issue calculon2 - Githubissues

[Thu May 9 19:56:40 2024] rule produce_fasta: input: results/data/subunits/subunits.json output: results/data/subunits/subunits/fasta jobid: 5 reason: Missing output files: results/data/subunits/subunits/fasta; Input files updated by another job: results/data/subunits/subunits.json wildcards: protein_complex=subunits resources: tmpdir=/tmp

✨ Pixi task (default): bash install.sh ⠁ updating packages in 'default' ⠁ updating packages in 'default' ⠁ downloading [00:00:00] [────────────────────] 0/247
× failed to link 'lib/libgfortran.so.5.0.0' ├─▶ unexpected io operation while removing clobbered file × failed to link 'bin/mmseqs' ├─▶ unexpected io operation while removing clobbered file ╰─▶ No such file or directory (os error 2)

[Thu May 9 19:56:40 2024] Error in rule produce_fasta: jobid: 5 input: results/data/subunits/subunits.json output: results/data/subunits/subunits/fasta shell:

# files={output.files}
# directory=${files%/*}
cd workflow/scripts/dependencies/CombFold
unset PIXI_PROJECT_MANIFEST
pixi run python3 scripts/prepare_fastas.py ../../../../results/data/subunits/subunits.json       --stage pairs --output-fasta-folder ../../../../results/data/subunits/subunits/fasta       --max-af-size 1800

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Thu May 9 19:56:41 2024] Error in rule setup_combfold: jobid: 2 output: results/checkpoints/setup_combfold shell:

echo "setting up combfold"
cd workflow/scripts/dependencies/CombFold
echo "We are in CombFold:"
ls
unset PIXI_PROJECT_MANIFEST
pixi run make
echo "compilation seems to have been a success!"
./CombinatorialAssembler/AF2trans.out --help

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Luke-ebbis / complex-prediction

issue calculon2 #6