Error (bug): version `GLIBC_PRIVATE' not found
phylars opened this issue · 1 comments
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.
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)
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"