Answers.Body: <p>It could be that <code>cellranger</code> does not have execute permissions. Try</p>
  
  <pre><code>chmod u+x [insert internal isilon path here]/[insert windows username here]/cellranger-3.0.1/cellranger-3.0.1/cellranger
  </code></pre>
  
  <p>(or the Windows equivalent, which seems to be to give Execute permission using the GUI)</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-28T14:43:20.427Z
Answers.Text: I tried this as you wrote and it says permission denied in linux command line. what is the windows equivalent? can I do this permission sharing in the Windows?
Answers.UserDisplayName: sv1234
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Answers.CreationDate: 2019-05-28T14:45:48.973Z
Answers.Text: This isn't a permissions issue, the error is about a wrong path. If the file existed but didn't have execute permissions, you would get a `Permission denied` error instead.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-28T15:05:30.107Z
Answers.Text: @terdon, I get a Permissions denied error
Answers.UserDisplayName: sv1234
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-28T17:35:11.793Z
Answers.Text: From your update, you seem to have the requisite permissions. @terdon Before OP's update, it could have been a permissions issue, and I wanted to ensure that was not the case. OP seems to be on a Windows machine, IDK how permissions work on Windows.
Answers.UserDisplayName: Ram RS
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Answers.CreationDate: 2019-05-28T17:40:11.143Z
Answers.Text: The OP is connecting to an AWS instance running Linux (according to the question, anyway) and the error messages on Linux are quite specific. If the file exists but isn't executable, you would never get a file not found error.
Answers.UserDisplayName: terdon
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Answers.CreationDate: 2019-05-28T18:18:10.133Z
Answers.Text: Sorry, I was going by windows user name that was in every path. OTOH, there's also the "linux" mentioned in the title and the tags. OP needs to be clearer about this
Answers.UserDisplayName: Ram RS
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Answers.CreationDate: 2019-05-28T18:39:31.113Z
Answers.Text: @RamRS, the linux AWS instance is mentioned in the 2nd line of my OP
Answers.UserDisplayName: sv1234
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-28T19:32:11.503Z
Answers.Text: And the question is tagged with `linux` :)
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-28T19:39:01.453Z
Answers.Text: @sv1234 "MobaXTerm linux command line" is confusing. Is it MobaXTerm (Windows-only app) or a linux command line interface? Like I said, you need to be clearer.
Answers.UserDisplayName: Ram RS
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Answers.CreationDate: 2019-05-28T14:17:46.490Z
Answers.LastActivityDate: 2019-05-28T14:17:46.490Z
Answers.UserDisplayName: Ram RS
Answers.Body: <p>this has been resolved. I downloaded the windows file and this caused trouble but when downloading the file within the Linux, it seems to be working. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-29T15:04:00.900Z
Answers.LastActivityDate: 2019-05-29T15:04:00.900Z
Answers.UserDisplayName: sv1234
Body: <p>I am trying to perform a cellranger count on fastq files generated from a 10x genomics single cell RNA Seq run.</p>
  
  <p>Just to provide some background, I ssh’d into the AWS using our AWS IP with MobaXTerm linux command line.</p>
  
  <p>My files are in the Isilon. The file folders are <code>path/to/runs/</code> - this folder contains the <code>.fastq</code> files for each sample (ex: <code>SI_GA_A1_S1</code>, <code>SI_GA_B1_S2</code>, <code>SI_GA_C1_S3</code>, and <code>SI_GA_D1_S4</code>). I can see these folders listed in the linux command line.</p>
  
  <p>The cellranger is found when I write the following: </p>
  
  <pre><code>path/to/cellranger-3.0.1/cellranger-3.0.1
  </code></pre>
  
  <p>then <code>ls</code> brings up 13 items located in the folder, one of them being <code>cellranger</code>.</p>
  
  <p>When I write the following command, </p>
  
  <pre><code>/path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger count \
      --id=run2\
      --transcriptome=/path/to/refseq/refdata-cellranger-hg19-3.0.0\
      --sample=sample1\
      --expect-cells=5000
  </code></pre>
  
  <p>and it gives me: </p>
  
  <pre><code>-bash: /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger: No such file or directory
  </code></pre>
  
  <p>This looks correct from what the 10x website says for single cell RNA Seq. Please advise.</p>
  
  <pre><code>$ ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger 
  -rwxrwx--- 1 1003080 1000000 460 Dec 5 19:41 /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-28T14:46:14.920Z
Comments.Text: You're using the wrong path. What does  `ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` return? Don't you want `/path/to/cellranger-3.0.1//cellranger` instead?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-28T15:02:48.400Z
Comments.Text: @terdon, an ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger returns: -rwxrwx--- 1 1003080 1000000 460 Dec  5 19:41 /[insert isilon path here]/[insert windowsID here]/cellranger-3.0.1/cellranger-3.0.1/cellranger.  why do you think it is the wrong path? if I do instead ls -l /path/to/cellranger-3.0.1//cellranger , it gives: ls: cannot access /[insert isilon path here]/[insert windowsID here]/cellranger-3.0.1/cellranger: No such file or directory
Comments.UserDisplayName: sv1234
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-28T16:07:36.983Z
Comments.Text: Please [edit] your question to add clarifications. Comments are easy to miss, hard to read and can be deleted without warning. Use the [formatting tools](https://bioinformatics.stackexchange.com/help/formatting) to format them as code so we can see what you are running.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-28T16:31:53.767Z
Comments.Text: Please try and use consistent paths. This sort of issue is usually caused by a tiny detail, and it's hard to catch when you use both `/path/to/` and `/[insert isilon path here]/[insert windowsID here]`. Also, the output of `ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` seems to have an extra `.` at the end. That isn't actually in your output, right?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-28T17:57:26.377Z
Comments.Text: As @terdon said, It's certainly a path problem, but it's really hard to spot given your code formatting.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-28T18:33:46.883Z
Comments.Text: hello, I have updated the original post. @terdon, the . at the end is not part of the output. I have updated the original post to contain only /path/to/ if that seems to simplify things. thank you.
Comments.UserDisplayName: sv1234
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-28T18:41:27.133Z
Comments.Text: Something is wrong here. The error tells you that `/path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` doesn't exist, but `ls /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` shows the file. Are you 100% _sure_ the paths you are using in your question are correct? Could you show us the real paths used? Are there any spaces in any of the paths? Any capital letters that you've changed to lowercase?
Comments.UserDisplayName: terdon
Tags: <linux><bash><cellranger>
Title: processing fastq files using cellranger on linux
ThreadText: # processing fastq files using cellranger on linux
  
  (Asked by: username_0 on 2019-05-28)
  
  I am trying to perform a cellranger count on fastq files generated from a 10x genomics single cell RNA Seq run.
  
  Just to provide some background, I ssh’d into the AWS using our AWS IP with MobaXTerm linux command line.
  
  My files are in the Isilon. The file folders are `path/to/runs/` - this folder contains the `.fastq` files for each sample (ex: `SI_GA_A1_S1`, `SI_GA_B1_S2`, `SI_GA_C1_S3`, and `SI_GA_D1_S4`). I can see these folders listed in the linux command line.
  
  The cellranger is found when I write the following:
  
  ```
  path/to/cellranger-3.0.1/cellranger-3.0.1
  
  ```
  
  then `ls` brings up 13 items located in the folder, one of them being `cellranger`.
  
  When I write the following command,
  
  ```
  /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger count \
      --id=run2\
      --transcriptome=/path/to/refseq/refdata-cellranger-hg19-3.0.0\
      --sample=sample1\
      --expect-cells=5000
  
  ```
  
  and it gives me:
  
  ```
  -bash: /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger: No such file or directory
  
  ```
  
  This looks correct from what the 10x website says for single cell RNA Seq. Please advise.
  
  ```
  $ ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger 
  -rwxrwx--- 1 1003080 1000000 460 Dec 5 19:41 /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger
  
  ```
  
  **Tags:** linux, bash, cellranger
  
  > **Comments:**
  > **username_1**: You're using the wrong path. What does  `ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` return? Don't you want `/path/to/cellranger-3.0.1//cellranger` instead?  
  > **username_0**: @username_1, an ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger returns: -rwxrwx--- 1 1003080 1000000 460 Dec  5 19:41 /[insert isilon path here]/[insert windowsID here]/cellranger-3.0.1/cellranger-3.0.1/cellranger.  why do you think it is the wrong path? if I do instead ls -l /path/to/cellranger-3.0.1//cellranger , it gives: ls: cannot access /[insert isilon path here]/[insert windowsID here]/cellranger-3.0.1/cellranger: No such file or directory  
  > **username_1**: Please [edit] your question to add clarifications. Comments are easy to miss, hard to read and can be deleted without warning. Use the [formatting tools](https://bioinformatics.stackexchange.com/help/formatting) to format them as code so we can see what you are running.  
  > **username_1**: Please try and use consistent paths. This sort of issue is usually caused by a tiny detail, and it's hard to catch when you use both `/path/to/` and `/[insert isilon path here]/[insert windowsID here]`. Also, the output of `ls -l /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` seems to have an extra `.` at the end. That isn't actually in your output, right?  
  > **username_2**: As @username_1 said, It's certainly a path problem, but it's really hard to spot given your code formatting.  
  > **username_0**: hello, I have updated the original post. @username_1, the . at the end is not part of the output. I have updated the original post to contain only /path/to/ if that seems to simplify things. thank you.  
  > **username_1**: Something is wrong here. The error tells you that `/path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` doesn't exist, but `ls /path/to/cellranger-3.0.1/cellranger-3.0.1/cellranger` shows the file. Are you 100% _sure_ the paths you are using in your question are correct? Could you show us the real paths used? Are there any spaces in any of the paths? Any capital letters that you've changed to lowercase?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2019-05-29. Score: 1
  
  this has been resolved. I downloaded the windows file and this caused trouble but when downloading the file within the Linux, it seems to be working.
  
  
  ---
  
  ### Answer by username_3 on 2019-05-28. Score: 0
  
  It could be that `cellranger` does not have execute permissions. Try
  
  ```
  chmod u+x [insert internal isilon path here]/[insert windows username here]/cellranger-3.0.1/cellranger-3.0.1/cellranger
  
  ```
  
  (or the Windows equivalent, which seems to be to give Execute permission using the GUI)
  
  > **Comments:**
  > **username_0**: I tried this as you wrote and it says permission denied in linux command line. what is the windows equivalent? can I do this permission sharing in the Windows?  
  > **username_1**: This isn't a permissions issue, the error is about a wrong path. If the file existed but didn't have execute permissions, you would get a `Permission denied` error instead.  
  > **username_0**: @username_1, I get a Permissions denied error  
  > **username_3**: From your update, you seem to have the requisite permissions. @username_1 Before OP's update, it could have been a permissions issue, and I wanted to ensure that was not the case. OP seems to be on a Windows machine, IDK how permissions work on Windows.  
  > **username_1**: The OP is connecting to an AWS instance running Linux (according to the question, anyway) and the error messages on Linux are quite specific. If the file exists but isn't executable, you would never get a file not found error.  
  > **username_3**: Sorry, I was going by windows user name that was in every path. OTOH, there's also the "linux" mentioned in the title and the tags. OP needs to be clearer about this  
  > **username_0**: @username_3, the linux AWS instance is mentioned in the 2nd line of my OP  
  > **username_1**: And the question is tagged with `linux` :)  
  > **username_3**: @username_0 "MobaXTerm linux command line" is confusing. Is it MobaXTerm (Windows-only app) or a linux command line interface? Like I said, you need to be clearer.  
  
  ---
  
  