Running Diploid

[H]

I am trying to run diploid.sh

But I am having issues when I run 

diploid.sh -g hg19 -s ~/Desktop/Juicer/GSE63525_GM12878_SNPs.txt

I also tried running 

diploid_1.sh -g /references/chrom.sizes -s ~/Desktop/Juicer/GSE63525_GM12878_SNPs.txt

and I get this error

No input file specified, reading from input stream

No such file or directory at /home/hiruy/Desktop/Juicer/scripts/diploid.pl line 79.

diploid.pl file is in the scripts folder and I am running the code inside the aligned folder where the merged_nodups.txt file is.

[Muhammad Saad Shamim]

Hey Hiruy!

Have you tried using the absolute file path for ~/Desktop/Juicer/GSE63525_GM12878_SNPs.txt

Also, are read permissions enabled for the SNP file?

Best,

- Muhammad Saad Shamim

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/f927c174-4d2e-449e-9ef3-05fc13fe33df%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[H]

Tried running 

diploid.sh -g hg19 -s /home/hiruy/Desktop/Juicer/GSE63525_GM12878_SNPs.txt 

and still get 

No input file specified, reading from input stream

No such file or directory at /home/hiruy/Desktop/Juicer/scripts/diploid.pl line 79.

-rwxrwxrwx  1 hiruy hiruy 27928087 Sep 16 16:26 GSE63525_GM12878_SNPs.txt

[Muhammad Saad Shamim]

Which juicer version are you running?

- Muhammad Saad Shamim

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/51a4ecb5-2878-4a08-b315-2b1be835783b%40googlegroups.com.

[H]

I think I am running Juicer version 1.5

Just checked the README.md in the main Juicer folder

[Muhammad Saad Shamim]

Which system? (CPU, SLURM, UGER, etc)

- Muhammad Saad Shamim

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/5a299082-a0e4-4a52-9d1c-9b2a6f55e4ae%40googlegroups.com.

[H]

CPU

[Muhammad Saad Shamim]

Hmm looks like CPU version may have the wrong file.

UGER:

https://github.com/theaidenlab/juicer/blob/master/UGER/scripts/diploid.sh

vs CPU:

https://github.com/theaidenlab/juicer/blob/master/CPU/common/diploid.sh

Can you check that the diploid.sh file on your computer looks more like the UGER version, and not the CPU one (from these links above).

This seems to be a bug / I've added it to the github issues list:

https://github.com/theaidenlab/juicer/issues/78

- Muhammad Saad Shamim

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/908737e9-8eb1-4918-9207-f4578c7400ee%40googlegroups.com.

[H]

It does not look like the UGER file at all. It looks exactly like the CPU diploid.sh

[Muhammad Saad Shamim]

Note that CPU version is still in beta, so it's possible diploid.sh for that is not available.

Looking into it.

- Muhammad Saad Shamim

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/581d64c0-9173-4277-86c1-4e71b0fdd175%40googlegroups.com.

[H]

Thank you.

Also on a side note, do I have to generate phased vcf files per experiment or can i use the vcf file that I downloaded from Rao 2014?

[Wanying Xu]

Hi,  can I ask a quick question? The SNP file you provided is annotated by the b37 or hg19?

Thanks!

To unsubscribe from this group and stop receiving emails from it, send an email to 3d-ge...@googlegroups.com.

[Neva Durand]

b37

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/bbd34862-904c-49a9-9aac-28ee12a2b6e1%40googlegroups.com.

--

Neva Cherniavsky Durand, Ph.D.

Pronouns: she, her, hers

Assistant Professor, Aiden Lab

www.aidenlab.org