<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>

CC BY-SA 4.0
2024-04-02T13:31:05.997Z
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"
Simon
CC BY-SA 4.0
2024-04-02T14:13:40.757Z
Okay @Simon the last approach is described above.
M__
CC BY-SA 4.0
2024-04-02T10:30:06.627Z
2024-04-02T14:20:33.213Z
2024-04-02T14:20:33.213Z
M__
<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>

CC BY-SA 4.0
2024-04-06T20:17:31.793Z
2024-04-06T20:17:31.793Z
Simon
<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>

CC BY-SA 4.0
2024-12-23T10:31:51.433Z
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
user2274103
<cellranger><conda><kallisto>
problem with running Kallisto on single cell data
# 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:

installed miniconda
create an environment called "rnaseq" where I installed kallisto conda install -c bioconda kallisto (0.50.1)
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


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 @Simon  

---

## 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/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"  
> **username_2**: Okay @Simon 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)


---

