Segmentation fault with shipped example #835
Description
The bug is primarily related to salmon (bulk mode)
Describe the bug
After building salmon it segfaults with the example file shipped with the source tarball.
The problem is described in detail in the Debian bug tracking system. While the Debian bug is against version 1.9.0 I can perfectly reproduce the issue with a recent download of version 1.10.0
To Reproduce
Steps and data to reproduce the behavior:
Download your release tarball.
$ tar xaf v1.10.0.tar.gz
$ cd salmon-1.10.0
# build on Debian testing system
$ cmake -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE
$ make
$ tar xaf sample_data.tgz
$ src/salmon index -t sample_data/transcripts.fasta -i sample_salmon_quasi_index
Version Info: This is the most recent version of salmon.
[2023-03-08 17:30:38.873] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
[2023-03-08 17:30:38.873] [jLog] [info] building index
out : sample_salmon_quasi_index
[2023-03-08 17:30:38.873] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
[2023-03-08 17:30:38.879] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2023-03-08 17:30:38.879] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
wrote 15 cleaned references
Segmentation fault.
- Version 1.9.0 as well as version 1.10.0 are affected. Unfortunately we did not managed to package version 1.7.0 and 1.8.0 but I confirm that version 1.6.0 was not affected by the described problem.
- Salmon was build as Debian package as well as built from source (see above)
- The reference was taken from the
sample_datashipped with the release tarball
Expected behavior
Clean processing without SEGFAULT.
Desktop (please complete the following information):
- OS: Debian (testing or unstable)
Additional context
- You can find some debug logs inside the Debian bug log.
- There is a build log which includes the said salmon call above as build time test
- When ignoring the package build time test the Continuous Integration log might be interesting as well
Kind regards, Andreas.