# Snakemake step error

**URL:** <https://nextstrain.discourse.group/t/snakemake-step-error/304>\
**Category:** Help and Getting Started\
**Created:** [January 26, 2021, 12:59pm UTC](https://nextstrain.discourse.group/t/snakemake-step-error/304 "2021-01-26T12:59:41Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![ibseq](https://avatars.discourse-cdn.com/v4/letter/i/22d042/32.png) [@ibseq](https://nextstrain.discourse.group/u/ibseq)\
**Post date:** [January 26, 2021, 12:59pm UTC](https://nextstrain.discourse.group/t/snakemake-step-error/304/1 "2021-01-26T12:59:41Z")

</div>

Hi all  
got this error trying to install the test data. any advice?  
Thanks, ibz

(nextstrain) ibz@C02DW5NDMD6T ncov % snakemake --cores 4 --profile ./my\_profiles/getting\_started

localrules directive specifies rules that are not present in the Snakefile:  
upload

Building DAG of jobs…  
Using shell: /bin/bash  
Provided cores: 4  
Rules claiming more threads will be scaled down.  
Conda environments: ignored  
Job counts:  
count jobs  
1 align  
1 all  
1 ancestral  
1 clades  
1 combine\_samples  
1 diagnostic  
1 export  
1 filter  
1 finalize  
1 incorporate\_travel\_history  
1 mask  
1 recency  
1 refilter  
1 refine  
1 rename\_subclades  
1 subclades  
1 subsample  
1 tip\_frequencies  
1 traits  
1 translate  
1 tree  
21

[Tue Jan 26 12:53:31 2021]  
Job 22:  
Aligning sequences to defaults/reference\_seq.fasta  
- gaps relative to reference are considered real

```
    mafft --auto --thread 4 --keeplength --addfragments results/prefiltered.fasta defaults/reference_seq.fasta > results/aligned.fasta 2> logs/align.txt

```

[Tue Jan 26 12:53:44 2021]  
Finished job 22.  
1 of 21 steps (5%) done

[Tue Jan 26 12:53:44 2021]  
Job 23: Scanning aligned sequences results/aligned.fasta for problematic sequences

```
    python3 scripts/diagnostic.py --alignment results/aligned.fasta --metadata data/example_metadata.tsv --reference defaults/reference_seq.gb --mask-from-beginning 100 --mask-from-end 50 --output-flagged results/flagged-sequences.tsv --output-diagnostics results/sequence-diagnostics.tsv --output-exclusion-list results/to-exclude.txt 2>&1 | tee logs/diagnostics.txt

```

[Tue Jan 26 12:53:44 2021]  
Job 12: Use metadata on submission date to construct submission recency field

```
    python3 scripts/construct-recency-from-submission-date.py --metadata data/example_metadata.tsv --output results/global/recency.json 2>&1 | tee logs/recency_global.txt

```

Traceback (most recent call last):  
File “scripts/construct-recency-from-submission-date.py”, line 3, in   
from augur.utils import read\_metadata  
ModuleNotFoundError: No module named ‘augur’  
[Tue Jan 26 12:53:44 2021]  
Error in rule recency:  
jobid: 12  
output: results/global/recency.json  
log: logs/recency\_global.txt (check log file(s) for error message)  
shell:

```
    python3 scripts/construct-recency-from-submission-date.py --metadata data/example_metadata.tsv --output results/global/recency.json 2>&1 | tee logs/recency_global.txt
    
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

```

Logfile logs/recency\_global.txt:  
Traceback (most recent call last):  
File “scripts/construct-recency-from-submission-date.py”, line 3, in   
from augur.utils import read\_metadata  
ModuleNotFoundError: No module named ‘augur’

Traceback (most recent call last):  
File “scripts/diagnostic.py”, line 8, in   
from Bio.SeqIO.FastaIO import SimpleFastaParser  
ModuleNotFoundError: No module named ‘Bio’  
[Tue Jan 26 12:53:44 2021]  
Error in rule diagnostic:  
jobid: 23  
output: results/sequence-diagnostics.tsv, results/flagged-sequences.tsv, results/to-exclude.txt  
log: logs/diagnostics.txt (check log file(s) for error message)  
shell:

```
    python3 scripts/diagnostic.py --alignment results/aligned.fasta --metadata data/example_metadata.tsv --reference defaults/reference_seq.gb --mask-from-beginning 100 --mask-from-end 50 --output-flagged results/flagged-sequences.tsv --output-diagnostics results/sequence-diagnostics.tsv --output-exclusion-list results/to-exclude.txt 2>&1 | tee logs/diagnostics.txt
    
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

```

Logfile logs/diagnostics.txt:  
Traceback (most recent call last):  
File “scripts/diagnostic.py”, line 8, in   
from Bio.SeqIO.FastaIO import SimpleFastaParser  
ModuleNotFoundError: No module named ‘Bio’

Shutting down, this might take some time.  
Exiting because a job execution failed. Look above for error message  
Complete log: /Users/ibz/ncov/.snakemake/log/2021-01-26T125331.400352.snakemake.log  
(nextstrain) ibz@C02DW5NDMD6T ncov %