Answers.Body: <p>You should be able to use the <code>--output-dir</code> argument to specify a folder of your choice and use <code>--id=demux_10x</code> as before.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-11T13:46:32.047Z
Answers.Text: that works partially. All arguments passed to `mkfastq` were `--id=demux_10x --output-dir=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc`. The fastqs are being saved at `/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10` while there is still a directory `demux_10x` and the file `__demux_10x.mro` at `/home/ngs` (from where the script was called). Hoping these files will be moved by completion of cellranger
Answers.UserDisplayName: BCArg
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-11T15:23:12.453Z
Answers.Text: The aforementioned files were not moved to the directory specified in `--output-dir`, even though the fastqs were saved there. On the `_invocatoin` file under `/home/ngs/demux_10x` there is an entry like `interop_output_path   = null,`, though apparently this cannot be specified by `cellranger mkfastq`. Guess the only solution will be to change directory back and forth
Answers.UserDisplayName: BCArg
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-12T07:09:40.167Z
Answers.Text: I remove quite a number of "such files" after my `cellranger count` runs, so this might be a deliberate design choice for some reason. BTW, the 10x customer service is very prompt, helped me in the course of a few hours in the past in case you would like to contact them.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-08T17:03:40.327Z
Answers.LastActivityDate: 2020-05-08T17:03:40.327Z
Answers.UserDisplayName: haci
Answers.Body: <p>I suspect the error message is a bit exaggerated.  Try removing the slash at the end of your --id</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-10T16:03:06.500Z
Answers.Text: tried that way too though it did not work
Answers.UserDisplayName: BCArg
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-08T16:24:04.603Z
Answers.LastActivityDate: 2020-05-08T16:24:04.603Z
Answers.UserDisplayName: swbarnes2
Body: <p>I have always used <code>cellranger mkfastq</code> to demultiplex 10x genomics runs manually, though recently the commands to do so have been incorporated into a script that should call the <code>cellranger</code> whenever it detects that a run is finished (and can be demultiplexed).</p>
  
  <p>The main difference when calling manually compared to being called automatically by the script is <strong>from where</strong> the commands are being called.</p>
  
  <p>So calling the commands manually <strong>from the directory where the samplesheet is and where the outputs shall be saved</strong> with:</p>
  
  <pre><code>/home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=demux_10x --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc 
  </code></pre>
  
  <p>does the job.</p>
  
  <p>but now cellranger is being called (automatically) from <code>/home/ngs</code>. The error message that I am getting from cellranger is:</p>
  
  <pre><code>/home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/bin
  cellranger mkfastq (3.1.0)
  Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
  -------------------------------------------------------------------------------
  
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/tenkit/bin/_mkfastq: line 531: __/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/.mro: No such file or directory
  Martian Runtime - '3.1.0-v3.2.3'
  
  Invalid name: /nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ (only numbers, letters, dash, and underscore allowed)
  </code></pre>
  
  <p>According to the error message I cannot use slashes <code>/</code> in the <code>--id</code> flag.</p>
  
  <p>Does anyone what I should pass to <code>--id</code> in order to get the outputs saved as
  <code>/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/</code>?</p>
  
  <p>I already know that if I just pass <code>--id=demux_10x</code> the outputs will be saved at <code>/home/ngs/demux_10x</code>. (again, I am calling the script that calls <code>cellranger</code> from <code>/home/ngs/</code>)</p>
  
  <p>Obviously I could change to the desired output directory i.e. <code>/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/</code> and do <code>--id=demux_10</code>, though I am trying to avoid that for now.</p>
  
Tags: <rna-seq><10x-genomics><cellranger><demultiplexing>
Title: cellranger mkfastq with full path to --id flag
ThreadText: # cellranger mkfastq with full path to --id flag
  
  (Asked by: username_0 on 2020-05-08)
  
  I have always used `cellranger mkfastq` to demultiplex 10x genomics runs manually, though recently the commands to do so have been incorporated into a script that should call the `cellranger` whenever it detects that a run is finished (and can be demultiplexed).
  
  The main difference when calling manually compared to being called automatically by the script is **from where** the commands are being called.
  
  So calling the commands manually **from the directory where the samplesheet is and where the outputs shall be saved** with:
  
  ```
  /home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=demux_10x --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc 
  
  ```
  
  does the job.
  
  but now cellranger is being called (automatically) from `/home/ngs`. The error message that I am getting from cellranger is:
  
  ```
  /home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/bin
  cellranger mkfastq (3.1.0)
  Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
  -------------------------------------------------------------------------------
  
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/tenkit/bin/_mkfastq: line 531: __/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/.mro: No such file or directory
  Martian Runtime - '3.1.0-v3.2.3'
  
  Invalid name: /nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ (only numbers, letters, dash, and underscore allowed)
  
  ```
  
  According to the error message I cannot use slashes `/` in the `--id` flag.
  
  Does anyone what I should pass to `--id` in order to get the outputs saved as
  `/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/`?
  
  I already know that if I just pass `--id=demux_10x` the outputs will be saved at `/home/ngs/demux_10x`. (again, I am calling the script that calls `cellranger` from `/home/ngs/`)
  
  Obviously I could change to the desired output directory i.e. `/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/` and do `--id=demux_10`, though I am trying to avoid that for now.
  
  **Tags:** rna-seq, 10x-genomics, cellranger, demultiplexing
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2020-05-08. Score: 1
  
  You should be able to use the `--output-dir` argument to specify a folder of your choice and use `--id=demux_10x` as before.
  
  > **Comments:**
  > **username_0**: that works partially. All arguments passed to `mkfastq` were `--id=demux_10x --output-dir=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc`. The fastqs are being saved at `/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10` while there is still a directory `demux_10x` and the file `__demux_10x.mro` at `/home/ngs` (from where the script was called). Hoping these files will be moved by completion of cellranger  
  > **username_0**: The aforementioned files were not moved to the directory specified in `--output-dir`, even though the fastqs were saved there. On the `_invocatoin` file under `/home/ngs/demux_10x` there is an entry like `interop_output_path   = null,`, though apparently this cannot be specified by `cellranger mkfastq`. Guess the only solution will be to change directory back and forth  
  > **username_1**: I remove quite a number of "such files" after my `cellranger count` runs, so this might be a deliberate design choice for some reason. BTW, the 10x customer service is very prompt, helped me in the course of a few hours in the past in case you would like to contact them.  
  
  ---
  
  ### Answer by username_2 on 2020-05-08. Score: 0
  
  I suspect the error message is a bit exaggerated. Try removing the slash at the end of your --id
  
  > **Comments:**
  > **username_0**: tried that way too though it did not work  
  
  ---
  
  