Is it possible to export weka results after execute it via command line?
What I am doing:
java -cp "./weka.jar" weka.classifiers.bayes.NaiveBayes -t "iris.arff" -i
But then, I have all the statistics in console, is there any way to export this? Or I have to read and write by myself?
Thanks!
An example from the Weka Primer:
java -Xmx1024m weka.classifiers.trees.J48 -t data.arff -i -k -d J48-data.model >&! J48-data.out &
So no, WEKA doesn't have a specific output parameter on the command line, but you simply redirect the output and errors to a file using >&! or only the output without errors using >.
In your case you could use this command to save the output to the file NaiveBayes-iris.out:
java -cp "./weka.jar" weka.classifiers.bayes.NaiveBayes -t "iris.arff" -i > NaiveBayes-iris.out
Related
I have tried to submit the script below to HPC
#!/bin/bash
#PBS -N bwa_mem_tumor
#PBS -q batch
#PBS -l walltime=02:00:00
#PBS -l nodes=2:ppn=2
#PBS -j oe
sample=x
ref=absolute/path/GRCh38.p13.genome.fa
fwd=absolutepath/forward_read.fq.gz
rev=absolutepath/reverse_read.fq.gz
module load bio/samtools/1.9
bwa mem $ref $fwd $rev > $sample.tumor.sam && samtools view -S $sample.tumor.sam -b > $sample.tumor.bam && samtools sort $sample.tumor.bam > $sample.tumor.sorted.bam
However as an output I can get only the $sample.tumor.sam and log file says that
Lmod has detected the following error: The following module(s) are unknown:
"bio/samtools/1.9"
Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
$ module --ignore-cache load "bio/samtools/1.9"
Also make sure that all modulefiles written in TCL start with the string
#%Module
However when I input modeles avail it shows that bio/samtools/1.9 is on the list.
Also when i use the option module --ignore-cache load "bio/samtools/1.9"
the result is the same
If i try to continue working with the sam file and input manually the command line
samtools view -b RS0107.tumor.sam > RS0107.tumor.bam
it shows
[W::sam_read1] Parse error at line 200943
[main_samview] truncated file.
What's possibly wrong with the samtools module ir we with the script?
This question is in addition to the question asked here: https://unix.stackexchange.com/questions/163145/how-to-get-whole-command-line-from-a-process. On my system, the following command results in a PID (as expected):
CUDA_VISIBLE_DEVICES=4,5 python3 main.py 1> out.txt 2> err.txt &
Now, the methods in the stack exchange link above provide many solutions. However, when trying these solutions, I only receive the following information:
python3 main.py
Is there a way to return the entire command line "CUDA_VISIBLE_DEVICES=4,5 python3 main.py 1> out.txt 2> err.txt &", not just the portion "python3 main.py"?
No.
Assuming you're on a Linux system, you can find the individual bits, but you can't put it together.
Assume also that the process's PID is in $pid
The CUDA_VISIBLE_DEVICES=4,5 variable gets added to the environment of the python command. You can find it in /proc/$pid/environ but you can't tell which of those variables were specified on the command line: the user could have written
export CUDA_VISIBLE_DEVICES=4,5
python3 main.py 1> out.txt 2> err.txt &
The file redirections are available in /proc/$pid/fd:
/proc/$pid/fd/1 is a symbolic link to out.txt
/proc/$pid/fd/2 is a symbolic link to err.txt
I don't know how to tell if a process is running in the background.
Since you're just interested in the environment: with bash
declare -A environ
while IFS='=' read -r -d '' var value; do
environ["$var"]="$value"
done < /proc/$pid/environ
echo "process has CUDA_VISIBLE_DEVICE value ${environ[CUDA_VISIBLE_DEVICE]}"
So in the terminal, I can run my program with
./letter --stack -b ship -e shot -c --output W < input.txt > output.txt
How do I achieve the same functionality in Eclipse? I've figured out how to do --stack -b ship -e shot -c --output W by going to the arguments tab under Run configuration.
I've looked online and seen a lot of posts about using the Common tab to input and output redirection but I can't get it working. When I check only the input file, it doesn't work and the Debug perspective shows it's stuck somewhere trying to read from a stream. When I check allocate console and input file, then it gets stuck on user input (aka I can manually type stuff) in the console.
So how do I get < input.txt and by extension > output.txt working?
I understand that -i flag takes a file (which may contain list of URLs) and I know that -o followed by a name can be specified to rename a item being downloaded using wget.
example:
wget -i list_of_urls.txt
wget -o my_custom_name.mp3 http://example.com/some_file.mp3
I have a file that looks like this:
file name: list_of_urls.txt
http://example.com/some_file.mp3
http://example.com/another_file.mp3
http://example.com/yet_another_file.mp3
I want to use wget to download these files with the -i flag but also save each file as 1.mp3, 2.mp3 and so on.
Can this be done?
You can use any script language (PHP or Python) for generate batch file. In thin batch file each line will contains run wget with url and -O options.
Or you can try write cycle in bash script.
I ran a web search again and found https://superuser.com/questions/336669/downloading-multiple-files-and-specifying-output-filenames-with-wget
Wget can't seem to do it but Curl can with -K flag, the file supplied can contain url and output name. See http://curl.haxx.se/docs/manpage.html#-K
If you are willing to use some shell scripting then https://unix.stackexchange.com/questions/61132/how-do-i-use-wget-with-a-list-of-urls-and-their-corresponding-output-files has the answer.
When I run isql with a script file:
isql.exe -q -e -i %1 -o %~n1.log
Then in the output file I see commands, but the error of commands I see on the screen when it run.
The Error doesn't isn't written to the output file. Which command should I use so the errors are also written to the output file?
You have to use the -m(erge) command line switch in order to send the error messages into the output file.