deepconsensus.scripts.run_deepconsensus errors

google / deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

BSD 3-Clause "New" or "Revised" License

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deepconsensus.scripts.run_deepconsensus errors #13

Closed zhoudreames closed 2 years ago

zhoudreames commented 2 years ago

i got some errors show in blow when i run python3 -m deepconsensus.scripts.run_deepconsensus --input_subreads_aligned=P05TYD21354128-1_r64114_20210126_052631_1_A02.subreads_to_ccs.bam --input_subreads_unaligned=DRC_chr3_20Mb_rmTail.P05TYD21354128-1_r64114_20210126_052631_1_A02.bam --input_ccs_fasta=P05TYD21354128-1_r64114_20210126_052631_1_A02.ccs.fasta --output_directory=1.tmp --checkpoint=01.DeepConsusModel i dont know how to solve it ,could you help me ?thanks~

danielecook commented 2 years ago

@zhoudreames can you try installing bzip2 in the conda env you are using?

Something like this...

conda install -c conda-forge -c bioconda bzip2

pichuan commented 2 years ago

Hi @zhoudreames , we've made a release in January that cleaned up a code quite a bit. And it now includes a Docker solution as well. If you're still encountering issues, please feel free to report again!