# Error in jobid: 22

**URL:** <https://nextstrain.discourse.group/t/error-in-jobid-22/1236>\
**Category:** Help and Getting Started\
**Created:** [September 5, 2022, 8:50pm UTC](https://nextstrain.discourse.group/t/error-in-jobid-22/1236 "2022-09-05T20:50:15Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![mead000](https://avatars.discourse-cdn.com/v4/letter/m/73ab20/32.png) [@mead000](https://nextstrain.discourse.group/u/mead000)\
**Post date:** [September 5, 2022, 8:50pm UTC](https://nextstrain.discourse.group/t/error-in-jobid-22/1236/1 "2022-09-05T20:50:15Z")

</div>

Hello,

I am trying to run some custom/local COVID sequencing data through the nextstrain custom data tutorial, replacing the suggested GISAID data with local data. I was able to run the custom data tutorial as written, and also using downloaded GISAID data. I just have a problem with the local data. I tried running a minimized version of the local data using the columns that the data preparation tutorial defines as required: strain, date,

I get an error in job 22:

> Note: You did not provide a sequence index, so Augur will generate one. You can generate your own index ahead of time with `augur index` and pass it with `augur filter --sequence-index`.  
> ERROR: Query contains a column that does not exist in metadata.  
> [Mon Sep 5 20:04:05 2022]  
> Error in rule filter:  
> jobid: 22  
> output: results/custom-build/filtered.fasta, results/custom-build/filtered\_log.tsv  
> log: logs/filtered\_custom-build.txt (check log file(s) for error message)  
> shell:
> 
> ```
> augur filter --sequences results/custom-build/masked.fasta --metadata results/custom-build/metadata_with_index.tsv --include defaults/include.txt --query '(`reference_data` == '"'"'yes'"'"' & _length >= 27000) | (`custom_data` == '"'"'yes'"'"' & _length >= 27000)' --max-date 2022-09-06 --min-date 2019-12-01 --exclude-ambiguous-dates-by any --exclude defaults/exclude.txt results/custom-build/excluded_by_diagnostics.txt --exclude-where division='USA' --output results/custom-build/filtered.fasta --output-log results/custom-build/filtered_log.tsv 2>&1 | tee logs/filtered_custom-build.txt;
> 
> (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
> 
> ```

The obvious fix would have been to ensure that the metadata contained all the columns in the query - but I tried to include everything in my source metadata (including length), but it doesn’t translate when nextstrain writes metadata\_with\_index.tsv. That file contains functional reference data / custom data flags, but only has length values for reference data. The custom column I made in the original metadata gets re-labeled as “\_length\_x”. I think this is the source of my issue, but I cannot figure out how to overcome it. Is there a disconnect between the FASTA and my metadata? I can run this fasta through nextclade on the web, and the fasta gets through the masking stage without issue. Help!

Complete log: [2022-09-05T200355.712908.snakemake.log - Google Drive](https://drive.google.com/file/d/1WK9wm-fihOvbrk7GmGYmok-u22KNhspM/view?usp=sharing)