# Augur error while subsampling - updated **URL:** \ **Category:** Help and Getting Started\ **Created:** [November 21, 2020, 7:19am UTC](https://nextstrain.discourse.group/t/augur-error-while-subsampling-updated/203 "2020-11-21T07:19:28Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![phemarajata](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/phemarajata/32/47_2.png) [@phemarajata](https://nextstrain.discourse.group/u/phemarajata)\ **Post date:** [November 21, 2020, 7:19am UTC](https://nextstrain.discourse.group/t/augur-error-while-subsampling-updated/203/1 "2020-11-21T07:19:28Z")
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