Update: Hi, I took this topic down last night because I thought my metadata file had issues and that fixing it would resolve this error but it did not, so I undeleted this topic. Any suggestion would be greatly appreciated. Thank you!
Hi all! I am running into an error while running snakemake during the subsampling processes. There may be something wrong with my build. I was wondering if anybody could help me figure out. Thank you so much in advance! Below is the error log:
[Fri Nov 20 22:39:29 2020]
Job 99:
Subsample all sequences by ‘region’ scheme for build ‘north-america’ with the following parameters:
- group by: division year month
- sequences per group: --sequences-per-group 48
- subsample max sequences:
- min-date:
- max-date:
- exclude: --exclude-where 'region!=North America'
- include:
- query:
- priority:
augur filter --sequences results/masked.fasta --metadata data/metadata-snf.tsv --include defaults/include.txt --exclude-where 'region!=North America' --group-by division year month --sequences-per-group 48 --output results/north-america/sample-region.fasta 2>&1 | tee logs/subsample_north-america_region.txt
[Fri Nov 20 22:39:43 2020]
Error in rule subsample:
jobid: 94
output: results/north-america_usa/sample-country.fasta
log: logs/subsample_north-america_usa_country.txt (check log file(s) for error message)
shell:
augur filter --sequences results/masked.fasta --metadata data/metadata-snf.tsv --include defaults/include.txt --exclude-where 'country!=USA' --group-by division year month --sequences-per-group 200 --output results/north-america_usa/sample-country.fasta 2>&1 | tee logs/subsample_north-america_usa_country.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Fri Nov 20 22:39:45 2020]
Error in rule subsample:
jobid: 103
output: results/global/sample-global.fasta
log: logs/subsample_global_global.txt (check log file(s) for error message)
shell:
augur filter --sequences results/masked.fasta --metadata data/metadata-snf.tsv --include defaults/include.txt --group-by country year month --sequences-per-group 20 --output results/global/sample-global.fasta 2>&1 | tee logs/subsample_global_global.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Fri Nov 20 22:39:48 2020]
Error in rule subsample:
jobid: 83
output: results/north-america_usa_la_county/sample-focal.fasta
log: logs/subsample_north-america_usa_la_county_focal.txt (check log file(s) for error message)
shell:
augur filter --sequences results/masked.fasta --metadata data/metadata-snf.tsv --include defaults/include.txt --query "(country == 'USA') & (division == 'California') & (location == 'Los Angeles County')" --group-by year month --sequences-per-group 300 --output results/north-america_usa_la_county/sample-focal.fasta 2>&1 | tee logs/subsample_north-america_usa_la_county_focal.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Fri Nov 20 22:39:53 2020]
Error in rule subsample:
jobid: 85
output: results/north-america_usa_la_county/sample-contextual.fasta
log: logs/subsample_north-america_usa_la_county_contextual.txt (check log file(s) for error message)
shell:
augur filter --sequences results/masked.fasta --metadata data/metadata-snf.tsv --include defaults/include.txt --exclude-where 'location=Los Angeles County' --group-by country year month --sequences-per-group 10 --output results/north-america_usa_la_county/sample-contextual.fasta 2>&1 | tee logs/subsample_north-america_usa_la_county_contextual.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Fri Nov 20 22:40:02 2020]
Error in rule subsample:
jobid: 88
output: results/north-america_usa_california/sample-division.fasta
log: logs/subsample_north-america_usa_california_division.txt (check log file(s) for error message)
shell:
augur filter --sequences results/masked.fasta --metadata data/metadata-snf.tsv --include defaults/include.txt --exclude-where 'region!=North America' 'country!=USA' 'division!=California' --group-by year month --sequences-per-group 300 --output results/north-america_usa_california/sample-division.fasta 2>&1 | tee logs/subsample_north-america_usa_california_division.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Fri Nov 20 22:40:52 2020]
Finished job 99.
1354 of 1446 steps (94%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/phemarajata/ncov/.snakemake/log/2020-11-20T194601.048130.snakemake.log