I have a problem in running rnaseqtrinity, my command line is here:
/home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/
Trinity --seqType fq --max_memory 4G --left /home/marziyeh/Data/RNA-seq\ data/Main\ data/paired_32_L3_1_trimmed.fq.gz paired_33_L3_1_
trimmed.fq.gz --right paired_32_L3_2_trimmed.fq.gz paired_33_L3_2_trimmed.fq.gz --CPU 2 --output trinity_out_dir_32_32.fq.gz
but the following error occours:
Error, cannot locate file: paired_33_L3_1_trimmed.fq.gz at /home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/Trinity line
2429. main::create_full_path(ARRAY(0x555a78a86df0), 1) called at /home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/Trinity line
1159
Thanks so much for your suggestions.
Look, your pramater of --left have a fatal error .
You command line indicates that your reads is paired end. But your path of left read have some problems.
1. Your should use \ to instead of /.
2. Your command shouldn't have the space， and the space in linux means a delimiter.
Related
My Python 3.7.1 script generates a fasta file called
pRNA.sites.fasta
Within the same script, I call following system command:
cmd = "weblogo -A DNA < pRNA.sites.fasta > OUT.eps"
os.system(cmd)
print(cmd) #for debugging
I am getting the following error message and debugging message on the command line.
Error: Please provide a multiple sequence alignment
weblogo -A DNA < pRNA.sites.fasta > OUT.eps
"OUT.eps" file is generated but it's emtpy. On the other hand, if I run the following 'weblogo' command from the command line, It works just find. I get proper OUT.eps file.
$ weblogo -A DNA<pRNA.sites.fasta>OUT.eps
I am guessing my syntax for os.system call is wrong. Can you tell me what is wrong with it? Thanks.
Never mind. It turned out to be that I was not closing my file, "pRNA.sites.fasta" before I make system call that uses this file.
I am getting following error while executing sparkling-shell2.cmd bat file. I walked through and I am getting this error while executing spark-shell.cmd with following paramters
cd %TOPDIR%
%SPARK_HOME%/bin/spark-shell.cmd --jars %TOPDIR%/assembly/build/libs/%FAT_JAR% --driver-memory %DRIVER_MEMORY% --conf spark.driver.extraJavaOptions="-XX:MaxPermSize=384m" %*
Error: The input line is too long.
How do I solve this issue?
Thanks
In Windows the maximum length of command line is 260 characters and you are hitting the limit.
Your options are to change multiple of %DEF% operators into one single operator and reduce the overall length with some experimentation.
For example, I want to resize my partition under Ubuntu and use the command line tool: parted. Usually I need several steps to answer its questions.
root#intel-corei7-64:~# parted /dev/mmcblk0 resizepart 3 29000M
Warning: Not all of the space available to /dev/mmcblk0 appears to be used, you can fix the GPT to use all of the space (an extra 53420032 blocks) or continue with the current setting?
parted: invalid token: 3
Fix/Ignore? Fix
Partition number? 3
Warning: Partition /dev/mmcblk0p3 is being used. Are you sure you want to continue?
Yes/No? Yes
End? [3914MB]? 29000MB
Information: You may need to update /etc/fstab.
The first command line is parted /dev/mmcblk0 resizepart 3 29000M
Then I answer Fix for its first question. Then 3 for the 2nd question. Then Yes for the 3rd question. Then 29000MB for the last question.
I need to do all these steps automatically by one script, how to make such a script?
have you tried something like:
echo -e "Fix\n3\nYes\n29000MB" | parted /dev/mmcblk0 resizepart 3 29000M
This is my first ever post on stackoverflow, hope I don't break any rules. I'm a complete Linux newbie (installed Lubuntu 14.04 64bit last night) so be duly warned.
In short, I'm trying to get my laptop touchpad toggle to work (Fn+F3 on my Inspiron5110). I have a bash script:
#!/bin/bash
if [ $(synclient -l | grep TouchpadOff | awk '{print $3}') == 1 ] ; then
synclient touchpadoff=0;
else
synclient touchpadoff=1;
fi
I got it from http://crunchbang.org/forums/viewtopic.php?id=10996 . If I paste the script code in the terminal and execute it, it works (touchpad goes on/off). However, I want to bind it to a key so in my lubuntu-rc.xml I've added the following:
<!-- disable touchpad -->
<keybind key="XF86TouchpadToggle">
<action name="Execute">
<command>/usr/local/bin/touchpad.sh</command>
</action>
</keybind>
When I press the necessary key combo however I get "Failure to execute child process "/usr/local/bin/touchpad.sh" (No such file or directory)". However I can see in this directory, both in the file manager and when I use ls in the terminal that the file is there:
/usr/local/bin$ ls -l
total 4
-rwxrwxr-x 1 paspaldzhiev paspaldzhiev 145 юни 2 22:54 touchpad.sh
I used chmod +x touchpad.sh to make it executable.
Now, where this gets even more confusing:
If I use bash /usr/local/bin/touchpad.sh I get:
paspaldzhiev#areuexperienced:/usr/local/bin$ bash touchpad.sh
touchpad.sh: line 6: syntax error near unexpected token `fi'
touchpad.sh: line 6: `fi'
Though as I've said above I know for a fact that the code works if I just paste it in the terminal.
Further, if I use ./touchpad.sh I get :
paspaldzhiev#areuexperienced:/usr/local/bin$ ./touchpad.sh
bash: ./touchpad.sh: /bin/bash^M: bad interpreter: No such file or directory
Just to note that I'm not very sure what the difference between bash touchpad.sh and ./touchpad.sh is in terms of execution, it's just that my more Linux-savvy friends told me to try these :D.
In any case, I have no idea how to proceed henceforth, could anyone please shed a light on what I'm doing wrong?
Thank you very much!
The ^M in your last error msg is your big hint ; -). Somehow you have used a windows editor, file transfer or something. Try dos2unix touchpad.sh. It will remove all the CR (^M) chars from end of lines. It should work then. Good luck. – shellter
There is no need for script, since there is no need for if instruction.
Place this piece of code in your lubuntu-rc.xml
<keybind key="XF86TouchpadToggle">
<action name="Execute">
<command>synclient TouchpadOff=$((1-$(synclient | grep TouchpadOff | awk '{print $3}')))</command>
</action>
</keybind>
I'm trying to get PHP phar command line tool installed on my Debian VM, how here described:
(1) download the php-src, I assume it's in /tmp/php/src
(2) make the dir /tmp/phar
(3) Save this as /tmp/php-src/ext/phar/Makefile.
(4) cd /tmp/php-src/ext/phar
(5) run sudo make
Now after step 5 I get an error:
:/tmp/php-src/ext/phar# make
Makefile:11: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
As I know, there can be two possible causes for this error message:
Tabs in the make file. I've tested the file with od -t c Makefile. The file contains no tabs (\t).
It could be a bug of make v3.81 and need a patch or an upgrade to (yet instable: "Warning: This package is from the experimental distribution.") v3.82. I've downloaded and istalled (dpkg -i make_3.82-1_amd64.deb) it, but the error is still occuring.
What causes the error? How can it be avoided?
Thx
(Answered in a comment: See Question with no answers, but issue solved in the comments (or extended in chat))
#Beta wrote:
The line should begin with a tab, not a bunch of spaces.
The OP wrote:
I've replaced all 8-spaces sequences with tabs and can execute the make script now.
I used:
cat Makefile|sed "s/ /\t/" > Makefile