I have used kallisto in the past, but am now struggling to get it to work on a new computer (MacBook M1).
- When I download kallisto using brew, and try to run kallisto quant, I get an error not generating bootstraps 'Warning: kallisto was not compiled with HDF5 support so no bootstrapping will be performed. Run quant with --plaintext option or recompile with HDF5 support to obtain bootstrap estimates.'
% for file in *fastq.gz; do kallisto quant -i kallisto_index_musmus.idx -o "$file.kallisto" -b 100 --single --rf-stranded -l 260 -s 20 "$file"; done
[quant] fragment length distribution is truncated gaussian with mean = 260, sd = 20 Warning: kallisto was not compiled with HDF5 support so no bootstrapping will be performed. Run quant with --plaintext option or recompile with HDF5 support to obtain bootstrap estimates. [index] k-mer length: 31 [index] number of targets: 118,489 [index] number of k-mers: 100,614,952
I have read that this might be an issue installing kallisto from brew. I installed conda and tried to install kallisto using condo, but get the following
~ % conda install kallisto Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.PackagesNotFoundError: The following packages are not available from current channels:
- kallisto
Could you please help me to resolve this?
Make sure you have the appropriate channels specified.
Thank you! I have tried that, still the same error. Any idea what else I could try?
Looks like there might not be a kallisto for M1 macs on anaconda. If you search specifically for kallisto for ARM64 nothing comes up.
However, if you search for the old AMD64, kallisto does show up.
If you go to the kallisto github they do have binaries available (listed as Rock64). It might be worth trying those.
Someone with more knowledge of running/installing kallisto on ARM64 might be able to give more specific advice.
Thank you!! I am not sure if doing binaries vs building from the source is the same thing? Sorry this might be a very silly question. When trying to build, the following ran OK:
But then I got the following error after running 'make':
In the latter attempt I am not really sure what exactly I am doing, so probably would need to learn that first unless there is something what is obviously wrong to you?..
Here is why it's failing to build from source and here's a simple solution to fix it (after this, it will work):
https://github.com/pachterlab/kallisto/issues/303#issuecomment-884612169
thank you so much! I ran the indicated code, but am getting the following error. I also tried to manually delete previously generated kallisto folders (did not find an uninstall option). Could there be files associated with autoconf that I should delete? Or should I try to install autoconf2.69, as also suggested in the reply?
It seems like you're missing aclocal. You need to make sure you have all the automake tools installed and that they're in your path. Try brew install automake
Binaries are them building it for you, whereas what you're doing is building it yourself form source. I would start off trying the binaries first.
tar -xf kallisto_rock64-v0.46.1.tar.gzchmod +x kallisto/kallistomv kallisto/kallisto /usr/local/binThank you so much for still bearing with me!! After untar, still an error...
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