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Makefile not able to run in one go #1
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Dear Citu, |
Dear Najla, rsat_user@cde778d90cbd:~/rsat_results$ make -f peak-motifs.mk all Thanks in advance |
Hi Citu, Thanks |
Hi Najal, Thanks |
Thanks @Citugulia40 , I have tested the container running Docker version 20.10.6, build 370c289 in two hosts: This is apparently related to the way arguments to scripts are handled by the shell within the container. We will investigate and produce a new container, but this will take us some time. Our only suggestion for the moment is to run it in Ubuntu, hope this helps, |
In your running container, if you type ps, which shell is running? |
Thank you so much. |
I have another question regarding de novo motif discovery using RSAT-peak motifs. I have a set of co-expressed genes and I have used your pipeline to discover de novo motifs in my genes of interest but I am not getting any significant motif in my gene list. Can you please recommend me any parameter that can be changed to get statistical significant motifs in my set of genes. |
Hi Citu,
|
Thanks.
|
Hi, Thanks in advance |
Good morning @Citugulia40 , at this point I have 2 suggestions:
Please let us know how that goes, |
Hi
I am using docker image for analysis. But Makefile is not running in one go, it is stopping after first step.
rsat_user@cde778d90cbd:~/rsat_results$ make -f peak-motifs.mk
Creating the result directories
Retrieving 4 upstream sequences boundaries from the genes of module M11
~/rsat_results/upstream1/regulonM11_up1.rm.fna
~/rsat_results/upstream2/regulonM11_up2.rm.fna
~/rsat_results/upstream3/regulonM11_up3.rm.fna
~/rsat_results/upstream4/regulonM11_up4.rm.fna
Retrieving 4 upstream sequences boundaries from all Prunus persica genome
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