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Error in rule hmm_align: HIV in Vpipe #138
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Hello, I can't really imagine why this error is happening. Could you provide:
please? |
Hello,
Thank you for the reply. By the way, I already figured out the error from
the previous one that I posted and right now Im keep getting an error in
HAPLOCLIQUE and even in SAVAGE.
Here is the screenshot:
[image: image.png]
Here are the needed information attached in this email. I have tried
exploring config file and even double check the hierarchy of the directory
of the samples.
Hoping for your reply soon.
Cheers,
Van
…On Sat, Mar 18, 2023 at 5:02 PM DrYak ***@***.***> wrote:
Hello, I can't really imagine why this error is happening. Could you
provide:
- your configuration file
- your samples.tsv
please?
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Hello, I would like to ask what does this error mean and how will I solve this error?
Activating conda environment: .snakemake/conda/0a11ef3f67c5c382159134f72bbed3ac_
ERROR: Count argument '2-testing-work-results-2VM-sim-20170904' is not an integral/floating point value! Aborting.
[Thu Feb 2 15:03:36 2023]
Error in rule hmm_align:
jobid: 3
input: /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/references/initial_consensus.fasta, /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/preprocessed_data/R1.fastq, /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/preprocessed_data/R2.fastq
output: /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/full_aln.sam, /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/rejects.sam, /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/references/ref_ambig.fasta, /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/references/ref_majority.fasta
log: /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/ngshmmalign.out.log, /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/ngshmmalign.err.log (check log file(s) for error details)
conda-env: /home/diamantev/HIV/Vpipe/working_2/.snakemake/conda/0a11ef3f67c5c382159134f72bbed3ac_
shell:
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-02-02T150334.285845.snakemake.log
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