kallisto quant synthax error when trying to generate log file for multiqc

[dscdscdscs]

When I try to run the following in RStudio, I get the subsequent error:

kallisto quant -i file.index -o test -t 4 sample_1.fastq.gz sample_2.fastq.gz &> sample.log The syntax of the command is incorrect.

However, if I remove "&> sample.log", it will run just fine but will of course not provide me with a log file to use with MultiQC

Any ideas why this might be happening?

[kascchmc]

Did you ever find a solution to this? I'm also having the same problem

[oelakad]

Hi, did you find a solution for this issue?

[kascchmc]

Did you ever find a solution to this? I'm also having the same problem

Yes, Kallisto doesn't run on Windows. I ran it through at Linux subsystem and everything worked.

[kascchmc]

Did you ever find a solution to this? I'm also having the same problem

Yes, Kallisto doesn't run on Windows. I ran it through at Linux subsystem and everything worked.

Yes, Kallisto doesn't run on Windows. I ran it through at Linux subsystem and everything worked.

[Yenaled]

^kallisto runs on windows and through RStudio, but the issue is probably the &> at the end of the command. I can't really fix this on the kallisto end as this is not a kallisto-specific issue (&> is a linux/unix redirection thing, and multiqc seems to require you to make a file through this).

[oelakad]

^kallisto runs on windows and through RStudio, but the issue is probably the &> at the end of the command. I can't really fix this on the kallisto end as this is not a kallisto-specific issue (&> is a linux/unix redirection thing, and multiqc seems to require you to make a file through this).

I think so, as I faced the same thing running it on mac. is there away to get around this on mac?

[Yenaled]

^It works on the Mac command-line terminal. Not sure about RStudio though (I don't usually run things on it)

[oelakad]

it worked yes (was just slow and did not show any responce till finished, which brought the confusion), thanks much.