Kallisto missing Bootstrap

Question

[dr.fatemeh.askari]

Hey all,

I am trying Kallisto for RNA-seq Fastq.gz file. For me, Kallisto runs without bootstraps. I have also tried to download the binary from pkgsrc using the following codes

bootstrap

cvs [e-mail]:/cvsroot checkout pkgsrc
cd pkgsrc/bootstrap
./bootstrap

Build package

cd pkgsrc/devel/memcached

Under pkgsrc, I have

Macs-MacBook-Pro-6:pkgsrc mac$ ls
CVS             filesystems         pkglocate           tex-babel-croatian
Makefile            finance             pkgtools            tex-babel-czech
README.md           fonts               plan9               tex-babel-danish
archivers           games               print               tex-babel-dutch
athena              geography           py-flask-uploads        tex-babel-esperanto
audio               graphics            regress             tex-babel-estonian
benchmarks          ham             security            tex-babel-french
biology             inputmethod         shells              tex-babel-friulan
**bootstrap**           japanese            sysutils            tex-babel-georgian
cad             lang                templates           tex-babel-greek
chat                licenses            tex-FAQ-en-doc          tex-babel-hebrew
comms               lxqt-notificationd      tex-MemoirChapStyles-doc    tex-babel-hungarian
converters          mail                tex-Type1fonts-doc      tex-babel-icelandic
corba               math                tex-amslatex-primer-doc     tex-babel-interlingua
cross               mbone               tex-around-the-bend-doc     tex-babel-irish
crosspkgtools           meta-pkgs           tex-ascii-chart-doc     tex-components-of-TeX-doc
crypto              misc                tex-babel-albanian      textproc
databases           mk              tex-babel-bahasa        time
devel               multimedia          tex-babel-basque        wm
distfiles           net             tex-babel-bosnian       www
doc             news                tex-babel-breton        x11
editors             packages            tex-babel-bulgarian     xdo
emulators           parallel            tex-babel-catalan

I don't know what to do else? Should I move bootstrap to kallisto?

[dr.fatemeh.askari]

Thanks Kevin,

I had set a value of 100 for bootstrap. It gives me the following warning. What to do?

Macs-MacBook-Pro-6:test mac$ kallisto quant -i transcripts.idx -b 100 -o output reads_1.fastq.gz reads_2.fastq.gz

[quant] fragment length distribution will be estimated from the data
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: 14
[index] number of k-mers: 22,118
[index] number of equivalence classes: 20
[quant] running in paired-end mode
[quant] will process pair 1: reads_1.fastq.gz
                             reads_2.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 10,000 reads, 9,413 reads pseudoaligned
[quant] estimated average fragment length: 178.02
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds

[dsull]

Download the binaries rather than compiling from source. If you do want to build it from source, be sure to specify-DUSE_HDF5=ON when running cmake.

[dr.fatemeh.askari]

Hey Dsull and Kevin, At this step, I am not sure whether my installed Kallisto is with binaries. I tried to follow their manual. However, when I run on the test still I don't get the abundance.h5 file in the output. I get only abundance.tsv and run_info.json. In the command Line I also specify -b function.

Macs-MacBook-Pro-6:~ mac$ cd kallisto
Macs-MacBook-Pro-6:kallisto mac$ ls
CMakeLists.txt  astyle.txt  gen_release.sh  src
INSTALL.md  build       gulpfile.js test
README.md   ext     license.txt unit_tests
Macs-MacBook-Pro-6:kallisto mac$ cd build
Macs-MacBook-Pro-6:build mac$ ls
CMakeCache.txt      Makefile        install_manifest.txt
CMakeFiles      cmake_install.cmake src
Macs-MacBook-Pro-6:build mac$ cd src
Macs-MacBook-Pro-6:src mac$ ls
CMakeFiles      cmake_install.cmake libkallisto_core.a
Makefile        kallisto

for the HDF5

Macs-MacBook-Pro-6:~ mac$ brew install HDF5
Updating Homebrew...
Warning: hdf5 1.12.0_1 is already installed and up-to-date

[dsull]

You cannot use your current kallisto installation to get the abundance.h5 files containing the bootstraps.

You have to re-install kallisto (see my previous comment).

[dr.fatemeh.askari]

Dear Dsull,

Recently, I have downloaded Kallisto with binary. Below is the details;

acs-MacBook-Pro-6:kallisto mac$ ls -al total 8792 drwxr-xr-x@ 7 mac staff 224 Aug 17 21:51 . drwx------+ 77 mac staff 2464 Aug 18 14:25 .. -rw-r--r--@ 1 mac staff 6148 Aug 17 22:01 .DS_Store -rw-r--r--@ 1 mac staff 2250 Mar 20 2017 README.md -rwxr-xr-x@ 1 mac staff 4484056 Nov 4 2019 kallisto -rw-r--r--@ 1 mac staff 1357 Mar 20 2017 license.txt drwxr-xr-x@ 11 mac staff 352 Aug 17 22:11 test Macs-MacBook-Pro-6:kallisto mac$ Macs-MacBook-Pro-6:kallisto mac$ ./kallisto -h Error: invalid command -h kallisto 0.46.1

Usage: kallisto <cmd> [arguments] ..

Where <cmd> can be one of:

index         Builds a kallisto index 
quant         Runs the quantification algorithm 
bus           Generate BUS files for single-cell data 
pseudo      Runs the pseudoalignment step 
merge        Merges several batch runs 
h5dump      Converts HDF5-formatted results to plaintext
inspect       Inspects and gives information about an index
version       Prints version information
cite          Prints citation information

Running kallisto <cmd> without arguments prints usage information for <cmd>

However, when I ask the system it gives me a different version of kallisto (kallisto 0.46.2) Macs-MacBook-Pro-6:~ mac$ kallisto kallisto 0.46.2

Usage: kallisto <cmd> [arguments] ..

Where <cmd> can be one of:

index         Builds a kallisto index 
quant         Runs the quantification algorithm 
bus           Generate BUS files for single-cell data 
pseudo        Runs the pseudoalignment step 
merge         Merges several batch runs 
h5dump        Converts HDF5-formatted results to plaintext
inspect       Inspects and gives information about an index
version       Prints version information
cite          Prints citation information

Running kallisto <cmd> without arguments prints usage information for <cmd>

Macs-MacBook-Pro-6:~ mac$

I am worried that the computer is riding the old version. I made sure to to delete that, but I don't know why I have it. What to do?

Another thing, how to make sure that HDF5 is working?

[GenoMax]

dr.fatemeh.askari : @dsull has already clarified that you will need to compile kallisto from source code. You can't use the binary provided by since it appears to have been compiled without support for bootstrap. That is probably true of either binaries you have.

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question

Answer 1

[dr.fatemeh.askari]

Thanks all,

I have solved the problem by installing miniconda3 and conda install kallisto. Apparently the brew install HDF5 was not functioning in my computer and that's why I couldn't invoke the bootstrapping.

[Kevin Blighe]

Great work

Answer 2

[Kevin Blighe]

I am not sure what you mean. To invoke the bootstrapping, you set a value for the command line parameter, --bootstrap-samples. Please see https://pachterlab.github.io/kallisto/manual

Example:

kallisto quant \
  --index=index \
  --bootstrap-samples=50 \
  --output-dir=output \
  pairA_1.fastq pairA_2.fastq pairB_1.fastq pairB_2.fastq

Kevin