I’m getting an error message when I try to run the basic nexstrain example :
snakemake --profile my_profiles/example -p
The error messages i get say that the code can’t find an auger command (see below). The dry run (using the -np flag) works fine.
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Stacia Wyman
Nov 22, 2021, 12:13 PM (22 hours ago)
Hi Erik, I’ve created a directory for you in: /groups/wyman/users/ on igi.biotite where you can work. Conda is installed on biotite. You should sign up for a GI
Erik Nelson
Nov 22, 2021, 12:37 PM (22 hours ago)
Hi Stacia, I’ll get started on this. I noticed that rule #6 of Rohan’s “biotite code” says “I will not use Conda”, yet Conda is installed on biotite. Seems like
Stacia Wyman
Nov 22, 2021, 12:44 PM (22 hours ago)
Policy changed on Conda on biotite, right Rohan? Time to update the docs. 
Erik Nelson
Nov 22, 2021, 12:51 PM (22 hours ago)
. . one more thing, I started registering on GSAID, however, they say to use my institutional email, and that using web email addresses such as gmail or yahoo w
Stacia Wyman
Nov 22, 2021, 12:53 PM (22 hours ago)
Yes you should wait. They are overwhelmed and who knows how long it would take. They are pretty strict.
Erik Nelson
Nov 22, 2021, 12:58 PM (22 hours ago)
got it, thanks
Rohan Sachdeva
Nov 22, 2021, 2:02 PM (20 hours ago)
Hi - It’s technically still banned (that’s why I haven’t updated the docs). I’m trying to figure a standardized install/systemwide install. But with that said I
Stacia Wyman
Nov 22, 2021, 2:05 PM (20 hours ago)
Ah! Sorry I thought it was system-wide. Thanks!
Erik Nelson nelsonerikd@gmail.com
Attachments
Nov 22, 2021, 2:58 PM (20 hours ago)
to Stacia
Hi Stacia, I’m getting an error message when I try to run the basic nexstrain example :
snakemake --profile my_profiles/example -p
(see the attached .txt file for details). The dry run (using the -np flag) runs fine. Also, is there some package you would recommend to view the JSON output files (trees) on a Mac?
Attachments area
Erik Nelson
Nov 22, 2021, 3:12 PM (19 hours ago)
ok, I see, use Auspice
Stacia Wyman
9:26 AM (1 hour ago)
Did you figure out your snakemake error? If you search the error message on the discussion board, you might find it. That’s what I did when I was figuring it ou
Erik Nelson
10:34 AM (26 minutes ago)
Not yet. The error says that it can’t find an auger command. This is their own example, so it should work. I didn’t change anything in the ncov/ directory, and
Erik Nelson
10:35 AM (24 minutes ago)
Did you try running the example yourself when you installed the code?
Stacia Wyman
10:40 AM (20 minutes ago)
I got through the tutorial. I recommend doing that since the video didn’t help.
Erik Nelson nelsonerikd@gmail.com
10:49 AM (11 minutes ago)
to Stacia
I got through the tutorial. I recommend doing that since the video didn’t help.
Do you mean the written instructions (the video is called “video tutorial walkthrough”)? I’ve read / watched both.
enelson@igi-biotite:/groups/wyman/projects/ncov$ snakemake --profile my_profiles/example -p
Building DAG of jobs…
Using shell: /bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job count min threads max threads
aa_muts_explicit 5 1 1
add_branch_labels 5 1 1
adjust_metadata_regions 5 1 1
all 1 1 1
ancestral 5 1 1
build_align 5 2 2
calculate_epiweeks 5 1 1
clades 5 1 1
colors 5 1 1
combine_samples 5 1 1
distances 5 1 1
emerging_lineages 5 1 1
export 5 1 1
filter 1 1 1
finalize 5 1 1
include_hcov19_prefix 5 1 1
index_sequences 1 1 1
logistic_growth 5 1 1
mutational_fitness 5 1 1
priority_score 4 1 1
proximity_score 4 1 1
recency 5 1 1
refine 5 1 1
rename_emerging_lineages 5 1 1
subsample 13 1 1
tip_frequencies 5 1 1
traits 5 1 1
translate 5 1 1
tree 5 2 2
total 139 1 2
Select jobs to execute…
[Mon Nov 22 12:49:02 2021]
Job 9:
Filtering alignment results/masked_example-data.fasta.xz → results/filtered_example-data.fasta.xz
- excluding strains in defaults/exclude.txt results/to-exclude_example-data.txt
- including strains in defaults/include.txt
- min length: 27000
augur filter --sequences results/masked_example-data.fasta.xz --metadata results/sanitized_metadata_example-data.tsv.xz --include defaults/include.txt --max-date 2021-11-23 --min-date 2019.74 --exclude-ambiguous-dates-by any --exclude defaults/exclude.txt results/to-exclude_example-data.txt --exclude-where division='USA' --min-length 27000 --output results/filtered_example-data.fasta 2>&1 | tee logs/filtered_example-data.txt;
xz -2 results/filtered_example-data.fasta
/bin/bash: line 1: augur: command not found
[Mon Nov 22 12:49:03 2021]
Error in rule filter:
jobid: 9
output: results/filtered_example-data.fasta.xz
log: logs/filtered_example-data.txt (check log file(s) for error message)
shell:
augur filter --sequences results/masked_example-data.fasta.xz --metadata results/sanitized_metadata_example-data.tsv.xz --include defaults/include.txt --max-date 2021-11-23 --min-date 2019.74 --exclude-ambiguous-dates-by any --exclude defaults/exclude.txt results/to-exclude_example-data.txt --exclude-where division='USA' --min-length 27000 --output results/filtered_example-data.fasta 2>&1 | tee logs/filtered_example-data.txt;
xz -2 results/filtered_example-data.fasta
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/filtered_example-data.txt:
/bin/bash: line 1: augur: command not found
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /groups/wyman/projects/ncov/.snakemake/log/2021-11-22T124901.715352.snakemake.log
enelson@igi-biotite:/groups/wyman/projects/ncov$
error.txt
Displaying error.txt.