Using Python 3.8.1 code, I unzipped the distribution of postgresql12 in a specific folder of root C, inside the code it creates two other folders, data and log. In the code I write the following line to set up a first database:
subP = subprocess.run([link_initdb, "-U NewDataBase", "-A AlphaBeta", "-E utf8", "-D C:\\Database\\pgsql\\data"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8")
But I get the following error message:
ubP.stderr: initdb: error: could not create directory " C:": Invalid argument
I don't know what I'm wrong!
For whatever reason there should be no space between -D and the filename.
To solve it you can use:
subP = subprocess.run([
link_initdb,
"-U postgres",
"-A password",
"-E utf8",
"--pgdata=C:\Database\pgsql\data",
],
shell=True,
)
Related
I'm passing a command to powershell
Dim command As String
command = "ffmpeg -vsync 0 –hwaccel cuvid -c:v h264_cuvid –resize 1280x720 -i D:\Imagens\nova\bol.mkv -c:a copy -c:v h264_nvenc -b:v 5M D:\Imagens\nova\bol_encod.mkv"
with
Dim powerShell As String = "C:\Windows\System32\WindowsPowerShell\v1.0\powershell.exe"
Process.Start("powershell", "-noexit " + command)
but powershell returns
Unable to find a suitable output format for 'ÔÇôhwaccel' ÔÇôhwaccel:
Invalid argument
where I believe 'ÔÇôhwaccel' to be –hwaccel; That's completely strange, once when I past the code directly on PowerShell it works fine.
Is that a problem with my string?
thank you!
I'm assuming powershell 5 and not core, I copied the test and pasted it into the terminal and found this u instead of a '-'. I would start by retyping and avoiding what looks like it may be a long hyphen or something else which is breaking the terminal.
I am trying to launch spotfire application from VBA like following
Dim retval As Double
retval = Shell("Path\Spotfire.Dxp.exe", vbNormalFocus)
It works. It launches spotfire with the default servername,username and password
But I want to launch the application by giving the servername, username and password as parameters in the script. How do I do it?
I tried this
retval = Shell("Path\Spotfire.Dxp.exe -s http://spotfire.abcd.com -u ABCD\A7 -p ABC", vbNormalFocus)
But it launched the application with default parameters and gives error at the end "Unable to load file. Could not find the specified file : -s"
Please suggest the possible solution.
after checking our support db, I found a few references to / notation instead of -. so the following command should work:
c:\path\Spotfire.Dxp.exe /server:http://localhost:8080/ /username:user /password:pass
I have a folder with multiple sub-folders that each contain .fastq files(s) that I would like to align to a genome. I am trying to create a snakemake workflow for it. First I access each sub-directory and the files in them using wildcards. Then I use the expand function to store all the paths to the files and write a rule to map the files to the genome. The code is as follows:
from snakemake.io import glob_wildcards, expand
import sys
import os
directories, files = glob_wildcards("data/samples/{dir}/{file}.fastq")
print(directories, files)
rule all:
input:
expand("data/samples/{dir}/{file}.fastq", zip, dir=directories,
file=files)
rule bwa_map:
input:
G = "data/genome.fa",
r1 = expand("data/samples/{dir}/{file}.fastq", zip,
dir=directories, file=files)
output:
r2 = expand("data/results/{dir}/{file}.bam", zip, dir=directories,
file=files)
shell:
"./bwa mem {input.G} {input.r1} | ./samtools sort -o - > {output.r2}"
However, when I execute this code as "snakemake bwa_map", I get the following error:
Error in job bwa_map while creating output files data/results/SRR5923/A.bam, data/results/SRR5924/B.bam, data/results/SRR5925/C.bam.
RuleException:
CalledProcessError in line 19 of /Users/rewatitappu/PycharmProjects/RNA-seq_Snakemake/Snakefile:
Command './bwa mem data/genome.fa data/samples/SRR5923/A.fastq data/samples/SRR5924/B.fastq data/samples/SRR5925/C.fastq | ./samtools sort -o - > data/results/SRR5923/A.bam data/results/SRR5924/B.bam data/results/SRR5925/C.bam' returned non-zero exit status 1.
File "/Users/rewatitappu/PycharmProjects/RNA-seq_Snakemake/Snakefile", line 19, in __rule_bwa_map
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Removing output files of failed job bwa_map since they might be corrupted:
data/results/SRR5923/A.bam
Will exit after finishing currently running jobs.
Am I wrongly executing the snakemake command or could there be a problem with the code?
The error message suggests that the error occurred at the execution of the following shell command:
./bwa mem data/genome.fa data/samples/SRR5923/A.fastq data/samples/SRR5924/B.fastq data/samples/SRR5925/C.fastq | ./samtools sort -o - > data/results/SRR5923/A.bam data/results/SRR5924/B.bam data/results/SRR5925/C.bam
The problem could be caused by the fact that you have two bam files as output.
You probably shouldn't use expand in the bwa_map rule. The expand already took place in the all rule.
I wrote the below code, which will extract the directory name along with the file name and I will use purge command on that extracted Text.
$ sear VAXMANAGERS_ROOT:[PROC]TEMP.LIS LOG/out=VAXMANAGERS_ROOT:[DEV]FVLIM.TXT
$ OPEN IN VAXMANAGERS_ROOT:[DEV]FVLIM.TXT
$ LOOP:
$ READ/END_OF_FILE=ENDIT IN ABCD
$ GOTO LOOP
$ ENDIT:
$ close in
$ ERROR=F$EXTRACT(0,59,ABCD)
$ sh sym ERROR
$ purge/keep=1 'ERROR'
The output is as follows:
ERROR = "$1$DKC102:[PROD_LIVE.LOG]DP2017_TMP2.LIS;27392 "
Problem here is --- Every time the directory length varies (Length may be 59 or 40 or some other value, but the directory and filename length will not exceed 59 characters in my system). So in the above output, the system is also fetching the Version number of that file number. So I am not able to purge the file along with the version number.
%PURGE-E-PURGEVER, version numbers not permitted
Any suggestion -- How to eliminate the version number from the output ?
I cannot use the exact length of the directory, as directory length varies everytime.... :(
The answer with F$ELEMENT( 0, ";", ABCD ) should work, as confirmed. I might script something like this:
$ ERROR = F$PARSE(";",ERROR) ! will return $1$DKC102:[PROD_LIVE.LOG]DP2017_TMP2.LIS;
$ ERROR = ERROR - ";"
$ PURGE/KEEP=1 'ERROR'
Not sure why you have the read loop. What you will get is the last line in the file, but assuming that's what you want.
While HABO explained it, some more explanations
Suppose I use f$search to check if a file exists
a = f$search("sys$manager:net$server.log")
then I find I it exists
wr sys$output a
shows
SYS$SYSROOT:[SYSMGR]NET$SERVER.LOG;9
From the help of f$parse I get
help lex f$parse arg
shows, among other things
`Specifies a character string containing the name of a field
in a file specification. Specifying the field argument causes
the F$PARSE function to return a specific portion of a file
specification.
Specify one of the following field names (do not abbreviate):
NODE Node name
DEVICE Device name
DIRECTORY Directory name
NAME File name
TYPE File type
VERSION File version number`
So I can do
wr sys$output f$parse(a,,,"DEVICE")
which shows
SYS$SYSROOT:
and also
wr sys$output f$parse(a,,,"DIRECTORY")
so I get
[SYSMGR]
and
wr sys$output f$parse(a,,,"NAME")
shows
NET$SERVER
and
wr sys$output f$parse(a,,,"TYPE")
shows
.LOG
the version is
wr sys$output f$parse(a,,,"VERSION")
shown as
;9
The lexicals functions can be handy, check it using
help lexical
it shows
F$CONTEXT F$CSID F$CUNITS F$CVSI F$CVTIME F$CVUI F$DELTA_TIME F$DEVICE F$DIRECTORY F$EDIT
F$ELEMENT F$ENVIRONMENT F$EXTRACT F$FAO F$FID_TO_NAME F$FILE_ATTRIBUTES F$GETDVI F$GETENV
F$GETJPI F$GETQUI F$GETSYI F$IDENTIFIER F$INTEGER F$LENGTH F$LICENSE F$LOCATE F$MATCH_WILD
F$MESSAGE F$MODE F$MULTIPATH F$PARSE F$PID F$PRIVILEGE F$PROCESS F$READLINK F$SEARCH
F$SETPRV F$STRING F$SYMLINK_ATTRIBUTES F$TIME F$TRNLNM F$TYPE F$UNIQUE F$USER
I have a pig script where in the beginning I would like to generate a string of the dates of the past 7 days from a certain date (later used to retrieve log files for those days).
I attempt to do this with this line:
%declare CMD7 input= ; for i in {1..6}; do d=$(date -d "$DATE -i days" "+%Y-%m-%d"); input="\$input\$d,"; done; echo \$input
I get an error :
" ERROR 2999: Unexpected internal error. Error executing shell command: input= ; for i in {1..6}; do d=$(date -d "2012-07-10 -i days" "+%Y-%m-%d"); input="$input$d,"; done;. Command exit with exit code of 127"
however the shell command runs perfectly fine outside of pig. I am really not sure what is going wrong here.
Thank you!
I have got a working solution but not as streamlined as you want, essentially I don't manage to get Pig to execute a complex shell statement in the declare.
I first wrote a shell script (let's call it 6-days-back-from.sh):
#!/bin/bash
DATE=$1
for i in {1..6}; do d=$( date -d "$DATE -$i days" +%F ) ; echo -n "$d "; done
Then a pig script as follow (let's call it days.pig):
%declare my_date `./6-days-back-from.sh $DATE`
A = LOAD 'dual' USING PigStorage();
B = FOREACH A GENERATE '$my_date';
DUMP B
note that dual is a directory containing a text file with a single line of text, for the purpose of displaying our variable
I called the script as follow:
pig -x local -param DATE="2012-08-03" days.pig
and got the following output:
({(2012-08-02),(2012-08-01),(2012-07-31),(2012-07-30),(2012-07-29),(2012-07-28)})