I have used Trimmomatic-0.39 few times already for trimming some sequencing data. This time I tried the option -baseout as stated in the manual but it does not recognise it as a valid option and the command does not run. If I run the command, as I usually I do with all the output files listed, it works though.
I type in the command line:
java -jar trimmomatic-0.39.jar PE -phred33 -trimlog trimmed_file18_log.log -baseout file18.fastq.gz file18-R1.fastq.gz file18-R2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 MAXINFO:25:0.2 MINLEN:20
What I get back is:
Unknown option -baseout file18.fastq.gz
Usage:
PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or: .....
I get back the same error message even if I move the '-baseout file18.fastq.gz' option after '...jar PE' and before the list of all the other options.
Related
I have created a unix script to be executed after the session finished.
The script basically counts the lines of specific file and then creates a trailer with this specific structure:
T000014800000000000000000000000000000
T - for trailer
0000148 - number of lines
00000000000000000000000000000 - filler
I have tested the script in Mac, I know already that environments are totally different, but I want to know what is needed to be changed in order to execute this script successfully in IPC.
After execution I get the following error message:
The shell command failed with exit code 126.
I invoke the script as follows:
sh -c "$PMRootDir/scripts/exec_trailer_unix.sh $PMRootDir/TgtFiles"
#! /bin/sh
TgtFiles=$1
TgtFilesBody=$TgtFiles/body.txt
TgtFilesTrailer=$TgtFiles/trailer.txt
string1=$(sed -n '$=' $TgtFilesBody)
pad=$(printf '%0.1s' "0"{1..8})
padlength=8
string2='T'
string3=$(printf '%s%*.*s%s\n' "$string2" 0 $((padlength - ${#string1} - ${#string2} )) "$pad" "$string1")
string4='00000000000000000000000000000'
string5=$(printf '%s%*.*s%s\n' "$string3" 0 $((${#string3} - ${#string4} )) "$string4")
echo $string5 > $TgtFilesTrailer
Any idea would be great.
Thanks in advance.
Please check below points.
it looks like permission issue. Please login using informatica user(the user that runs infa demon) and run this command. You should be able to get the errors.
sh -c "$PMRootDir/scripts/exec_trailer_unix.sh $PMRootDir/TgtFiles"
Sometime the server variable $PMRootDir in UNIX doesnt get interpreted and can result null value. Please use echo $PMRootDir to check if its working after logging into UNIX using above user.
You can create trailer file using Infa easily.
Just add an aggregator transformation right before actual target( group by a dummy field to calculate count(*)). Then add an expression transformation to create those strings. And then trailer file target. Just 3 more transformations.
| --> AGG --> EXP --> Trailer Target file
Final Tr --|--> Final Target
I use the Linux kernel style in my C code, even though it's not related to the kernel. Running checkpatch.pl produces ERROR: Missing Signed-off-by: line(s). How to ignore it?
To intentionally silence the ERROR: Missing Signed-off-by: line(s) one can pass the --no-signoff parameter, e.g.:
git show | checkpatch.pl --no-tree --no-signoff
This can also be added on a new line to the .checkpatch.conf file to avoid having to type it.
All, I am running the following script to load the data on to the Oracle Server using unix box and sqlldr. Earlier it gave me an error saying sqlldr: command not found. I added "SQLPLUS < EOF", it still gives me an error for unexpected end of file syntax error on line 12 but it is only 11 line of code. What seems to be the problem according to you.
#!/bin/bash
FILES='ls *.txt'
CTL='/blah/blah1/blah2/name/filename.ctl'
for f in $FILES
do
cat $CTL | sed "s/:FILE/$f/g" >$f.ctl
sqlplus ID/'PASSWORD'#SERVERNAME << EOF sqlldr SCHEMA_NAME/SCHEMA_PASSWORD control=$f.ctl data=$f EOF
done
sqlplus will never know what to do with the command sqlldr. They are two complementary cmd-line utilities for interfacing with Oracle DB.
Note NO sqlplus or EOF etc required to load data into a schema:
#!/bin/bash
#you dont want this FILES='ls *.txt'
CTL_PATH=/blah/blah1/blah2/name/'
CTL_FILE="$CTL_PATH/filename.ctl"
SCHEMA_NM=SCHEMA_NAME
SCHEMA_PSWD=SCHEMA_PASSWORD
for f in *.txt
do
# don't need cat! cat $CTL | sed "s/:FILE/$f/g" >"$f".ctl
sed "s/:FILE/$f/g" "$CTL_FILE" > "$CTL_PATH/$f.ctl"
#myBad sqlldr "$SCHEMA_NAME/$SCHEMA_PASSWORD" control="$CTL_PATH/$f.ctl" data="$f"
sqlldr $SCHEMA_USER/$SCHEMA_PASSWORD#$SERVER_NAME control="$CTL_PATH/$f.ctl" data="$f" rows=10000 direct=true errors=999
done
Without getting too philosophical, using assignments like FILES=$(ls *.txt) is a bad habit to get into. By contrast, for f in *.txt will deal correctly for files with odd characters in them (like spaces or other syntax breaking values). BUT the other habit you do want to get into is to quote all variable references (like $f), with dbl-quotes : "$f", OK? ;-) This is the otherside of protection for files with spaces etc embedded in them.
In the edit update, I've varibalized your CTL_PATH and CTL_FILE. I think I understand your intent, that you have 1 std CTL_FILE that you pass thru sed to create a table specific .ctl file (a good approach in my experience). Note that you don't need to use cat to send a file to sed, but your use to create a altered file via redirection (> $f.ctl) is very shell-like too.
In 2nd edit update, I looked here on S.O. and found an example sqlldr cmdline that has the correct syntax and have modified to work with your variable names.
To finish up,
A. Are you sure the Oracle Client package is installed on the machine
that you are running your script on?
B. Is the /path/to/oracle/client/tools/bin included in your working
$PATH?
C. try which sqlldr. If you don't get anything, either its not
installed or its not in the path.
D. If not installed, you'll have to get it installed.
E. Once installed, note the directory that contains the sqlldr cmd.
find / -name 'sqlldr*' will take a long time to run, but it will
print out the path you want to use.
F. Take the "path" part of what is returned (like
/opt/oracle/11.2/client/bin/ (but not the sqlldr at the end), and
edit script at 2nd line with
(Txt added to appease the S.O. Formatter ;-) )
export ORCL_PATH="/path/you/found/to/oracle/client"
export PATH="$ORCL_PATH:$PATH"
These steps should solve any remaining issues. If this doesn't work, see if there is someone where you work that understands your local computing environment that can help explain any missing or different steps.
IHTH
Here is a basic script with getopt command and assigned variables.
If someone were to type in
MyScript -a
with no words or numbers added after the -a, then an error message would pop up! The same happens if you replace -a with any other assigned variables. If I wanted no error message to appear, how would I go about doing this?
Hints/advice is preferred over a simply strict answer!
From the bash manual:
getopts can report errors in two ways. If the first character of optstring is a colon, silent error reporting is used. In normal operation diagnostic messages are printed when invalid options or missing option arguments are encountered. If the variable OPTERR is set to 0, no error messages will be displayed, even if the first character of optstring is not a colon.
Since you tag the question with Unix and don't mention bash, you may or may not be so lucky, but the answer is to read the manual page carefully.
It's a bit annoying that when I hit a break point in XCode 4, values of Watch Expressions are always grayed out. I have to create dummy variables pointing to the thing I want to watch in order to get around it.
The log says the following errors when I run the app:
warning: Unable to read symbols for /Developer/Platforms/iPhoneOS.platform/DeviceSupport/4.3.3 (8J2)/Symbols/System/Library/Frameworks/IOKit.framework/IOKit (file not found).
warning: Tried to remove a non-existent library: /Developer/Platforms/iPhoneOS.platform/DeviceSupport/4.3.3 (8J2)/Symbols/System/Library/Frameworks/IOKit.framework/IOKit
Current language: auto; currently objective-c++
warning: Unable to read symbols for /Developer/Platforms/iPhoneOS.platform/DeviceSupport/4.3.3 (8J2)/Symbols/Developer/usr/lib/libXcodeDebuggerSupport.dylib (file not found).
How can I fix this?
As for myself, I debug variables using two handy GDB console commands. You can enter them when in debug mode in debug console after GDB mark. I use "p" command for printing basic C type variables:
p [[[self pointerToMyClass] anotherPointerToOtherClass] someIntValue]
And I use "po" command for printing content of arrays, for checking objects:
po [[[self pointerToMyClass] anotherPointerToOtherClass] someNSArray]
po [[[self pointerToMyClass] anotherPointerToOtherClass] myUIImageView]