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Issue with python libraries in singularity #67

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Shoooosh opened this issue Dec 16, 2024 · 0 comments
Open

Issue with python libraries in singularity #67

Shoooosh opened this issue Dec 16, 2024 · 0 comments

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@Shoooosh
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Hi everyone.

I've been trying to make Mitofinder work with metaspades, using mitofinder's container on singularity. I couldn't install directly singularity and so I installed it via conda (Singularity version 3.8.7) on an environment loaded with python 2.7.

I am running the following command:

singularity run \
-B /hpc/archive/G_BIOANTHRO/GiacomoM:/hpc/archive/G_BIOANTHRO/GiacomoM \
-B /hpc/home/giacomo.mercuri/.conda/envs/mitofinder2:/env \
-B /hpc/home/giacomo.mercuri/.conda/envs/mitofinder2/lib:/opt/conda/lib \
/hpc/archive/G_BIOANTHRO/GiacomoM/mitofinder_v1.4.2.sif \
-j SRR11921218_metaspades \
-1 $indir/SRR11921218_1.fastq.gz \
-2 $indir/SRR11921218_2.fastq.gz \
--metaspades \
--max-contig-size 30000 \
-r /hpc/archive/G_BIOANTHRO/GiacomoM/data/no_backup/Macaca/ReferenceMacaca/Macaca.gb \
-o 2 -p 6 -m 260

But I am getting this error in the metaspades log:
/opt/conda/bin/python: error while loading shared libraries: libpython2.7.so.1.0: cannot open shared object file: No such file or directory

I get that the issue is probably with my singularity and the binding process, but I'm not sure how to tackle this.

Here is the full .log from metaspades
spades.log

Any help would be much appreciated.
Thanks

PS: when I try to run the script "compress_all.py" from the singularity shell through the container it does seem to work by itself...

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