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problem in install cellranger

Hello,

I am trying to install cellranger-3.1.0 in my server.

Thanks in advance for great help!

Best,

Yue

Welcome to Ubuntu 18.04.3 LTS (GNU/Linux 5.0.0-23-generic x86_64)


~/opt01/cellranger-3.1.0$ export PATH="/home/yli1/opt01/cellranger-3.1.0:$PATH"
~/opt01/cellranger-3.1.0$ cellranger
/home/yli1/opt01/cellranger-3.1.0
/home/yli1/opt01/cellranger-3.1.0/cellranger: line 31: /home/yli1/opt01/cellranger-3.1.0/../tenkit/bin/common/_master: No such file or directory
rna-seq
• 7,074 views • link
updated by Fatima Fatima • written by yueli7 yueli7

This seems like you've messed up your path somehow. On a new terminal, what does it say both before and after your export PATH line if you just type $PATH?

• 0 views • link
written by jared.andrews07 jared.andrews07

Hello, jared.andrews07,

Thank you so much for your response!

You are absolutely right!

What I can do at present stage?

Thank you in advance for your great help!

Best,

Yue

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ $PATH
-bash: /home/yli1/opt01/cellranger-3.1.0:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-
• 0 views • link
written by yueli7 yueli7

2 answers

You can use ls /tenkit/bin/common/ to see if the file (_master) is there. You can use chmod u+rx * -R in cellranger folder to give read and run permissions for all the files in the folder. Use ll command to see the current permissions.

There might be files missing from your folder. You can download the folder again. If you mention which link you used to download cellranger and what other commands you used prior to export path, it can be useful in finding the problem.

Also, try: 

export PATH=/opt01/cellranger-3.1.0:$PATH

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in

• 0 views • link
written by Fatima Fatima

Hello, Fatima,

Thank you so much for your kindly response!

Thank you in advance for your great help!

Is that possible I messed up my path?

Best,

Yue

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ $PATH
-bash: /home/yli1/opt01/cellranger-3.1.0:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/hom




yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ls /tenkit/bin/common/
ls: cannot access '/tenkit/bin/common/': No such file or directory
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ chmod u+rx * -R
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ll
total 60
drwxr-xr-x 9 yli1 yli1 4096 Feb  1 17:59 ./
drwxr-xr-x 4 yli1 yli1 4096 Feb  1 17:57 ../
-rwxr--r-- 1 yli1 yli1  661 Feb  1 17:58 builtwith.json*
-rwxr-xr-x 1 yli1 yli1  460 Feb  1 17:57 cellranger*
drwxr-xr-x 3 yli1 yli1 4096 Feb  1 17:59 cellranger-cs/
-rwxr-xr-x 1 yli1 yli1 1246 Feb  1 17:57 cellranger-shell*
drwxr-xr-x 3 yli1 yli1 4096 Feb  1 17:57 cellranger-tiny-fastq/
drwxr-xr-x 3 yli1 yli1 4096 Feb  1 17:57 cellranger-tiny-ref/
drwxr-xr-x 3 yli1 yli1 4096 Feb  1 17:57 lz4/
drwxr-xr-x 3 yli1 yli1 4096 Feb  1 17:58 martian-cs/
drwxr-xr-x 3 yli1 yli1 4096 Feb  1 17:57 miniconda-cr-cs/
-rwxr--r-- 1 yli1 yli1  200 Feb  1 17:59 product.json*
-rwxr--r-- 1 yli1 yli1 3014 Feb  1 17:57 sourceme.bash*
-rwxr--r-- 1 yli1 yli1 2199 Feb  1 17:58 sourceme.csh*
drwxr-xr-x 3 yli1 yli1 4096 Feb  1 17:58 STAR/
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ export PATH=/opt01/cellranger-3.1.0:$PATH
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ cellranger
/home/yli1/opt01/cellranger-3.1.0
/home/yli1/opt01/cellranger-3.1.0/cellranger: line 31: /home/yli1/opt01/cellranger-3.1.0/../tenkit/bin/common/_master: No such file or directory
• 0 views • link
written by yueli7 yueli7

what's the output of 

 cellranger sitecheck > sitecheck.txt
 cat sitecheck.txt

And

find -iname "_master"
• 0 views • link
written by Fatima Fatima

Hello, Fatima,

Thank you so much for your great help!

I think I messed up my path.

Same steps, I did well in my local PC, but have problems in remote computer.

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in

I did this command:

echo 'export PATH="/home/yli1/yard/apps/cellranger-3.0.2/cellranger":$PATH' >> ~/.bashrc
source ~/.bashrc

The remote computer always running, never stop.

    yli1@rsch-rnk-srv01:/bin$ bash
    cellranger: command not found
    cellranger: command not found
    cellranger: command not found
    cellranger: command not found
    cellranger: command not found


    bash: /usr/lib/command-not-found: Argument list too long
    bash: /usr/bin/lesspipe: Argument list too long
    bash: /usr/bin/dircolors: Argument list too long
    bash: /usr/lib/command-not-found: Argument list too long
    bash: /usr/bin/lesspipe: Argument list too long
    bash: /usr/bin/dircolors: Argument list too long

My path is messed.

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ $PATH
-bash: /home/yli1/opt01/cellranger-3.1.0:~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger





yli1@rsch-rnk-srv01:~$ /home/yli1/opt01/cellranger-3.1.0/cellranger testrun --id=tiny
/home/yli1/opt01/cellranger-3.1.0
/home/yli1/opt01/cellranger-3.1.0/cellranger: line 31: /home/yli1/opt01/cellranger-3.1.0/../tenkit       /bin/common/_master: No such file or directory


yli1@rsch-rnk-srv01:~$ cellranger sitecheck > sitecheck.txt
/home/yli1/opt01/cellranger-3.1.0/cellranger: line 31: /home/yli1/opt01/cellranger-3.1.0/../tenkit/bin/common/_master: No such file or directory


yli1@rsch-rnk-srv01:~$ cat sitecheck.txt
/home/yli1/opt01/cellranger-3.1.0


yli1@rsch-rnk-srv01:~$ find -iname "_master"
./opt01/cellranger-3.1.0/cellranger-cs/3.1.0/tenkit/bin/common/_master
• 0 views • link
written by yueli7 yueli7

I think the problem as another user suggested might be the PATH

Maybe you need to remove the wrong paths from ~/.bashrc and ~/.bash_profile?

The correct path is:

/home/yli1/opt01/cellranger-3.1.0
• 0 views • link
written by Fatima Fatima

Hello, Fatima,

You are absolutely right!

How I can remove the wrong paths from ~/.bashrc and ~/.bash_profile?

Thank you so much for your great help!

Really appreciate your time and help!

Best,

Yue

• 0 views • link
written by yueli7 yueli7

You can open them using vi

vi ~/.bashrc

Remove the wrong paths related to cellranger. Press ESC then type :wq enter to save and exit.

You can also use other apps emacs, vim, nano,...

Also check this link: https://askubuntu.com/a/833927

• 0 views • link
written by Fatima Fatima

Hello, Fatima,

Thank you so much!

My path is 

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$.

How I can make the change?

Really appreciate your help!

Best,

Yue

vi ~/.bashrc

export PATH="/home/yli1/yard/apps/cellranger-3.0.2/cellranger":$PATH
export PATH="/home/yli1/yard/apps/cellranger-3.0.2/cellranger":$PATH
export PATH="~/home/yli1/yard/apps/cellranger-3.1.0/cellranger":$PATH
export PATH="~/home/yli1/yard/apps/cellranger-3.1.0:$PATH"
export PATH="~/home/yli1/yard/apps/cellranger-3.1.0/cellranger":$PATH
export PATH="/home/yli1/yard/apps/cellranger-3.1.0/cellranger":$PATH
export PATH="/home/yli1/yard/apps/opt/cellranger-3.1.0/cellranger":$PATH
export PATH="~/yard/apps/opt/cellranger-3.1.0:$PATH" >> ~/.bashr
cellranger
source ~/.bashrc
cellranger
echo export PATH=~/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/opt/cellranger-   3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/opt/cellranger-3.1.0:/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/home/yli1/yard/apps/cellranger-3.1.0/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:/home/yli1/yard/apps/cellranger-3.0.2/cellranger:~/home/yli1/yard/apps/opt/cellranger-3.1.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
• 0 views • link
written by yueli7 yueli7

In Vi pess d to delete each line. Delete all the lines containing cellranger press ESC and then type :wq enter to save. Then use the export command only once and run cellranger again.

Correct path: /home/yli1/opt01/cellranger-3.1.0

You don't need to add the full path, let's stick to the instructions for now.

If your bashrc only contains the lines you posted here, instead of deleting those lines you can use this command 

echo "source ~/.bashrc" > ~./bashrc

> this character will overwrite therefore deleting the previous bashrc

>> this will append to the previous bashrc but you don't need it for this command. (so use this if you want to keep your old bashrc)

• 0 views • link
written by Fatima Fatima

Hello, Fatima,

Thank you so much for your detailed explanation!

Just as you said. I deleted all the lines containing cellranger , but the ESC botton does not work.

I only can do is ctrl+z, then: vi ~/.bashrc.

What I can do?

Thank you in advance for your great help

Best,

Yue

E325: ATTENTION
Found a swap file by the name "~/.bashrc.swp"
      owned by: yli1   dated: Mon Feb  3 11:28:38 2020
     file name: ~yli1/.bashrc
      modified: YES
     user name: yli1   host name: rsch-rnk-srv01
    process ID: 8019 (still running)
While opening file "/home/yli1/.bashrc"
         dated: Fri Jan 31 18:53:18 2020

(1) Another program may be editing the same file.  If this is the case,
be careful not to end up with two different instances of the same
file when making changes.  Quit, or continue with caution.
(2) An edit session for this file crashed.
If this is the case, use ":recover" or "vim -r /home/yli1/.bashrc"
to recover the changes (see ":help recovery").
If you did this already, delete the swap file "/home/yli1/.bashrc.swp"
to avoid this message.

Swap file "~/.bashrc.swp" already exists!
[O]pen Read-Only, (E)dit anyway, (R)ecover, (Q)uit, (A)bort: 




# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi
source ~/.bashrc
~                                                                                                     ~                                                                                                              ~
• 0 views • link
written by yueli7 yueli7

You can run these commands instead: 

rm -f ~/.bashrc.swp
rm -f ~/.bashrc 
echo "source ~/.bashrc" > ~/.bashrc
echo 'export PATH="/home/yli1/opt01/cellranger-3.0.2":$PATH' >> ~/.bashrc
echo 'export PATH="/home/yli1/opt01/cellranger-3.0.2/cellranger":$PATH' >> ~/.bashrc

You don't need to use vi for now, but here is a tutorial: https://ryanstutorials.net/linuxtutorial/vi.php

• 0 views • link
updated by jared.andrews07 jared.andrews07 • written by Fatima Fatima

Hello, Fatima,

Thank you so much for your quick response!

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ pwd
/home/yli1/opt01/cellranger-3.1.0
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ export PATH="home/yli1/opt01/cellranger-3.1.0:$PATH"
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ cellranger
/usr/bin/env: ‘bash’: No such file or directory

If I print vi ~/.bashrc,

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi
"~/.bashrc" [readonly] 117L, 3771C
• 0 views • link
written by yueli7 yueli7

Since ~/.bashrc is [readonly] you need to add write access 

chmod u+wx ~/.bashrc

Please don't forget the / before home in the path

echo "source ~/.bashrc" > ~/.bashrc
echo 'export PATH="/home/yli1/opt01/cellranger-3.0.2":$PATH' >> ~/.bashrc
echo 'export PATH="/home/yli1/opt01/cellranger-3.0.2/cellranger":$PATH' >> ~/.bashrc
cellranger

No need to run export PATH="/home/yli1/opt01/cellranger-3.1.0:$PATH" over and over again.

• 0 views • link
written by Fatima Fatima

Hello, Fatima,

Thank you for your kindly reply!

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ chmod u+wx ~/.bashrc
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ echo "source ~/.bashrc" > ~/.bashrc
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ echo 'export PATH="/home/yli1/opt01/cellranger-3.1.0":$PATH' >> ~/.bashrc
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ echo 'export PATH="/home/yli1/opt01/cellranger-3.1.0/cellranger":$PATH' >> ~/.bashrc
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ cellranger
/home/yli1/opt01/cellranger-3.1.0
/home/yli1/opt01/cellranger-3.1.0/cellranger: line 31: /home/yli1/opt01/cellranger-3.1.0/../tenkit/bin/common/_master: No such file or directory
• 0 views • link
written by yueli7 yueli7

Please forget about the PATH for now. I just downloaded cellranger to be able to help you better. I didn't export path for simplicity. I was able to run it using ./cellranger while in the cellranger-3.1.0 folder.

All I did was download using curl, tar -zxvf the downloaded file, cd to the folder, ./cellranger and it worked.

• 0 views • link
written by Fatima Fatima

If bash command doesn't work try exec bash

[fsharifi@fsharifi cellranger-3.1.0]$ ll
total 40
-rw------- 1 fsharifi   fsharifi 661 Jul 23  2019 builtwith.json
lrwxrwxrwx 1 fsharifi fsharifi    34 Jul 23  2019 cellranger -> cellranger-cs/3.1.0/bin/cellranger
drwx------ 3 fsharifi fsharifi    27 Jul 23  2019 cellranger-cs
-rwx------ 1 fsharifi fsharifi 1246 Jul 23  2019 cellranger-shell
drwx------ 3 fsharifi fsharifi   27 Jul 23  2019 cellranger-tiny-fastq
drwx------ 3 fsharifi fsharifi   27 Jul 23  2019 cellranger-tiny-ref
drwx------ 3 fsharifi fsharifi    30 Jul 23  2019 lz4
drwx------ 3 fsharifi fsharifi    28 Jul 23  2019 martian-cs
drwx------ 3 fsharifi fsharifi    48 Jul 23  2019 miniconda-cr-cs
-rw------- 1 fsharifi fsharifi   200 Jul 23  2019 product.json
-rw------- 1 fsharifi fsharifi 18974 Feb  3 16:19 sitecheck.txt
-rw------- 1 fsharifi fsharifi 3014 Jul 23  2019 sourceme.bash
-rw------- 1 fsharifi fsharifi  2199 Jul 23  2019 sourceme.csh
drwx------ 3 fsharifi fsharifi    29 Jul 23  2019 STAR

[fsharifi@fsharifi cellranger-3.1.0]$ ll ./cellranger
lrwxrwxrwx 1 fsharifi fsharifi 34 Jul 23  2019 ./cellranger -> cellranger-cs/3.1.0/bin/cellranger

[fsharifi@fsharifi cellranger-3.1.0]$ ./cellranger
/home/fsharifi/Apps/cellranger-3.1.0/cellranger-cs/3.1.0/bin
cellranger  (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------

Usage:
    cellranger mkfastq

    cellranger count
    cellranger aggr
    cellranger reanalyze
    cellranger mat2csv

    cellranger mkgtf
    cellranger mkref

    cellranger vdj

    cellranger mkvdjref

    cellranger testrun
    cellranger upload
    cellranger sitecheck
• 0 views • link
written by Fatima Fatima

Hello, Fatima,

I downloaded all the file again.

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ll
total 60
drwxr-xr-x 9 yli1 yli1 4096 Feb  3 13:52 ./
drwxr-xr-x 4 yli1 yli1 4096 Feb  3 13:54 ../
-rw-r--r-- 1 yli1 yli1  661 Feb  3 13:52 builtwith.json
-rwxr-xr-x 1 yli1 yli1  460 Feb  3 13:50 cellranger*
drwxr-xr-x 3 yli1 yli1 4096 Feb  3 13:52 cellranger-cs/
-rwxr-xr-x 1 yli1 yli1 1246 Feb  3 13:50 cellranger-shell*
drwxr-xr-x 3 yli1 yli1 4096 Feb  3 13:50 cellranger-tiny-fastq/
drwxr-xr-x 3 yli1 yli1 4096 Feb  3 13:50 cellranger-tiny-ref/
drwxr-xr-x 3 yli1 yli1 4096 Feb  3 13:50 lz4/
drwxr-xr-x 3 yli1 yli1 4096 Feb  3 13:52 martian-cs/
drwxr-xr-x 3 yli1 yli1 4096 Feb  3 13:50 miniconda-cr-cs/
-rw-r--r-- 1 yli1 yli1  200 Feb  3 13:52 product.json
-rw-r--r-- 1 yli1 yli1 3014 Feb  3 13:50 sourceme.bash
-rw-r--r-- 1 yli1 yli1 2199 Feb  3 13:52 sourceme.csh
drwxr-xr-x 3 yli1 yli1 4096 Feb  3 13:52 STAR/


yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ll ./cellranger
-rwxr-xr-x 1 yli1 yli1 460 Feb  3 13:50 ./cellranger*



yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ./cellranger
/home/yli1/opt01/cellranger-3.1.0
./cellranger: line 31: /home/yli1/opt01/cellranger-3.1.0/../tenkit/bin/common/_master: No such file or directory
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written by yueli7 yueli7

Sorry I don't know what's wrong :(

Maybe try: 

  ./cellranger-cs/3.1.0/bin/cellranger

I don't know what are ../ and ./ in your ll result.

• 0 views • link
written by Fatima Fatima

You are so smart!

It work!

Really appreciated!

Thank you so much for your last try!

Thank you for your time, patient and the spirit of never give up!

Best,

Yue

• 0 views • link
written by yueli7 yueli7

No problem :)

If you try this command in the cellranger-3.1.0 folder, you can create a shortcut and run using ./cellranger directly

ln -s cellranger-cs/3.1.0/bin/cellranger cellranger

After creating the shortcut you might even be able to run using cellranger from other folders too.

Best of luck :)

• 0 views • link
written by Fatima Fatima

Hello, Fatima,

Thank you so much for your suggestion!

Actually I was playing well in my local Ubuntu system, but when I upload the file to my school server, Ubuntu 18.04.3 LTS (GNU/Linux 5.0.0-23-generic x86_64), totally mess.

Thank you again!

Best,

Yue

  yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ln -s cellranger-cs/3.1.0/bin/cellranger cellranger
  ln: failed to create symbolic link 'cellranger': File exists
• 0 views • link
written by yueli7 yueli7

Or you can try something like this, just please make sure the path is correct:

echo "source ~/.bashrc" > ~/.bashrc
echo 'export PATH="/home/yli1/opt01/cellranger-3.0.2":$PATH' >> ~/.bashrc
echo 'export PATH="/home/yli1/opt01/cellranger-3.0.2/cellranger":$PATH' >> ~/.bashrc

Use pwd to find the correct path as mentioned in the tutorial 

cd cellranger-3.0.2 
pwd

If this didn't work, maybe you can remove the folder and it's files and download again and try again following the instructions:

rm -rf cellranger-3.1.0

This command will remove the cellranger-3.1.0 folder and every file/folder inside it.

Please read the instructions more carefully and when you use a command please make sure you understand it. You can always google the command to find its purpose. I'm suggesting this based on different commands that you had added to bashrc. It would be a good approach to understand the basics for example some of those paths start with ~/home, some with /home You can try ls before each of those paths to see if they are correct. 

ll /home/yli1/opt01/cellranger-3.0.2/
ll /home/yli1/opt01/cellranger-3.0.2/cellranger

https://www.ubuntupit.com/the-50-best-linux-commands-to-run-in-the-terminal/ https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in https://medium.com/@tzhenghao/a-guide-to-building-a-great-bashrc-23c52e466b1c

• 0 views • link
written by Fatima Fatima

I don't know what's wrong with your current cellranger, 

rm -f cellranger 
ln -s cellranger-cs/3.1.0/bin/cellranger cellranger
• 0 views • link
written by Fatima Fatima

It work!

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ rm -f cellranger 
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ln -s cellranger-cs/3.1.0/bin/cellranger cellranger
yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0$ ./cellranger
/home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin
cellranger  (3.1.0)
     Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
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written by yueli7 yueli7

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