Segmentation fault in version 0.46.1

[yeroslaviz]

I try to run kallisto pseudo after installing the latest version 0.46.1 from the binary version for linux.

The command I use:

kallisto pseudo -i transcripts.idx -o Kallisto -b batch.txt 

my batch.txt file looks like that:

#id file1 file 2
cell1 reads_1.fastq.gz reads_1.fastq.gz

and what I get is this:

[quant] fragment length distribution will be estimated from the data
[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_1.fastq.gz
[quant] finding pseudoalignments for all files ...Segmentation fault (core dumped)

When running kallisto quant instead it works without problems.

I have tried both my own data as well as the test data from the repository.
It seems that this is an evergoing problem. Is there a solution for this problem?

[yeroslaviz]

I have tried to install directly from the github repo, but encounter error messages, when running the make command

yeroslaviz@supercube005:build$ make
Scanning dependencies of target htslib
[  3%] Creating directories for 'htslib'
[  6%] No download step for 'htslib'
[ 10%] No patch step for 'htslib'
[ 13%] No update step for 'htslib'
[ 17%] Performing configure step for 'htslib'
/bin/sh: 1: autoheader: not found
CMakeFiles/htslib.dir/build.make:105: recipe for target '../ext/htslib/src/htslib-stamp/htslib-configure' failed
make[2]: *** [../ext/htslib/src/htslib-stamp/htslib-configure] Error 127
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/htslib.dir/all' failed
make[1]: *** [CMakeFiles/htslib.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

any ideas?

the complete output is shown below:

 git clone https://github.com/pachterlab/kallisto.git
Cloning into 'kallisto'...
remote: Enumerating objects: 208, done.
remote: Counting objects: 100% (208/208), done.
remote: Compressing objects: 100% (140/140), done.
remote: Total 3771 (delta 120), reused 112 (delta 67), pack-reused 3563
Receiving objects: 100% (3771/3771), 4.06 MiB | 6.09 MiB/s, done.
Resolving deltas: 100% (2419/2419), done.
yeroslaviz@supercube005:software$ cd kallisto/
yeroslaviz@supercube005:kallisto$ mkdir build 
yeroslaviz@supercube005:kallisto$ cd build/
yeroslaviz@supercube005:build$ cmake -DCMAKE_INSTALL_PREFIX:PATH=$HOME ..
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
shared build
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.0.1")  
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/yeroslaviz/software/kallisto/build
yeroslaviz@supercube005:build$ make
Scanning dependencies of target htslib
[  3%] Creating directories for 'htslib'
[  6%] No download step for 'htslib'
[ 10%] No patch step for 'htslib'
[ 13%] No update step for 'htslib'
[ 17%] Performing configure step for 'htslib'
/bin/sh: 1: autoheader: not found
CMakeFiles/htslib.dir/build.make:105: recipe for target '../ext/htslib/src/htslib-stamp/htslib-configure' failed
make[2]: *** [../ext/htslib/src/htslib-stamp/htslib-configure] Error 127
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/htslib.dir/all' failed
make[1]: *** [CMakeFiles/htslib.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

[yeroslaviz]

Rerunning the exact same commands with kallisto version 0.43.0 works!

[pmelsted]

The compilation fails because you are missing autoheader, install autoconf to fix this.

I'll check if I can reproduce the error with batch.txt with the latest kallisto version

[pmelsted]

Thanks for reporting this, the issue is fixed in the development branch and will make it into the next release.

Note that your batch file has the same file repeated, but that wasn't the problem.