I have a *.w file, referring to two include files ({incl\include_file.i}, {incl\do_something_file.i}). That first include-file contains the definition of a RECID variable "recordid":
DEF INPUT-OUTPUT PARAMETER recordid AS RECID.
I am capable to compile the *.w file, the listing file looks as follows: (just a fragment)
Prompt>findstr "recordid do_something" listing.txt
...
1 x DEF INPUT-OUTPUT PARAMETER recordid AS RECID.
...
1 x 1 {incl\do_something_file.i
2 x 1 INPUT-OUTPUT recordid
So, the compilation works. In top of that, I've checked the pairs of "&ANALYZE-SUSPEND" and "&ANALYZE-RESUME" clauses and everything is fine.
Nevertheless, I can't open the *.w file, as the mentioned RECID seems not to be known (errors 201 and 196).
Edit after first comments
This the exact error message I get while opening the *.w file, using the AppBuilder (I'm working with a Dutch version of the tool, hence the Dutch words in between):
---------------------------
Fout
---------------------------
This file cannot be analyzed by the AppBuilder.
Please check these problems in your file or environment:
** Onbekende veld- of variabelenaam - recordid. (201)
** .\incl\<do_something_file>.i Compilatiefout op regel 7. (196)
---------------------------
OK
---------------------------
Edit with more information on ANALYZE- clauses
I've launched following findstr command on my code with the following results:
Prompt>findstr /I "ANALYZE-RESUME ANALYZE-SUSPEND" <filename>.w
&ANALYZE-SUSPEND _VERSION-NUMBER ... GUI
&ANALYZE-RESUME
&ANALYZE-SUSPEND _UIB-CODE-BLOCK _CUSTOM _DEFINITIONS ...
&ANALYZE-RESUME
...
I confirm that the number of &ANALYZE-SUSPEND clauses equals the number of &ANALYZE-RESUME clauses, they are in the right sequence (first a SUSPEND and then a RESUME) and none of them is commented out.
Does anybody have an idea what's going wrong?
The problem was caused by an include, being outside of an suspend resume clause, in order to solve such a situation the following command might be useful:
findstr /I "ANALYZE {incl" <source_file>.w
The result should look like the following:
...
&ANALYZE-SUSPEND _UIB-CODE-BLOCK _CONTROL C-Win
&ANALYZE-RESUME
&ANALYZE-SUSPEND _UIB-CODE-BLOCK _CUSTOM _MAIN-BLOCK C-Win
{incl\something.i}
{incl\something_else.i}
&ANALYZE-RESUME
...
You see following rules:
The number of suspends and resumes must be equal.
Every suspend is to be closed by a resume.
Not one of those can be commented out.
It is advised to have includes between the suspend and the resume.
Related
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.
I have written a snakemake code to run bwa_map. Fastq files are with different folder name and different sample name (paired end). It shows error as 'SAMPLES' is not defined. Please help.
Error:
$snakemake --snakefile rnaseq.smk mapped_reads/EZ-123-B_IGO_08138_J_2_S101_R2_001.bam -np
*NameError in line 2 of /Users/singhh5/Desktop/tutorial/rnaseq.smk:
name 'SAMPLES' is not defined
File "/Users/singhh5/Desktop/tutorial/rnaseq.smk", line 2, in *
#SAMPLE DIRECTORY
fastq
Sample_EZ-123-B_IGO_08138_J_2
EZ-123-B_IGO_08138_J_2_S101_R1_001.fastq.gz
EZ-123-B_IGO_08138_J_2_S101_R2_001.fastq.gz
Sample_EZ-123-B_IGO_08138_J_4
EZ-124-B_IGO_08138_J_4_S29_R1_001.fastq.gz
EZ-124-B_IGO_08138_J_4_S29_R2_001.fastq.gz
#My Code
expand("~/Desktop/{sample}/{rep}.fastq.gz", sample=SAMPLES)
rule bwa_map:
input:
"data/genome.fa",
"fastq/{sample}/{rep}.fastq"
conda:
"env.yaml"
output:
"mapped_reads/{rep}.bam"
threads: 8
shell:
"bwa mem {input} | samtools view -Sb -> {output}"
The specific error you are seeing is because the variable SAMPLES isn't set to anything before you use it in expand.
Some other issues you may run into:
Output file is missing the {sample} wildcard.
The value of threads isn't passed into bwa or samtools
You should place your expand into the input directive of the first rule in your snakefile, typically called all to properly request the files from bwa_map.
You aren't pairing your reads (R1 and R2) in bwa.
You should look around stackoverflow or some github projects for similar rules to give you inspiration on how to do this mapping.
I'm trying to implement the touch command from the unix command line, but it seems that my last line throws an exception: ** Exception: ~/.todo: openFile: does not exist (No such file or directory)
main = touch "~/.todo"
touch :: FilePath -> IO ()
touch name = do
exists <- doesFileExist name
unless exists $ appendFile name ""
If there is any OS specific behavior, I'm testing from macOS Sierra.
I feel as if this error is strange in that the documentation for openFile states that
If the file does not exist and it is opened for output, it should be created as a new file.
Any suggestions as to how to fix this?
Edit: According to #chi, the touch command should always open the file, even if it already exists, because it will then update the file's last modified date.
touch :: FilePath -> IO ()
touch name = appendFile name ""
Use touchFile from the unix package (System.Posix.Files.ByteString).
appendFile name "" does not work like touch; appendFile is a no-op when the string to append is empty.
You can confirm this by running stat on the file before and after and comparing the modification times.
In the future please paste all the code you are using that creates the error. This includes both the imports and the invocation. In your case it seems you are running something with a shell expansion character:
*Main> touch "~/foobar"
*** Exception: ~/foobar: openFile: does not exist (No such file or directory)
The ~ is typically expanded by a shell (there also exists a C library that can do that rewriting for you). Most languages actually interpret that as a literal part of the path... but the ~ directory probably doesn't exist or that symbol might not even be valid depending on your platform.
Instead try a valid file path:
*Main> touch "/tmp/thisfile"
*Main>
Leaving GHCi.
% ls -l /tmp/thisfile
-rw-rw-r--. 1 theuser theuser 0 Feb 3 12:51 /tmp/thisfile
I've tried to find a table with the definition for each COMPSTAT (related to the tool Control-M workload Automation) return code but without any success.
Can anyone tell me if such a table exists?
Thank you.
It's the return code from whatever task was being executed at that time. By convention, a zero value means 'OK', and anything non-zero means an error of some kind.
Different utilities (i.e. external commands) have different possible return codes, so if the command were SCP then you would look up the code in the SCP documentation, and find that for example, '67' meant 'key exchange failed'.
There is no table that contains the definition of each COMPSTAT return code.
OSCOMPSTAT stand for Control-M Operating System Completion Status.
The value of COMPSTAT is set by the exit code of the command that was called.
Example:
After calling the command [cat file1.txt] the value of COMPSTAT will be:
0 if the file "file1.txt" is found
1 if the file "file1.txt" is not found
After calling the command [ctmfw] the value of COMPSTAT will be:
0 if the specified file is found
7 if the specified file is not found
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