Answers.Body: <blockquote>
  <p>created another environment called &quot;kb&quot;, where I installed Kallisto-bustools</p>
  </blockquote>
  <p>This is known to work well. What about installing bustools in the same env as Kallisto?</p>
  <p>Alternatively you can create a new conda environment</p>
  <pre><code>conda create --name kba
  conda activate kba
  conda install -c bioconda kallisto
  conda install conda-build
  conda skeleton pypi kb_python
  conda build kb_python
  conda install --use-local kb_python
  kb count \
  pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
  -i Homo_sapiens.GRCh38.cdna.all.index \
  -x 10XV3 \
  -g t2g.txt \
  -t 8 \
  --cellranger
  </code></pre>
  <p>If the above doesn't work you simply delete the env</p>
  <pre><code>conda deactivate
  conda env remove --name kba
  </code></pre>
  <hr />
  <p>Okay <code>skeleton</code> didn't work. The last option is to use Docker. There is a Docker file of kallisto <a href="https://pachterlab.github.io/kallisto/download" rel="nofollow noreferrer">https://pachterlab.github.io/kallisto/download</a>
  It's a bit weird it's not in the Docker repo. The Docker builder file is <a href="https://github.com/cyverse/docker-builds/blob/master/kallisto/Dockerfile" rel="nofollow noreferrer">https://github.com/cyverse/docker-builds/blob/master/kallisto/Dockerfile</a></p>
  <p>I assume most people know how to use a Docker file. If not, i.e. you want a tutorial, then please post as a separate question (quite alot of text to explain).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-02T13:31:05.997Z
Answers.Text: Unfortunately installing bustools and Kallisto in the same env returned the same error.
  
  Creating a new env did not help either. After running "conda skeleton pypi kb_python" I got the following error message:
  
  "Error: command failed: /Users/simon/miniconda/envs/kb/conda-bld/skeleton_1712064046833/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/python setup.py install"
Answers.UserDisplayName: Simon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-02T14:13:40.757Z
Answers.Text: Okay @Simon the last approach is described above.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-02T10:30:06.627Z
Answers.LastActivityDate: 2024-04-02T14:20:33.213Z
Answers.LastEditDate: 2024-04-02T14:20:33.213Z
Answers.UserDisplayName: M__
Answers.Body: <p>Well, it's embarassing to say but...I didn't have Autotools, CMake, and Make installed! Once I installed them, I could run the command. However, I am running now in another problem: even though the process starts, it gets stuck very quickly at the step &quot;generating count matrix&quot; (over night).
  But bustools is running, using 99% CPU but only 1 thread (even if I said &quot;-t 8&quot;. My &quot;counts_unfiltered&quot; folder is of course empty.
  I never get an error message but I don't think that even on my modest laptop a dataset of 1K cells should take so long, or am I wrong?
  <a href="https://i.sstatic.net/udAoC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/udAoC.png" alt="enter image description here" /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-06T20:17:31.793Z
Answers.LastActivityDate: 2024-04-06T20:17:31.793Z
Answers.UserDisplayName: Simon
Body: <p>I am totally new to bioinformatics, therefore apologies if the terminology is not correct or the question is dumb :) I have been trying the following:</p>
  <ol>
  <li>installed miniconda</li>
  <li>create an environment called &quot;rnaseq&quot; where I installed kallisto <code>conda install -c bioconda kallisto (0.50.1)</code></li>
  <li>created another environment called &quot;kb&quot;, where I installed Kallisto-bustools</li>
  </ol>
  <pre><code>conda create -y --name kb python=3.8
  conda activate kb
  pip install kb-python
  </code></pre>
  <ol start="4">
  <li>run the following line of code from terminal:</li>
  </ol>
  <pre><code>kb count \
  pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
  -i Homo_sapiens.GRCh38.cdna.all.index \
  -x 10XV3 \
  -g t2g.txt \
  -t 8 \
  --cellranger
  </code></pre>
  <p>I get this error message:
  ````kb_python.config.UnsupportedOSError: Failed to find compatible kallisto binary. Provide a compatible binary with the <code>--kallisto</code> option or run <code>kb compile</code>.</p>
  <pre><code>I have a MacBook Pro 2020, Intel Core i5, OS Sonoma 14.4. I used the same &quot;.index&quot; file and ran Kallisto on bulk RNA-seq data and it worked. I tried now to redownload the fastq files (they belong to one of the test datasets from 10x), regenerate the index file, remove all the conda envs and reinstall everything but nothing worked. Thanks for any help you could provide!
  
       
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-23T10:31:51.433Z
Comments.Text: I am experiencing the same issue with some of my single cell datasets, But bustools is running, using 99% CPU but only 1 thread, I get no error message, and the process is stuck at the "Generating count matrix" step.
  Did you figure out what caused the error in your case?
  Sorry, I don't have enough reputation to comment, this is not an answer, but a response to the last answer of @Simon
Comments.UserDisplayName: user2274103
Tags: <cellranger><conda><kallisto>
Title: problem with running Kallisto on single cell data
ThreadText: # problem with running Kallisto on single cell data
  
  (Asked by: username_0 on 2024-04-02)
  
  I am totally new to bioinformatics, therefore apologies if the terminology is not correct or the question is dumb :) I have been trying the following:
  
  1. installed miniconda
  2. create an environment called "rnaseq" where I installed kallisto `conda install -c bioconda kallisto (0.50.1)`
  3. created another environment called "kb", where I installed Kallisto-bustools
  
  ```
  conda create -y --name kb python=3.8
  conda activate kb
  pip install kb-python
  
  ```
  
  4. run the following line of code from terminal:
  
  ```
  kb count \
  pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
  -i Homo_sapiens.GRCh38.cdna.all.index \
  -x 10XV3 \
  -g t2g.txt \
  -t 8 \
  --cellranger
  
  ```
  
  I get this error message:
  ````kb\_python.config.UnsupportedOSError: Failed to find compatible kallisto binary. Provide a compatible binary with the `--kallisto` option or run `kb compile`.
  
  ```
  I have a MacBook Pro 2020, Intel Core i5, OS Sonoma 14.4. I used the same ".index" file and ran Kallisto on bulk RNA-seq data and it worked. I tried now to redownload the fastq files (they belong to one of the test datasets from 10x), regenerate the index file, remove all the conda envs and reinstall everything but nothing worked. Thanks for any help you could provide!
  
       
  
  ```
  
  **Tags:** cellranger, conda, kallisto
  
  > **Comments:**
  > **username_1**: I am experiencing the same issue with some of my single cell datasets, But bustools is running, using 99% CPU but only 1 thread, I get no error message, and the process is stuck at the "Generating count matrix" step. Did you figure out what caused the error in your case? Sorry, I don't have enough reputation to comment, this is not an answer, but a response to the last answer of @username_0  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2024-04-02. Score: 2
  
  > created another environment called "kb", where I installed Kallisto-bustools
  
  This is known to work well. What about installing bustools in the same env as Kallisto?
  
  Alternatively you can create a new conda environment
  
  ```
  conda create --name kba
  conda activate kba
  conda install -c bioconda kallisto
  conda install conda-build
  conda skeleton pypi kb_python
  conda build kb_python
  conda install --use-local kb_python
  kb count \
  pbmc_1k_v3_S1_mergedLanes_R1.fastq.gz pbmc_1k_v3_S1_mergedLanes_R2.fastq.gz \
  -i Homo_sapiens.GRCh38.cdna.all.index \
  -x 10XV3 \
  -g t2g.txt \
  -t 8 \
  --cellranger
  
  ```
  
  If the above doesn't work you simply delete the env
  
  ```
  conda deactivate
  conda env remove --name kba
  
  ```
  
  ---
  
  Okay `skeleton` didn't work. The last option is to use Docker. There is a Docker file of kallisto <https://pachterlab.github.io/kallisto/download>
  It's a bit weird it's not in the Docker repo. The Docker builder file is <https://github.com/cyverse/docker-builds/blob/master/kallisto/Dockerfile>
  
  I assume most people know how to use a Docker file. If not, i.e. you want a tutorial, then please post as a separate question (quite alot of text to explain).
  
  > **Comments:**
  > **username_0**: Unfortunately installing bustools and Kallisto in the same env returned the same error.  Creating a new env did not help either. After running "conda skeleton pypi kb_python" I got the following error message:  "Error: command failed: /Users/username_0/miniconda/envs/kb/conda-bld/skeleton_1712064046833/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/python setup.py install"  
  > **username_2**: Okay @username_0 the last approach is described above.  
  
  ---
  
  ### Answer by username_0 on 2024-04-06. Score: 1
  
  Well, it's embarassing to say but...I didn't have Autotools, CMake, and Make installed! Once I installed them, I could run the command. However, I am running now in another problem: even though the process starts, it gets stuck very quickly at the step "generating count matrix" (over night).
  But bustools is running, using 99% CPU but only 1 thread (even if I said "-t 8". My "counts\_unfiltered" folder is of course empty.
  I never get an error message but I don't think that even on my modest laptop a dataset of 1K cells should take so long, or am I wrong?
  [![enter image description here](https://i.sstatic.net/udAoC.png)](https://i.sstatic.net/udAoC.png)
  
  
  ---
  
  