stl_vector.h error

[fdecarpentier]

Bug primarily related to salmon (bulk mode)

Using files from the tutorial (https://combine-lab.github.io/salmon/getting_started/) did not trigger the bug so I had to make an example with my data. C. reinhardtii annotation and assembly available here : https://data.jgi.doe.gov/refine-download/phytozome?q=Chlamydomonas+reinhardtii+CC-4532 Reads available here : https://www.ncbi.nlm.nih.gov/sra/SRR10737773

Gentrome and Transcriptome indexes where generate as follows :

grep "^>" <(gunzip -c CreinhardtiiCC_4532_707_v6.0.hardmasked.fa.gz) | cut -d " " -f 1 > decoys.txt
sed -i.bak -e 's/>//g' decoys.txt

cat CreinhardtiiCC_4532_707_v6.1.transcript_primaryTranscriptOnly.fa.gz CreinhardtiiCC_4532_707_v6.0.hardmasked.fa.gz > gentrome.fa.gz

salmon index -t gentrome.fa.gz -d decoys.txt -p 12 -i index_gentrome
salmon index -t CreinhardtiiCC_4532_707_v6.1.transcript_primaryTranscriptOnly.fa.gz -p 12 -i index_transcriptome

Salmon quant was run as follows:

salmon quant -i index_gentrome -l A -1 SRR10737773_1.fastq -2 SRR10737773_2.fastq -p 12 -o quant_gentrome
salmon quant -i index_transcriptome -l A -1 SRR10737773_1.fastq -2 SRR10737773_2.fastq -p 12 -o quant_transcriptome

I get this error when quantifying on gentrome and not transcriptome (full log : salmon.log)

/usr/include/c++/14.1.1/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Transcript; _Alloc = std::allocator<Transcript>; reference = Transcript&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
salmon.sh: line 3: 54621 Aborted (core dumped) salmon quant -i index_gentrome -l A -1 SRR10737773_1.fastq -2 SRR10737773_2.fastq -p 12 -o quant_gentrome

Detail OS : Arch Linux x86_64 Kernel : 6.9.7-arch1-1 gcc: 14.1.1 20240522 Salmon version : 1.10.3 Salmon was installed through Arch AUR (https://aur.archlinux.org/packages/salmon) because conda triggers another bug. I suspect that this is the cause of the bug. I tried to clean up my dependencies/packages but could not fix the bug.

Thank you for this great program! Cheers!