Error (bug): version `GLIBC_PRIVATE' not found

[phylars]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? This bug is generated from Salmon.

Describe the bug To use Salmon, I installed windows subsystem for Linux (WLS), then newest Ubuntu, Anaconda, bioconda, and finally Salmon (via Bioconda) on my PC. However, when I run any order (making index or do quant), I get this error message:

salmon: /lib/x86_64-linux-gnu/libpthread.so.0: version `GLIBC_PRIVATE' not found (required by /home/plyric/anaconda3/share/salmon-0.8.1-0/bin/../lib/librt.so.1)

I checked what this means and thought this is because this Ubuntu may not have GLIBC C++ library, so I followed some tutorial to (1) update my Ubuntu, and (2) install the newest GBLIC library, but the problem still persist.

However, if I use the exact same code on a HPCC, it actually works.

To Reproduce Steps and data to reproduce the behavior: Totally following your index preparation tutorial like this:

grep "^>" <(gunzip -c TAIR10_chr_all.fas.gz) | cut -d " " -f 1 > decoys.txt sed -i.bak -e 's/>//g' decoys.txt cat Araport11_cdna_20240409.gz TAIR10_chr_all.fas.gz > gentrome.fasta.gz salmon index -t gentrome.fasta.gz -d decoys.txt -p 12 -i salmon_index --gencode

Then the error pops: salmon: /lib/x86_64-linux-gnu/libpthread.so.0: version `GLIBC_PRIVATE' not found (required by /home/plyric/anaconda3/share/salmon-0.8.1-0/bin/../lib/librt.so.1)

If I manage to get the index using an HPCC and run local quant like this: salmon quant -i Arabidopsis_index -l A -1 filtered_a234-f1_S10_L002_R1_001.fastq.gz -2 filtered_a234-f1_S10_L002_R2_001.fastq.gz --validateMappings -o test_transcripts_quant Then same error pops.

Specifically, please provide at least the following information:

• Which version of salmon was used? It is very strange. I am supposed to get v1.10.3 by bioconda default, but -v order get the same error. So I don't know how to get my version. The conda list says "0.8.1"
• How was salmon installed (compiled, downloaded executable, through bioconda)? Bioconda, official install order code
• Which reference (e.g. transcriptome) was used? Arabidopsis (not important for the issue)
• Which read files were used? Arabidopsis (not important for the issue)
• Which which program options were used? Default

Expected behavior I just want it work.

Screenshots

Desktop (please complete the following information):

• OS: Windows 11 => WSL => Ubuntu 22.04.4 LTS (GNU/Linux 5.10.16.3-microsoft-standard-WSL2 x86_64)

[phylars]

I somehow deleted it and forced it to install 1.10.3 and problem solved. "conda install bioconda::salmon=1.10.3" does not work I have to do "conda install salmon=1.10.3"