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MissingRuleException error #19
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I have the same issue |
Try to run the command without "all"
and it'll run the pipeline with default jobs (calc_depth, call, call_cutesv, filter_vcf, index_lra, index_vcf, map_lra,print_version and sort_vcf).
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Thank you for your comment! However, when I do this I get a further error: File "pysam/libcutils.pyx", line 115, in pysam.libcutils.encode_filename I have tried installing the different programmes in the command but still come up with the same error. Please can you help me? Thanks! |
Hi! I have the same problem. Have some of you managed to solve the issue? snakemake all is not working edit: MissingOutputException in line 111 of /data/ont/286/minread15K/cutesv/pipeline-structural-variation-2.0.2/Snakefile:
Job Missing files after 5 seconds:
/data/ont/hg38/hg38_dna.primary_assembly.fa.gli
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Job id: 6 completed successfully, but some output files are missing. 6
File "/home/prom/anaconda3/envs/ont/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 589, in handle_job_success
File "/home/prom/anaconda3/envs/ont/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 252, in handle_job_success
It means that rule index_lra that should generate reference.fa.gli is not working properly. Do you have any idea how to fix it? Tried to change --latency-wait, nothing changed |
Hi imdanique, I got the same error. To solve it I copied the reference genome fasta file (reference.fa) to another location in the server (a location where I have full access/permisson, such as your home) and then used that new path in the "reference_fasta" parameter. As the pipeline tries to write (output) the reference.fa.gli file in the same location where the reference.fa file is, in my cause would cause this error. Try this to exclude the same issue. |
Hi!
I am trying to use the pipeline with the default command: snakemake all --config input_fastq=/path/.fastq reference_fasta=/path/ref.fasta threads=16 --cores 4
(I got told to add the cores on by another error).
However I get this error: MissingRuleException: No rule to produce all (if you use input functions make sure that they don't raise unexpected exceptions).
I'm not too familiar with snakemake but can't seem to find 'all' in the snakefile or scripts? How do I resolve this?
Thanks!
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