I'm trying to study fetal fraction by using a seqff script from here.
The instruction says that I need a headless sam file to work so after alignment with bwa, I process my sam file by using samtools:
samtools view -S -q 20 target.sam > treated.sam
This process also remove the #SG header since there is no reference file. I also use grep to remove header of the target.sam got after alignment for comparison. However, when I compare, I noticed that ENet calculation on the treated.sam returned with NA results, so half of the method to calculate fetal fraction of this script was gone.
I have tested it in multiple cases and it seems that without using samtools, the script worked well but with samtools Enet calculaton not worked. Can someone tell me what is wrong with the script?
I'm using R 4.0 and all modification I made to the script is on the args since it cannot recognize args I input with anymore.
Related
For an example, I have created some feature for automation testing using Behave login_account.feature and choose_product.feature. To run on a single feature, I use this command on the terminal behave -f behave_html_formatter:HTMLFormatter -i login_account.feature.
I want to run on multiple feature login_account.feature and choose_product.feature in one command on the terminal. Anyone, can you give me the example command to run multiple feature using Behave in one command on the terminal?
Thank you in advance.
I think there might be two issues:
I'm not sure if that's the way to run with that formatter. See behave-html-formatter docs for config and example. I can't trial myself as I don't want/need this formatter installed. I would suggest you worry about this after you understand how to run multiple features, which is where issue #2 comes in.
-i expects a single argument, which is a regular expression pattern.
Assuming you are in your features folder, just list the two features with space separator after the behave command:
behave login_account.feature choose_product.feature
Better still, you could use tags. This makes way more sense if you want to run more than the two files in your example. Add a tag at the top of each of the feature files you want to execute e.g. #runme.
Then execute only the ones having the preferred tag:
behave -t #runme
I ran
mpiexec -n $nprocs julia --project myfile.jl
on a cluster, where myfile.jl has the following form
using Distributed; using Dates; using JLD2; using LaTeXStrings
#everywhere begin
using SharedArrays; using QuantumOptics; using LinearAlgebra; using Plots; using Statistics; using DifferentialEquations; using StaticArrays
#Defining some other functions and SharedArrays to be used later e.g.
MySharedArray=SharedArray{SVector{Nt,Float64}}(Np,Np)
end
#sync #distributed for pp in 1:Np^2
for jj in 1:Nj
#do some stuff with local variables
for tt in 1:Nt
#do some stuff with local variables
end
end
MySharedArray[pp]=... #using linear indexing
println("$pp finished")
end
timestr=Dates.format(Dates.now(), "yyyy-mm-dd-HH:MM:SS")
filename="MyName"*timestr
#save filename*".jld2"
#later on, some other small stuff like making and saving a figure. (This does give an error "no method matching heatmap_edges(::Surface{Array{Float64,2}}, ::Symbol)" but I think that this is a technical thing about Plots so not very related to the bigger issue here)
However, when looking at the output, there are a few issues that make me conclude that something is wrong
The "$pp finished" output is repeated many times for each value of pp. It seems that this amount is actually equal to 32=$nprocs
Despite the code not being finished, "MyName" files are generated. It should be one, but I get a dozen of them with different timestr component
EDIT: two more things that I can add
the output of the different "MyName" files is not identical, but this is expected since random numbers are used in the inner loops. There are 28 of them, a number that I don't easily recognize except that its again close to the 32 $nprocs
earlier, I wrote that the walltime was exceeded, but this turns out not to be true. The .o file ends with "BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES ... EXIT CODE :9", pretty shortly after the last output file.
$nprocs is obtained in the pbs script through
#PBS -l select=1:ncpus=32:mpiprocs=32
nprocs= `cat $PBS_NODEFILE|wc -l`
As pointed out by adamslc on the Julia discourse, the proper way to use Julia on a cluster is to either
Start a session with one core from the job script, add more with addprocs() in the Julia script itself
Use more specialized Julia packages
https://discourse.julialang.org/t/julia-distributed-redundant-iterations-appearing/57682/3
I have a series of sequential directories to gather files from on a linux server that I am logging into remotely and processing from an R terminal.
/r18_060, /r18_061, ... /r18_118, /r18_119
Each directory is for the day of year the data was logged on, and it contains a series of files with standard prefix such as "fl.060.gz"
I have to supply a function that contains multiple system() commands with a linux glob for the day. I want to divide the year into 60-day intervals to make the QA/QC more manageable. Since I'm crossing from 099 - 100 in the glob, I have to use brace expansion to match the correct sequence of days.
ls -d /root_driectory/r18_{0[6-9]?,1[0-1]?}
ls -d /root_driectory/r18_{060..119}
All of these work fine when I manually input these globs into my bash shell, but I get an error when the system() function provides a similar command through R.
day_glob <- {060..119}
system(paste("zcat /root_directory/r_18.", day_glob, "/fl.???.gz > tmpfile", sep = "")
>gzip: cannot access '/root_directory/r18_{060..119}': No such file or directory
I know that this could be an error in the shell that the system() function operates in, but when I query that it gives the correct environment and user name
system("env | grep ^SHELL=")
>SHELL=/bin/bash
system("echo $USER")
>tgw
Does anyone know why this fails when it is passed through R's system() command? What can I do to get around this problem without removing the system call altogether? There are many scripts that rely on these functions, and re-writing the entire family of R scripts would be time prohibitive.
Previously I had been using 50-day intervals which avoids this problem, but I thought this should be something easy to change, and make one less iteration of my QA/QC scripts per year. I'm new to the linux OS so I figured I might just be missing something obvious.
Writing my first script with after effects to automate some of my process. I want the script to run at startup of AE with some arguments passed via command line so I use the -s command.
Everything is done except for one problem, when I run AfterFX.exe with the -s, for example if i do this:
"PATH_TO_ADOBE_CS6\Support Files\AfterFX.exe" -s "alert('foo')"
It opens after effects and i do get that 'foo' dialog but for some reason After Effects is 'disabled'. What I mean is I can't do anything, not open any project, nothing. all options are grayed out.
Note that if after effects is already running, and I run the command, it doesnt 'disable' after effects and I get the desired result.
I am using windows and after effects CS6.
note: obviously I intend to do something more complex than alert('foo') which was used a minimalist example to show my issue.
figure it out. for those who find this later, the solution is to add app.exitAfterLaunchAndEval = false.. i.e,
"PATH_TO_ADOBE_CS6\Support Files\AfterFX.exe" -s "app.exitAfterLaunchAndEval = false; alert('foo')"
So I am trying to compare a binary file I make when I compile with gcc to an sample executable that is provided. So I used the command diff and went like this
diff asgn2 sample-asgn2
Binary files asgn2 and sample-asgn2 differ
Is there any way to see how they differ? Instead of it just displaying that differ.
Do a hex dump of the two binaries using hexdump. Then you can compare the hex dump using your favorite diffing tool, like kdiff3, tkdiff, xxdiff, etc.
Why don't you try Vbindiff? It probably does what you want:
Visual Binary Diff (VBinDiff) displays files in hexadecimal and ASCII (or EBCDIC). It can also display two files at once, and highlight the differences between them. Unlike diff, it works well with large files (up to 4 GB).
Where to get Vbindiff depends on which operating system you are using. If Ubuntu or another Debian derivative, apt-get install vbindiff.
I'm using Linux,in my case,I need a -q option to just show what you got.
diff -q file1 file2
without -q option it will show which line is differ and display that line.
you may check with man diff to see the right option to use in your UNIX.
vbindiff only do byte-to-byte comparison. If there is just one byte addition/deletion, it will mark all subsequent bytes changed...
Another approach is to transform the binary files in text files so they can be compared with the text diff algorithm.
colorbindiff.pl is a simple and open-source perl script which uses this method and show a colored side-by-side comparison, like in a text diff. It highlights byte changes/additions/deletions. It's available on GitHub.