RuntimeError: Decompression 'SNAPPY' not available

[iReprogram]

Running snakemake from Ubuntu 18.04 (on Windows Subsystem Linux) w/ 32GB of RAM Output from: snakemake --use-conda --cores $N (crashes during step 5 of 11)

Error in rule create_alignment_table: jobid: 6 output: results/align_table/DpnII_run01_GRCh38.at.catalog.yaml, results/align_table/DpnII_run01_GRCh38.at.alignment.parquet, results/align_table/DpnII_run01_GRCh38.at.read.parquet, results/align_table/DpnII_run01_GRCh38.at.overlap.parquet, results/align_table/DpnII_run01_GRCh38.at.alignment_summary.csv, results/align_table/DpnII_run01_GRCh38.at.read_summary.csv log: results/logs/results/align_table/DpnII_run01_GRCh38.at.catalog.yaml.log (check log file(s) for error message) shell: set +u; source ~/miniconda3/etc/profile.d/conda.sh ; conda activate ; conda activate poreC; pore_c alignments parse results/mapping/DpnII_run01_GRCh38.read_sort.bam results/virtual_digest/DpnII_GRCh38.vd.catalog.yaml results/align_table/DpnII_run01_GRCh38.at -n 5 2>results/logs/results/align_table/DpnII_run01_GRCh38.at.catalog.yaml.log (exited with non-zero exit code)

Error Message for yaml.log file: compression.py", line 128, in decompress_data (algorithm.upper(), sorted(decompressions))) RuntimeError: Decompression 'SNAPPY' not available. Options: ['BROTLI', 'GZIP', 'UNCOMPRESSED']

[aboyle]

Same problem - you can fix this by installing python-snappy in the poreC conda environment:

conda activate poreC conda install python-snappy

[eharr]

@iReprogram did @aboyle's suggestion fix this for you? If not please try the latest version of the pipeline and pore-c tools - they should have fixed some of the installation issues.