Error in rule add_refgenome

[rb520826]

Hi,

Thank you for making this pipeline. I am just starting to use it and having a few teething problems. Any advice would be really appreciated! Thank you!

This is the first error:

Error in rule add_refgenome: jobid: 4 output: results/refgenome/GRCh38.rg.catalog.yaml, results/refgenome/GRCh38.rg.metadata.csv, results/refgenome/GRCh38.rg.chromsizes, results/refgenome/GRCh38.rg.fa, results/refgenome/GRCh38.rg.fa.fai log: results/logs/results/refgenome/GRCh38.rg.catalog.yaml.log (check log file(s) for error message) conda-env: /scripts/poreC/Pore-C-Snakemake/.snakemake/conda/40889797 shell: pore_c --dask-scheduler-port 0 --dask-num-workers 5 refgenome prepare .test/resources/GRCh38.fasta.gz results/refgenome/GRCh38.rg --genome-id GRCh38 2> results/logs/results/refgenome/GRCh38.rg.catalog.yaml.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

And the second error:

CreateCondaEnvironmentException: Could not create conda environment from /scripts/poreC/Pore-C-Snakemake/wrappers/whatshap/haplotag/environment.yaml: Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... Building graph of deps: 0%| | 0/6 [00:00<?, ?it/s] Examining @/linux-64::__linux==3.10.0=0: 0%| | 0/6 [00:00<?, ?it/s] Examining @/linux-64::__unix==0=0: 17%|█▋ | 1/6 [00:00<00:00, 2460.00it/s] Examining @/linux-64::__glibc==2.17=0: 33%|███▎ | 2/6 [00:00<00:00, 2744.96it/s] Examining samtools==1.10.0: 50%|█████ | 3/6 [00:00<00:00, 3066.01it/s] Examining whatshap==1.0: 67%|██████▋ | 4/6 [00:00<00:00, 128.17it/s] Examining @/linux-64::__archspec==1=x86_64: 83%|████████▎ | 5/6 [00:00<00:00, 8.65it/s] Examining @/linux-64::__archspec==1=x86_64: 100%|██████████| 6/6 [00:00<00:00, 10.37it/s]

Determining conflicts: 0%| | 0/6 [00:00<?, ?it/s] Examining conflict for __glibc samtools whatshap: 0%| | 0/6 [00:00<?, ?it/s] Examining conflict for samtools whatshap: 17%|█▋ | 1/6 [00:00<00:01, 4.15it/s] Examining conflict for samtools whatshap: 33%|███▎ | 2/6 [00:00<00:00, 8.30it/s]

Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed Solving environment: ...working... Building graph of deps: 0%| | 0/6 [00:00<?, ?it/s] Examining @/linux-64::__linux==3.10.0=0: 0%| | 0/6 [00:00<?, ?it/s] Examining @/linux-64::__unix==0=0: 17%|█▋ | 1/6 [00:00<00:00, 6710.89it/s] Examining @/linux-64::__glibc==2.17=0: 33%|███▎ | 2/6 [00:00<00:00, 7319.90it/s] Examining samtools==1.10.0: 50%|█████ | 3/6 [00:00<00:00, 7903.84it/s] Examining whatshap==1.0: 67%|██████▋ | 4/6 [00:00<00:00, 184.12it/s] Examining @/linux-64::__archspec==1=x86_64: 83%|████████▎ | 5/6 [00:00<00:00, 9.01it/s] Examining @/linux-64::__archspec==1=x86_64: 100%|██████████| 6/6 [00:00<00:00, 10.82it/s]

Determining conflicts: 0%| | 0/6 [00:00<?, ?it/s] Examining conflict for __glibc samtools whatshap: 0%| | 0/6 [00:00<?, ?it/s] Examining conflict for samtools whatshap: 17%|█▋ | 1/6 [00:00<00:01, 4.01it/s] Examining conflict for samtools whatshap: 33%|███▎ | 2/6 [00:00<00:00, 8.03it/s]

Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package samtools conflicts for: whatshap==1.0 -> pysam[version='>=0.15'] -> samtools=1.9 samtools==1.10.0The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.17=0
• samtools==1.10.0 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
• whatshap==1.0 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.17

Note that strict channel priority may have removed packages required for satisfiability.