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Dependency libraries problem #1
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Ok, this seems like you are missing more than just libbz2 in your conda environment. You would need to install g++-10, gcc-10, build-essential and libbz2-dev if you want to compile and build taxor on your own. |
I also uploaded an updated binary of Taxor using the static bzip2 library. Please try it out and tell me if it worked or throws any other error messages. |
It seems like you are using older GCC and G++ versions on the system. However, I created a docker image, which you can find here. I hope this solves your issues. |
Unfortunately it's not clear to me from the error message which shared library in the docker image is missing. Did singularity tell you more about tha? |
BTW: I could successfully run the docker container image even on my windows laptop. So it seems more like an issue with singularity |
Hi, I recently tried to add some static libraries to the binary executable of Taxor. Now it includes the zlib, glibc and libstdc++. You may want to give it a try and report if it works or not. Unfortunately, all my Linux distributions have no issues with the executables and I could not reproduce your issues. |
Unfortunately, the latest binary still failed to run on our server. It said
So I created a conda environment and installed
However, it still reported the same error. So I configured the
Hmm, new error about the glibc version :
Then I installed a glibc (v2.33). While it still failed. I can't do anything with the
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Yeah, this is a weird behavior on some platforms when using the precompiled binary. I still need to figure out why the math library is making troubles. In the meantime, as you are using conda anyway, I recommend you to use the taxor bioconda package. This should fix your issue. |
Good to know that! The conda way should be added to the Installation section. BTW. In the Installation section of README, "executable binaries" links to KMCP. |
Oh damn...Thanks for pointing that out. I immediately resolved that and added the conda as in installation option. |
unfortunately, it failed to run with some sample data.
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The index file should be an indexed database (created with the |
Oh sorry, that line resulted from the wrong input. While it exits unexpectedly as well with
The other indexes worked!
BTW, if |
The error remains with redownloaded
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The md5sum is correct. Can you please check the taxor version, you are using. |
Installed with conda.
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I don't know what happened with the files but I rebuilt the indexes, tested, and uploaded them again. At least on our cluster, they work as expected. Please contact me again if they still cause a segmentation fault. |
Same error.
Here's the environment:
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I created a conda environtment with miniconda3 for taxor on a different laptop and had no issues when using the genbank -viral index. When looking at you package versions, the only two things that I recognized was that your environment is missing the
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Hi @JensUweUlrich, I'm having the same issue - Segmentation fault (core dumped) when I run <taxor search --index-file databases/gtdb-R214-k22-s12.hixf --query-file BC07_cdna2_filtered.fastq --output-file test.txt --error-rate 0.99 --threads 4> VERSION ` Thanks |
Did you check if the md5sum of your downloaded index file is correct? I also recognized that seom packages have different versions than the one I had in my conda environment. So you could also try to change to taxor version 0.1.2 or zstd vrsion 1.5.5. |
Looked like the downloaded database was the issue - works well with databases build from scratch - thanks |
Hello, I built database using
i get this error
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@bioinfo17 can you share your commands for building database with scracth. I downloaded my genomes as mentioned in document. But i still get the above error. |
Dear Jens-Uwe Ulrich,
I am notice you already provided a compiled version, but when I use it, it's says "./taxor: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory".
It looks like the software needs some libraries from the conda environment, and I don't have the root account of the cluster.
And also those libraries cannot be installed by myself.
Best wishes,
Yue Ma
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