I am checking to see if a process on a remote server has been killed. The code I'm using is:
if [ `ssh -t -t -i id_dsa headless#remoteserver.com "ps -auxwww |grep pipeline| wc -l" | sed -e 's/^[ \t]*//'` -lt 3 ]
then
echo "PIPELINE STOPPED SUCCESSFULLY"
exit 0
else
echo "PIPELINE WAS NOT STOPPED SUCCESSFULLY"
exit 1
fi
However when I execute this I get:
: integer expression expected
PIPELINE WAS NOT STOPPED SUCCESSFULLY
1
The actual value returned is "1" with no whitespace. I checked that by:
vim <(ssh -t -t -i id_dsa headless#remoteserver.com "ps -auxwww |grep pipeline| wc -l" | sed -e 's/^[ \t]*//')
and then ":set list" which showed only the integer and a line feed as the returned value.
I'm at a loss here as to why this is not working.
If the output of the ssh command is truly just an integer preceded by optional tabs, then you shouldn't need the sed command; the shell will strip the leading and/or trailing whitespace as unnecessary before using it as an operand for the -lt operator.
if [ $(ssh -tti id_dsa headless#remoteserver.com "ps -auxwww | grep -c pipeline") -lt 3 ]; then
It is possible that result of the ssh is not the same when you run it manually as when it runs in the shell. You might try saving it in a variable so you can output it before testing it in your script:
result=$( ssh -tti id_dsa headless#remoteserver.com "ps -auxwww | grep -c pipeline" )
if [ $result -lt 3 ];
The return value you get is not entirely a digit. Maybe some shell-metacharacter/linefeed/whatever gets into your way here:
#!/bin/bash
var=$(ssh -t -t -i id_dsa headless#remoteserver.com "ps auxwww |grep -c pipeline")
echo $var
# just to prove my point here
# Remove all digits, and look wether there is a rest -> then its not integer
test -z "$var" -o -n "`echo $var | tr -d '[0-9]'`" && echo not-integer
# get out all the digits to use them for the arithmetic comparison
var2=$(grep -o "[0-9]" <<<"$var")
echo $var2
if [[ $var2 -lt 3 ]]
then
echo "PIPELINE STOPPED SUCCESSFULLY"
exit 0
else
echo "PIPELINE WAS NOT STOPPED SUCCESSFULLY"
exit 1
fi
As user mbratch noticed I was getting a "\r" in the returned value in addition to the expected "\n". So I changed my sed script so that it stripped out the "\r" instead of the whitespace (which chepner pointed out was unnecessary).
sed -e 's/\r*$//'
Related
I have a shell script that works well if I just run it from command line. When I call it from a rule within snakemake it fails.
The script runs a for loop over a file of identifiers and uses those to grep the sequences from a fastq file followed by multiple sequence alignment and makes a consensus.
Here is the script. I placed some echo statements in there and for some reason it doesn't call the commands. It stops at the grep statement.
I have tried adding set +o pipefail; in the rule but that doesn't work either.
#!/bin/bash
function Usage(){
echo -e "\
Usage: $(basename $0) -r|--read2 -l|--umi-list -f|--outfile \n\
where: ... \n\
" >&2
exit 1
}
# Check argument count
[[ "$#" -lt 2 ]] && Usage
# parse arguments
while [[ "$#" -gt 1 ]];do
case "$1" in
-r|--read2)
READ2="$2"
shift
;;
-l|--umi-list)
UMI="$2"
shift
;;
-f|--outfile)
OUTFILE="$2"
shift
;;
*)
Usage
;;
esac
shift
done
# Set defaults
# Check arguments
[[ -f "${READ2}" ]] || (echo "Cannot find input file ${READ2}, exiting..." >&2; exit 1)
[[ -f "${UMI}" ]] || (echo "Cannot find input file ${UMI}, exiting..." >&2; exit 1)
#Create output directory
OUTDIR=$(dirname "${OUTFILE}")
[[ -d "${OUTDIR}" ]] || (set -x; mkdir -p "${OUTDIR}")
# Make temporary directories
TEMP_DIR="${OUTDIR}/temp"
[[ -d "${TEMP_DIR}" ]] || (set -x; mkdir -p "${TEMP_DIR}")
#RUN consensus script
for f in $( more "${UMI}" | cut -f1);do
NAME=$(echo $f)
grep "${NAME}" "${READ2}" | cut -f1 -d ' ' | sed 's/#M/M/' > "${TEMP_DIR}/${NAME}.name"
echo subsetting reads
seqtk subseq "${READ2}" "${TEMP_DIR}/${NAME}.name" | seqtk seq -A > "${TEMP_DIR}/${NAME}.fasta"
~/software/muscle3.8.31_i86linux64 -msf -in "${TEMP_DIR}/${NAME}.fasta" -out "${TEMP_DIR}/${NAME}.muscle.fasta"
echo make consensus
~/software/EMBOSS-6.6.0/emboss/cons -sequence "${TEMP_DIR}/${NAME}.muscle.fasta" -outseq "${TEMP_DIR}/${NAME}.cons.fasta"
sed -i 's/n//g' "${TEMP_DIR}/${NAME}.cons.fasta"
sed -i "s/EMBOSS_001/${NAME}.cons/" "${TEMP_DIR}/${NAME}.cons.fasta"
done
cat "${TEMP_DIR}/*.cons.fasta" > "${OUTFILE}"
Snakemake rule:
rule make_consensus:
input:
r2=get_extracted,
lst="{prefix}/{sample}/reads/cell_barcode_umi.count"
output:
fasta="{prefix}/{sample}/reads/fasta/{sample}.R2.consensus.fa"
shell:
"sh ./scripts/make_consensus.sh -r {input.r2} -l {input.lst} -f {output.fasta}"
Edit Snakemake error messages I changed some of the paths to a neutral filepath
RuleException:
CalledProcessError in line 29 of ~/user/scripts/consensus.smk:
Command ' set -euo pipefail; sh ./scripts/make_consensus.sh -r ~/user/file.extracted.fastq -l ~/user/cell_barcode_umi
.count -f ~/user/file.consensus.fa ' returned non-zero exit status 1.
File "~/user/scripts/consensus.smk", line 29, in __rule
_make_consensus
File "~/user/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
If there are better ways to do this than using a shell for loop please let me know!
thanks!
Edit
Script ran as standalone: first grep
grep AGGCCGTTCT_TGTGGATG R_extracted/wgs_5_OL_debug.R2.extracted.fastq | cut -f1 -d ' ' | sed 's/#M/M/' > ./fasta/temp/AGGCCGTTCT_TGTGGATG.name
Script ran through snakemake: first 2 grep statements
grep :::::::::::::: R_extracted/wgs_5_OL_debug.R2.extracted.fastq | cut -f1 -d ' ' | sed 's/#M/M/' > ./fasta/temp/::::::::::::::.name
I'm now trying to figure out where those :::: in snakemake are coming from. All ideas welcome
It stops at the grep statement
My guess is that the grep command in make_consensus.sh doesn't capture anything. grep returns exit code 1 in such cases and the non-zero exit status propagates to snakemake. (see also Handling SIGPIPE error in snakemake)
Loosely related... There is an inconsistency between the shebang of make_consensus.sh that says the script should be executed with bash (#!/bin/bash) and the actual execution using sh (sh ./scripts/make_consensus.sh). (In practice it shouldn't make any difference since sh is probably redirected to bash anyway)
I have a issue with my Script, i am just trying to fingure out if my screen session is running or not (line 19).
The rest of the script is working.
#!/bin/bash
echo $PATH // /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
echo "0"
content=$(wget http://interwebs.com/index.php?page=count -q -O -)
z=$(($content / 5))
z=$(($z + 1))
echo $z // 4
lockfile=/var/tmp/mylock
if ( set -o noclobber; echo "$$" > "$lockfile") 2> /dev/null; then
trap 'rm -f "$lockfile"; exit $?' INT TERM EXIT
# do stuff here
x=1
count=0
while [ $x -le $z ]
do
$req ="$(ps -ef | grep -i mystatus$count | grep -v grep)"
if [ "$req" = "" ]; then
# run bash script
screen -amds mystatus$count /usr/bin/wget --spider interwebs.com/index.php?page=cronwhatsoever$(( $count +1))-$(( $count +5))
else
echo "Cron running"
fi
x=$(( $x + 1 ))
count=$(( $count +5))
done
# clean up after yourself, and release your trap
rm -f "$lockfile"
trap - INT TERM EXIT
else
echo "Lock Exists: $lockfile owned by $(cat $lockfile)"
fi
sleep 15
It returns line 19: =: command not found. Actually running:
ps -ef | grep -i bukkit | grep -v grep
Works without issues if i run it directly in my Terminal, so any idea how to solve this issue?
I guess it something PATH related but grep is located in /bin/grep.
$req ="$(ps -ef | grep -i mystatus$count | grep -v grep)"
should be
req="$(ps -ef | grep -i mystatus$count | grep -v grep)"
Don't use $ on the left-hand side of an assignment, and you must not have spaces around the =
I have this bash script:
How I can call it the grep's output in the if else statement? If I suppress the output of the grep command with -q, also will work?
#!/usr/bin/env bash
DOMAINS=( '.com' '.biz' )
while read input; do
for (( i=0;i<${#DOMAINS[#]};i++)); do
jwhois --force-lookup --disable-cache --no-redirect -c jwhois.conf "$input${DOMAINS[$i]}" | MATCH="$(grep -oPa '^.*\b(clientTransferProhibited)\b.*$')"
if [ $? -eq 0 ]; then
echo -e "$input${DOMAINS[$i]}\tregistered\t" $(date +%y/%m/%d_%H:%M:%S) "\t" "$MATCH" |& tee --append output/registered.txt
else
echo -e "$input${DOMAINS[$i]}\tavailable\t" $(date +%y/%m/%d_%H:%M:%S) "\t" "$MATCH" |& tee --append output/available.txt
fi
done
done < "$1"
So MATCH="$(grep -oPa '^.*\b(clientTransferProhibited) used by "$MATCH" in the if else statement not outputting anything, but if I just use grep -oPa '^.*\b(clientTransferProhibited), it's printing the line without problem. The reason why I want to use as a variable, because I want to put in specific places in the if else statements.
Actual output:
$ domain1.com available 15/11/16_14:13:05
$ domain1.biz available 15/11/16_14:13:05
$ domain2.com registered 15/11/16_14:13:05
$ domain2.biz registered 15/11/16_14:13:05
Output that I want:
$ domain1.com available 15/11/16_14:13:05
$ domain1.biz available 15/11/16_14:13:05
$ domain2.com registered 15/11/16_14:13:05 Status: clientTransferProhibited http://www.icann.org/epp#clientTransferProhibited
$ domain2.biz registered 15/11/16_14:13:05 Status: clientTransferProhibited http://www.icann.org/epp#clientTransferProhibited
So the result of this line is what you want stored in a variable...
jwhois --force-lookup --disable-cache --no-redirect -c jwhois.conf "$input${DOMAINS[$i]}" | grep -oPa '^.*\b(clientTransferProhibited)\b.*$'
In that case, you want to evaluate that line and set the entire thing to your desired variable. The type of assignment you attempt in the middle of a pipeline will not be valid.
MATCH=$(jwhois --force-lookup --disable-cache --no-redirect -c jwhois.conf "$input${DOMAINS[$i]}" | grep -oPa '^.*\b(clientTransferProhibited)\b.*$')
Those are two different MATCH variables, because pipes execute subshells:
Bash subshell/pipelines - which parts are executing in subshells?
Try it this way instead:
MATCH="$(jwhois --force-lookup --disable-cache --no-redirect -c jwhois.conf "$input${DOMAINS[$i]}" | grep -oPa '^.*\b(clientTransferProhibited)\b.*$')"
I've written the bash script (searchuser) which should display all the users who are executing a specific program or a script (at least a bash script). But when searching for scripts fails because the command the SO is executing is something like bash scriptname.
This script acts parsing the ps command output, it search for all the occurrences of the specified program name, extracts the user and the program name, verifies if the program name is that we're searching for and if it's it displays the relevant information (in this case the user name and the program name, might be better to output also the PID, but that is quite simple). The verification is accomplished to reject all lines containing program names which contain the name of the program but they're not the program we are searching for; if we're searching gedit we don't desire to find sgedit or gedits.
Other issues I've are:
I would like to avoid the use of a tmp file.
I would like to be not tied to GNU extensions.
The script has to be executed as:
root# searchuser programname <invio>
The script searchuser is the following:
#!/bin/bash
i=0
search=$1
tmp=`mktemp`
ps -aux | tr -s ' ' | grep "$search" > $tmp
while read fileline
do
user=`echo "$fileline" | cut -f1 -d' '`
prg=`echo "$fileline" | cut -f11 -d' '`
prg=`basename "$prg"`
if [ "$prg" = "$search" ]; then
echo "$user - $prg"
i=`expr $i + 1`
fi
done < $tmp
if [ $i = 0 ]; then
echo "No users are executing $search"
fi
rm $tmp
exit $i
Have you suggestion about to solve these issues?
One approach might looks like such:
IFS=$'\n' read -r -d '' -a pids < <(pgrep -x -- "$1"; printf '\0')
if (( ! ${#pids[#]} )); then
echo "No users are executing $1"
fi
for pid in "${pids[#]}"; do
# build a more accurate command line than the one ps emits
args=( )
while IFS= read -r -d '' arg; do
args+=( "$arg" )
done </proc/"$pid"/cmdline
(( ${#args[#]} )) || continue # exited while we were running
printf -v cmdline_str '%q ' "${args[#]}"
user=$(stat --format=%U /proc/"$pid") || continue # exited while we were running
printf '%q - %s\n' "$user" "${cmdline_str% }"
done
Unlike the output from ps, which doesn't distinguish between ./command "some argument" and ./command "some" "argument", this will emit output which correctly shows the arguments run by each user, with quoting which will re-run the given command correctly.
What about:
ps -e -o user,comm | egrep "^[^ ]+ +$1$" | cut -d' ' -f1 | sort -u
* Addendum *
This statement:
ps -e -o user,pid,comm | egrep "^\s*\S+\s+\S+\s*$1$" | while read a b; do echo $a; done | sort | uniq -c
or this one:
ps -e -o user,pid,comm | egrep "^\s*\S+\s+\S+\s*sleep$" | xargs -L1 echo | cut -d ' ' -f1 | sort | uniq -c
shows the number of process instances by user.
I have a script which is checking a key in one file against a key in another to see if it exists in both. However in the script the grep never returns anything has been found but on the command line it does.
#!/bin/bash
# First arg is the csv file of repo keys separated by line and in
# this manner 'customername,REPOKEY'
# Second arg is the log file to search through
log_file=$2
csv_file=$1
while read line;
do
customer=`echo "$line" | cut -d ',' -f 1`
repo_key=`echo "$line" | cut -d ',' -f 2`
if [ `grep "$repo_key" $log_file` ]; then
echo "1"
else
echo "0"
fi
done < $csv_file
The CSV file is formatted as follows:
customername,REPOKEY
and the log file is as follows:
REPOKEY
REPOKEY
REPOKEY
etc
I call the script by doing ./script csvfile.csv logfile.txt
Rather then checking output of grep command use grep -q to check its return status:
if grep -q "$repo_key" "$log_file"; then
echo "1"
else
echo "0"
fi
Also your script can be simplified to:
log_file=$2
csv_file=$1
while IFS=, read -r customer repo_key; do
if grep -q "$repo_key" "$log_file"; then
echo "1"
else
echo "0"
fi
done < "$csv_file"
use the exit status of the grep command to print 1 or 0
repo_key=`echo "$line" | cut -d ',' -f 2`
grep -q "$repo_key" $log_file
if [ $? -eq 1 ]; then
echo "1"
else
echo "0"
fi
-q supresses the output so that no output is printed
$? is the exit status of grep command 1 on successfull match and 0 on unsuccessfull
you can have a much simpler version as
grep -q "$repo_key" $log_file
echo $?
which will produce the same output