Removing output files of failed job getbins since they might be corrupted:
M12/binning/metabat/bins
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-03-19T035013.317143.snakemake.log
Hi there -I'm running into an error when binning my samples. Here is the log message:
_[Wed Mar 20 04:13:50 2024] localrule get_bins: input: M12/binning/metabat/cluster_attribution.tsv, Assembly/fasta/M12.fasta output: M12/binning/metabat/bins log: M12/logs/binning/get_bins_metabat.log jobid: 230 reason: Missing output files: M12/binning/metabat/bins; Input files updated by another job: Assembly/fasta/M12.fasta, M12/binning/metabat/cluster_attribution.tsv wildcards: sample=M12, binner=metabat resources: tmpdir=/tmp/212440.1.long, mem_mb=244032, mem_mib=232728, time_min=300, runtime=300 Activating conda environment: atlas_analysis/databases/condaenvs/337744b4752a4601911c04f7a64ed693 Activating conda environment: atlas_analysis/databases/condaenvs/337744b4752a4601911c04f7a64ed693 [Wed Mar 20 04:13:51 2024] Error in rule get_bins: jobid: 230 input: M12/binning/metabat/cluster_attribution.tsv, Assembly/fasta/M12.fasta output: M12/binning/metabat/bins log: M12/logs/binning/get_bins_metabat.log (check log file(s) for error details) conda-env: /afs/crc.nd.edu/user/a/abadilla/genomics_project/atlas_analysis/databases/condaenvs/337744b4752a4601911c04f7a64ed693 Logfile M12/logs/binning/get_bins_metabat.log: 2024-03-20 04:13:51 index fasta file Assembly/fasta/M12.fasta for fast access 2024-03-20 04:13:51 Found 1 contigs ['M12_0'] 2024-03-20 04:13:51 Uncaught exception: Traceback (most recent call last): File "/afs/crc.nd.edu/user/a/abadilla/genomics_project/.snakemake/scripts/tmp6fk61sgv.get_fasta_of_bins.py", line 109, in
get_fasta_of_bins(
File "/afs/crc.nd.edu/user/a/abadilla/genomics_project/.snakemake/scripts/tmp6fk61sgv.get_fasta_of_bins.py", line 96, in get_fasta_of_bins
fasta_contigs = [contig_fasta_dict[c] for c in bin_contig_names]
File "/afs/crc.nd.edu/user/a/abadilla/genomics_project/.snakemake/scripts/tmp6fk61sgv.get_fasta_of_bins.py", line 96, in
fasta_contigs = [contig_fasta_dict[c] for c in bin_contig_names]
File "/afs/crc.nd.edu/user/a/abadilla/genomics_project/atlas_analysis/databases/condaenvs/337744b4752a4601911c04f7a64ed693/lib/python3.8/site-packages/Bio/File.py", line 422, in getitem
record = self._proxy.get(self._offsets[key])
KeyError: 'M12_0'
================================================================================
Removing output files of failed job getbins since they might be corrupted: M12/binning/metabat/bins Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-03-19T035013.317143.snakemake.log
Complete snakemake log is attached here: 2024-03-19T035013.317143.snakemake.log
I do have contigs in my samples according to the previous log from Megahit and the contig file (.fasta) for my M12 sample: M12.txt
The cluster attribution file, however, is showing a unique M12_0 contig that is not part of the M12.fasta table. cluster_attribution.csv
Any idea how to troubleshoot this? Thanks!!