Error in rule "align"

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1

Hi there!
I have installed nextstrain on a computer cluster I use, and I am trying to run the example runs included in the /ncov repository. When I run:
snakemake --cores 1 --profile /my_profiles/example/ -p

I get this error in the log: (the Logfile logs/align_example-data.txt: mentioned is empty)

Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job counts:
	count	jobs
	5	add_branch_labels
	5	adjust_metadata_regions
	1	align
	1	all
	5	ancestral
	5	annotate_metadata_with_index
	5	build_align
	5	calculate_epiweeks
	5	clade_files
	5	clades
	5	colors
	5	combine_samples
	5	diagnostic
	5	distances
	5	emerging_lineages
	5	export
	4	extract_subsampled_sequences
	5	filter
	5	finalize
	5	include_hcov19_prefix
	5	index
	1	index_sequences
	5	logistic_growth
	5	mask
	5	mutational_fitness
	4	priority_score
	4	proximity_score
	5	recency
	5	refine
	5	rename_emerging_lineages
	1	sanitize_metadata
	13	subsample
	5	tip_frequencies
	5	traits
	5	translate
	5	tree
	169

[Fri Jan 14 20:08:55 2022]
Job 11: 
        Aligning sequences to defaults/reference_seq.fasta
            - gaps relative to reference are considered real
        


        python3 scripts/sanitize_sequences.py             --sequences data/example_sequences.fasta             --strip-prefixes hCoV-19/ SARS-CoV-2/             --output /dev/stdout 2> logs/sanitize_sequences_example-data.txt             | nextalign             --jobs=1             --reference defaults/reference_seq.fasta             --genemap defaults/annotation.gff             --genes ORF1a,ORF1b,S,ORF3a,E,M,ORF6,ORF7a,ORF7b,ORF8,N,ORF9b             --sequences /dev/stdin             --output-dir results/translations             --output-basename seqs_example-data             --output-fasta results/aligned_example-data.fasta             --output-insertions results/insertions_example-data.tsv > logs/align_example-data.txt 2>&1;
        xz -2 results/aligned_example-data.fasta;
        xz -2 results/translations/seqs_example-data*.fasta
        
[Fri Jan 14 20:08:55 2022]
Error in rule align:
    jobid: 11
    output: results/aligned_example-data.fasta.xz, results/insertions_example-data.tsv, results/translations/seqs_example-data.gene.ORF1a.fasta.xz, results/translations/seqs_example-data.gene.ORF1b.fasta.xz, results/translations/seqs_example-data.gene.S.fasta.xz, results/translations/seqs_example-data.gene.ORF3a.fasta.xz, results/translations/seqs_example-data.gene.E.fasta.xz, results/translations/seqs_example-data.gene.M.fasta.xz, results/translations/seqs_example-data.gene.ORF6.fasta.xz, results/translations/seqs_example-data.gene.ORF7a.fasta.xz, results/translations/seqs_example-data.gene.ORF7b.fasta.xz, results/translations/seqs_example-data.gene.ORF8.fasta.xz, results/translations/seqs_example-data.gene.N.fasta.xz, results/translations/seqs_example-data.gene.ORF9b.fasta.xz
    log: logs/align_example-data.txt (check log file(s) for error message)
    shell:
        
        python3 scripts/sanitize_sequences.py             --sequences data/example_sequences.fasta             --strip-prefixes hCoV-19/ SARS-CoV-2/             --output /dev/stdout 2> logs/sanitize_sequences_example-data.txt             | nextalign             --jobs=1             --reference defaults/reference_seq.fasta             --genemap defaults/annotation.gff             --genes ORF1a,ORF1b,S,ORF3a,E,M,ORF6,ORF7a,ORF7b,ORF8,N,ORF9b             --sequences /dev/stdin             --output-dir results/translations             --output-basename seqs_example-data             --output-fasta results/aligned_example-data.fasta             --output-insertions results/insertions_example-data.tsv > logs/align_example-data.txt 2>&1;
        xz -2 results/aligned_example-data.fasta;
        xz -2 results/translations/seqs_example-data*.fasta
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/align_example-data.txt:


Removing output files of failed job align since they might be corrupted:
results/insertions_example-data.tsv
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Thanks!!!

2

Hi there, I think I have the same issue. I think it might be related to what is reported in the logfile logs/sanitize_sequences_example-data.txt, ie

Traceback (most recent call last):
  File "scripts/sanitize_sequences.py", line 2, in <module>
    from augur.io import open_file, read_sequences, write_sequences
ModuleNotFoundError: No module named 'augur'

the installation was smooth and the output of nextstrain check-setup --set-default was:

Testing your setup…

# docker is not supported
✘ no: docker is installed
✘ no: docker run works
? unknown: containers have access to >2 GiB of memory
✔ yes: image is new enough for this CLI version

# native is supported
✔ yes: snakemake is installed
✔ yes: augur is installed
✔ yes: auspice is installed

# aws-batch is not supported
✘ no: job description "nextstrain-job" exists
✘ no: job queue "nextstrain-job-queue" exists
✘ no: S3 bucket "nextstrain-jobs" exists

All good!  Supported Nextstrain environments: native

Setting default environment to native.

Thank you,

Domenico

3

Hi @Sanna! I would second @dsimone’s suggestion to check logs/sanitize_sequences_example-data.txt. If you have an error such as ModuleNotFoundError: No module named 'augur' then I would suggest reinstalling the nextstrain conda environment (if you are using that), or reinstalling augur within your current working environment. Let us know how you get on!

4

Hi @james thanks for your feedback. Indeed I deactivated the env and reactivated it and then it worked… I’ve probably missed something that happened but eventually it went through. Sorry I can’t be of so much help!

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