Error in rule hmm_align: HIV in Vpipe

[vfdiamante]

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:

        CONSENSUS_NAME=/home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904
        CONSENSUS_NAME="${CONSENSUS_NAME#*/}"
        CONSENSUS_NAME="${CONSENSUS_NAME//\//-}"

        # 1. clean previous run
        rm -rf   /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments
        rm -f    /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/references/ref_ambig.fasta
        rm -f    /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/references/ref_majority.fasta
        mkdir -p /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments
        mkdir -p /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/references

        # 2. perform alignment # -l = leave temps
        ngshmmalign -v  -R /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/references/initial_consensus.fasta -o /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/full_aln.sam -w /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/rejects.sam -t 1 -N "${CONSENSUS_NAME}"  /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 > /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/ngshmmalign.out.log 2> >(tee /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/alignments/ngshmmalign.err.log >&2)

        # 3. move references into place
        mv /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/{alignments,references}/ref_ambig.fasta
        mv /home/diamantev/HIV/Vpipe/working_2/testing/work/results/2VM-sim/20170904/{alignments,references}/ref_majority.fasta
        
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

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

[DrYak]

Hello, I can't really imagine why this error is happening. Could you provide:

• your configuration file
• your samples.tsv

please?

[vfdiamante]

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? — Reply to this email directly, view it on GitHub <#138 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5T6B6YFAOPTHLXHWE643CTW4V22TANCNFSM6AAAAAAUOXZC24> . You are receiving this because you authored the thread.Message ID: ***@***.***>