but I don't know what.

Does anybody have an idea ?

Thanks !

[Neva Durand]

Hello,

You should modify where it looks for the scripts/ directory.  You can do so either by modifying the Juicer script directly or by sending in the "-D" flag.

Here's the Quick Start example:  https://github.com/theaidenlab/juicer/wiki/Installation#example-with-cpu-version

Here's the directory structure expected: https://github.com/theaidenlab/juicer/wiki/Installation#directory-structure

If you are sending in the reference and restriction site file, you don't need to worry about those for the directory structure, just the scripts.

Best

Neva

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[remi.mo...@gmail.com]

So just to be sure:

file chimeric_blacklist.awk is in this location

/media/remi/Disk1/Juicer/scripts/CPU/common/

Just adding "-D /media/remi/Disk1/Juicer" to my original command line should be enough ?

Thanks a lot !

Le lundi 4 juin 2018 17:50:33 UTC+2, Neva Durand a écrit :

Hello,

You should modify where it looks for the scripts/ directory.  You can do so either by modifying the Juicer script directly or by sending in the "-D" flag.

Here's the Quick Start example:  https://github.com/theaidenlab/juicer/wiki/Installation#example-with-cpu-version

Here's the directory structure expected: https://github.com/theaidenlab/juicer/wiki/Installation#directory-structure

If you are sending in the reference and restriction site file, you don't need to worry about those for the directory structure, just the scripts.

Best

Neva

On Mon, Jun 4, 2018 at 11:33 AM, <remi.mo...@gmail.com> wrote:

Hello,

I am trying to run the CPU version of Juicer on my local machine but the program failed after creating the sam file.

Here is my command;

bash scripts/CPU/juicer.sh -g scW -z references/Scerevisiae_W303/Scerevisiae_W303.fna -p references/Scerevisiae_W303/scW.chrom.sizes -y references/Scerevisiae_W303/scW_DpnII.txt

And here is the result:

awk: fatal: can't open source file `/opt/juicer/scripts/common/chimeric_blacklist.awk' for reading (No such file or directory)
***! Failure during chimera handling of /media/remi/Disk1/Juicer/splits/AT147.pcrfree.fastq

There is actually no opt/ folder in my root folder so my best guess is that I missed something during the installation, but I don't know what.

Does anybody have an idea ?

Thanks !

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[Neva Durand]

Yes, that should work.

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[remi.mo...@gmail.com]

I also had to move the directory common from CPU/ to scripts/ but after that it worked fine for me.

Thank you for your help.

Yes, that should work.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/e292773f-bd0c-4e54-b120-8e3e002cf1f1%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.