Comments (6)
Hi @limh25, thank you for reporting this issue.
You should be able to run the example build using the command:
nextstrain build . --configfile profiles/ci/builds.yaml
I am updating the README to reflect this in #113.
from seasonal-flu.
Hi @joverlee521,
Thank you for your help. Now it runs, but produces error and stops. Error message below.
[Tue Jul 25 06:42:49 2023]
Job 16: Parsing fasta into sequences and metadata
Reason: Missing output files: data/h3n2/na.fasta, data/h3n2/metadata_na.tsv; Input files updated by another job: data/h3n2/raw_na.fasta
augur parse --sequences data/h3n2/raw_na.fasta --output-sequences data/h3n2/na.fasta --output-metadata data/h3n2/metadata_na.tsv --fields strain virus accession date date_submitted region country division location passage_category originating_lab submitting_lab age gender --prettify-fields region country division location originating_lab submitting_lab 2>&1 | tee logs/parse_h3n2_na.txt
[Tue Jul 25 06:42:49 2023]
Error in rule concat_titers_for_build:
jobid: 20
input: example_data/cdc_h3n2_cell_fra_titers.tsv
output: builds/ci_build/all_titers.tsv
log: logs/concat_titers_for_build_ci_build.txt (check log file(s) for error details)
conda-env: /app/limh25/seasonal-flu/.snakemake/conda/bda388b1eaf328dc458bca193b400f10_
shell:
tsv-append -H example_data/cdc_h3n2_cell_fra_titers.tsv > builds/ci_build/all_titers.tsv 2> logs/concat_titers_for_build_ci_build.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job concat_titers_for_build since they might be corrupted:
builds/ci_build/all_titers.tsv
[Tue Jul 25 06:42:49 2023]
Error in rule build_reference_strains_table:
jobid: 18
input: config/h3n2/reference_strains.txt
output: data/h3n2/reference_strains.tsv
log: logs/build_reference_strains_table_h3n2.txt (check log file(s) for error details)
conda-env: /app/limh25/seasonal-flu/.snakemake/conda/bda388b1eaf328dc458bca193b400f10_
shell:
csvtk add-header --names strain config/h3n2/reference_strains.txt | csvtk uniq | csvtk --out-tabs mutate2 --name is_reference --expression "'True'" > data/h3n2/reference_strains.tsv
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job build_reference_strains_table since they might be corrupted:
data/h3n2/reference_strains.tsv
[Tue Jul 25 06:42:50 2023]
Finished job 10.
3 of 88 steps (3%) done
[Tue Jul 25 06:42:50 2023]
Finished job 16.
4 of 88 steps (5%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-07-25T064248.960339.snakemake.log
Should I turn off the titer part? If so, how am I supposed to run it without titer part?
Complete log file attached.
Thank you again.
2023-07-25T064248.960339.snakemake.log
from seasonal-flu.
@limh25 Could you provide the logs for the first rule that failed (logs/concat_titers_for_build_ci_build.txt
)? It should contain more details on the error.
Could you also provide the output of nextstrain version --verbose
?
from seasonal-flu.
@joverlee521 The logs/concat_titers_for_build_ci_build.txt
shows only one line /usr/bin/bash: line 1: tsv-append: command not found
/
(nextstrain) [limh25@machine1 seasonal-flu]$ nextstrain version --verbose
nextstrain.cli 6.1.0.post1
Python
/home/limh25/anaconda3/envs/nextstrain/bin/python3.7
3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21)
[GCC 9.4.0]
Runners
docker
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?
unknown
conda
nextstrain-base unknown
singularity
docker://nextstrain/base (not present)
ambient (default)
augur 18.1.2
auspice 2.39.0
aws-batch
unknown
Thanks.
from seasonal-flu.
@joverlee521 The example build works fine with nextstrain build . --configfile profiles/ci/builds.yaml
. I have two machines where nextstrain is installed, and the one with newer installation works fine. I just have to update the older one.
from seasonal-flu.
Glad to hear you were able to get it working!
from seasonal-flu.
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from seasonal-flu.