Hi,
I've put the test suite line below (and others) into some autopkgtest
and for the moment forced the build time test to pass[1] to get some
package to test. I've built this and installed salmon as well as
salmon-dbgsym and was running the same test as Dominik via:
cp -a /usr/share/doc/salmon/examples/* .
gdb --args salmon index -t transcripts.fasta -i sample_salmon_quasi_index
(gdb) run
Starting program: /usr/bin/salmon index -t transcripts.fasta -i
sample_salmon_quasi_index
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
index ["sample_salmon_quasi_index"] did not previously exist . . . creating it
[2023-02-22 15:10:42.244] [jLog] [warning] The salmon index is being built
without any decoy sequences. It is recommended that decoy sequence (either
computed auxiliary decoy sequence oor 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-bsased-mode.
[2023-02-22 15:10:42.244] [jLog] [info] building index
out : sample_salmon_quasi_index
[2023-02-22 15:10:42.244] [puff::index::jointLog] [info] Running fixFasta
[New Thread 0x757ff6c0 (LWP 2115402)]
[Step 1 of 4] : counting k-mers
[Thread 0x757ff6c0 (LWP 2115402) exited]
[2023-02-22 15:10:42.248] [puff::index::jointLog] [info] Replaced 0 non-ATCG
nucleotides
[2023-02-22 15:10:42.248] [puff::index::jointLog] [info] Clipped poly-A tails
from 0 transcripts
wrote 15 cleaned references
Thread 1 "salmon" received signal SIGSEGV, Segmentation fault.
rapidjson::PrettyWriter,
rapidjson::UTF8, rapidjson::UTF8, rapidjson::CrtAllocator,
2u>::StartObject (this=0x7fff8168) at
/usr/include/rapidjson/prettywriter.h:113
113 new (Base::level_stack_.template Push())
typename Base::Level(false);
(gdb) bt 20
#0 rapidjson::PrettyWriter,
rapidjson::UTF8, rapidjson::UTF8, rapidjson::CrtAllocator,
2u>::StartObject (this=0x7fff8168)
at /usr/include/rapidjson/prettywriter.h:113
#1 cereal::JSONOutputArchive::writeName (this=0x7fff8030) at
/usr/include/cereal/archives/json.hpp:347
#2 0x55b04428 in cereal::prologue (ar=...) at
./external/pufferfish/include/cereal/archives/json.hpp:891
#3 cereal::OutputArchive::process
(head=@0x7fff7d55: false, this=0x7fff8030) at
./external/pufferfish/include/cereal/cereal.hpp:416
#4 cereal::OutputArchive::operator()
(this=) at ./external/pufferfish/include/cereal/cereal.hpp:311
#5 cereal::save (t=..., ar=...) at
./external/pufferfish/include/cereal/archives/json.hpp:944
#6 cereal::OutputArchive::processImpl,
(cereal::traits::detail::sfinae)0> (t=..., this=)
at ./external/pufferfish/include/cereal/cereal.hpp:505
#7 cereal::OutputArchive::process > (head=..., this=) at
./external/pufferfish/include/cereal/cereal.hpp:417
#8 cereal::OutputArchive::operator() > (this=0x7fff8030) at
./external/pufferfish/include/cereal/cereal.hpp:311
#9 fixFasta (parser=0x76076800, decoyNames=..., keepDuplicates=false,
k=31, sepStr=" \t", expect_transcriptome=true, noclip_polya=false, iomutex=...,
log=std::shared_ptr (use count 4, weak count 0) = {...},
outFile="sample_salmon_quasi_index/ref_k31_fixed.fa",
refIdExtensions=std::vector of length 15, capacity 15 = {...},
shortRefs=std::vector of length 0, capacity 0) at
./external/pufferfish/src/FixFasta.cpp:456 o
#10 0x55b08195 in fixFastaMain (args=std::vector of length 7, capacity
8 = {...}, refIdExtension=std::vector of length 15, capacity 15 = {...},
s
shortRefs=std::vector of length 0, capacity 0,
log=std::shared_ptr (use count 4, weak count 0) = {...},
hasFeatures=hasFeatures@entry=false)
at ./external/pufferfish/src/FixFasta.cpp:686
#11 0x55a8a510 in pufferfishIndex (indexOpts=...) at
./external/pufferfish/src/PufferfishIndexer.cpp:432
#12 0x5566399e in SalmonIndex::buildPuffIndex_ (idxOpt=...,
indexDir=..., this=0x7603e280) at ./include/SalmonIndex.hpp:111
#13 SalmonIndex::build (idxOpt=..., indexDir=..., this=0x7603e280) at
./include/SalmonIndex.hpp:76
#14 salmonIndex (argc=, argv=) at
./src/BuildSalmonIndex.cpp:247
#15 0x555fe9a0 in std::function
>&)>::operator()(int, char const**, std::unique_ptr >&) const
(__args#2=std::unique_ptr = {...}, __args#1=,
__args#0=, this=0x7604e1a8)
at /usr/include/c++/12/bits/std_function.h:591
#16 main (argc=, argv=0x7fffde98) at ./src/Salmon.cpp:267
The traceback with the latest Pufferfish is different before
./include/SalmonIndex.hpp:111
Interestingly the old pufferfish (used by Dominik) triggers failures in
spdlog while the updated pufferfish above triggers the problem in
rapidjson.
I now tried to check the original upstream tarball, have built it via
> cmake -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2
>
