Kallisto quantification fails to execute

[Mintxoklet]

• sRNA analysis pipeline version: 3.6.2
• Python version: 3.10.9
• Operating System: Windows

Description

I have used RNAlysis before, I was just trying to use the kallisto gene quantification tool for 8 paired end read fastq samplles, but when starting the quant a message error appears.

Traceback (most recent call last):
  File "rnalysis\gui\gui.py", line 3662, in finish_generic_job
  File "rnalysis\gui\gui_widgets.py", line 329, in run
  File "rnalysis\fastq.py", line 850, in kallisto_quantify_paired_end
  File "rnalysis\fastq.py", line 898, in _parse_kallisto_misc_args
  File "rnalysis\utils\io.py", line 1459, in generate_base_call
  File "rnalysis\utils\io.py", line 1400, in run_subprocess
  File "subprocess.py", line 858, in __init__
  File "subprocess.py", line 1311, in _execute_child
OSError: [WinError 193] %1 no es una aplicación Win32 válida

What could be causing the issue?

[GuyTeichman]

Hi,
It appears like RNAlysis fails to find the kallisto executable.
I have a few follow-up questions:

1. Did you specify the installation folder of kallisto? If so, what's the path you specified?
2. Are you using the RNAlysis stand-alone app or installed via Python?

Thanks,
Guy.

[Mintxoklet]

Hello,
So first I tried with the RNAlysis version 3.4 I had installed with Python. And that ocurred. When initializing RNAlysis it told me there was a newer verions available (3.6) but for some reason when trying to update, the app would just close and restart again, asking once more if I would like to update. So I tried updating it by downloading the standalone zip 3.6 version and executing it with the RNAlysis.exe as stated in the instructions. This way I had 2 rnalysis. I tried then using the 3.6 version, but the error prompt when performing the kallisto quantification was exactly the same.

Regarding question 1, I specified the kallisto folder which was "C:\Users\Jon\AppData\Local\kallisto". For instance RNalysis folder is in that same "Local" directory, if that is of any use to you.

[GuyTeichman]

Hi,
Could you please make sure that inside the folder "C:\Users\Jon\AppData\Local\kallisto" exists a file called "kallisto.exe"?

[Mintxoklet]

Yes there is. In fact, since kallisto wasnt working with RNAlysis, I have run kallisto alone on the PowerShell terminal. Then, following what RNAlysis does automatically, I have summarized the transcript abundances for genes with tximport in R. But still it would be nice to sort this out, as first time it worked flawlessly in RNAlysis and was is so much more convenient.

[GuyTeichman]

Hi,
Unfortunately I've been unable to replicate this issue on my local setup.
Since you ran into this problem when using the stand-alone version, I would suggest that you update your Python version of RNAlysis manually, and then try running kallisto again using the Python version of RNAlysis.

To manually update RNAlysis Python version, open your terminal and type the following command:
pip install --upgrade RNAlysis[alll]

Please let me know if that works (both the manual update and using kallisto afterwards).

Best,
Guy.

[Mintxoklet]

Hello again,
The manual pip update worked just fine to update to the latest 3.6.2 version.
However, the error I got when trying to perform the kallisto quantification was exactly the same.
:(