gabaldonlab / karyon Goto Github PK
View Code? Open in Web Editor NEWThis is the Karyon Pipeline
License: GNU General Public License v3.0
This is the Karyon Pipeline
License: GNU General Public License v3.0
Hi, I really like the nQuire plots included in this, and think those among the others could be really useful. I have the required files for the allplots.py script - vcf, pileup, etc - but cant get it working.
I am getting the following error message:
Traceback (most recent call last):
File "bin/allplots.py", line 100, in <module>
config_dict["KAT"][0],
KeyError: 'KAT'
I am running the following command:
python3 allplots.py \
-f redundans _reduced.fasta \
-v file.vcf -p file.mpileup \
-b file.bam \
-l library_to_make_fasta.fastq \
-o out_file
I have installed with both lightinstall.sh and install.sh and am getting the same message.
Can you help? I will try the docker image int he meantime, many thanks.
Hello,
I would like to use the pipeline for the mapping and variant calling, plotting but I would like to skip the first parts which are the assembly, reduction and proceed directly to the above steps. My assembly is already in a good state. However, bin/varcall_recipee.py does not come with documentation of the required arguments. Are the scripts also as a standalone version or does some one need to run the entire pipeline?
Thanks
Alex
Hello, I am trying to install karyon. I am installing it on a cluster environment (without admin rights or apt or apt-get) mostly using conda. I am running into small things I am able to resolve, but I thought I should keep track of them as it might be useful for you.
1 - 6. are just some small observations I run into while going through the manual and trying to get the plot done.
7. is something I would like to bring your attention to, because I am reviewing the manuscript right now and the software should work beforehand.
I think this line in the installation script should be
conda install -c bioconda -y sra-tools
instead. Because as it is, I am getting
conda install: error: argument -c/--channel: expected one argument
I installed GATK4 via conda instead
conda install -c bioconda gatk4
I think sudo chmod 777 nQuire
can be simply chmod 777 nQuire
(sudo in unnecessary)
At this point, I gave up on most of the software, because all I wanted to generate are the karyon plots for the already assembled genome. It would be handy to have a reduced installation procedure for people that would like to do the genome on their own.
Some parts of the manual pdf are not well typeset - some of the spaces in the code are not there and when one copy-pastes a bit, it will mess up the command. And oddly enough, only some parts of the manual file have this problem.
all_plots.py
in the manual should be allplots.py
(at least that's the name of a script). Furtheremore, the script requires -p <pileup>
file, while manual instruct to specify -m example.mpileup
file (thought -p example.mpileup
actually did the job). It also screamed when I tried to specify it 2 sequencing files (R1 and R2).
then I finally managed to get it run, but then I got
python3 install/karyon/bin/allplots.py -f data/reference/genome.fa -v freebayes_Afus1_raw.vcf -p Afus1.mpileup -b data/mapped_reads/Afus1.rg.sorted.rmdup.bam -l data/trimmed_reads/Afus1/ERR5959256-trimmed-pair1.fastq.gz -o data/Afus1/karyon_plots
Traceback (most recent call last):
File "/scratch/kjaron/install/karyon/bin/allplots.py", line 93, in <module>
allplots(window_size,
File "/scratch/kjaron/install/karyon/bin/karyonplots.py", line 496, in allplots
os.mkdir(kitchen)
FileNotFoundError: [Errno 2] No such file or directory: '/home/karyon/tmp/6X0UH5'
I have not installed all the components, I have just thoseI thought will be necessary for the analysis (nQuire and all the python libraries). This is something I would like to propose as well - could you perhaps create simpler installation instructions for people interested in the ploidy analysis and plots from existing assembly/vcf files?
Hi, i think that the nQuire ploidy/CN plots look great. Would you be able to pull them out as a standalone script i could use please?
Ive spent a lot of time trying to get the allplots.py script running but have had no luck yet.
Many thanks
Mike
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