# Broken workflow after updating runtime and CLI

**URL:** <https://nextstrain.discourse.group/t/broken-workflow-after-updating-runtime-and-cli/1290>\
**Category:** Help and Getting Started\
**Created:** [December 14, 2022, 7:27pm UTC](https://nextstrain.discourse.group/t/broken-workflow-after-updating-runtime-and-cli/1290 "2022-12-14T19:27:44Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![arodzh](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/arodzh/32/215_2.png) [@arodzh](https://nextstrain.discourse.group/u/arodzh)\
**Post date:** [December 14, 2022, 7:27pm UTC](https://nextstrain.discourse.group/t/broken-workflow-after-updating-runtime-and-cli/1290/1 "2022-12-14T19:27:44Z")

</div>

Hi Nextstrain team,

Got the following error after updating the runtime and CLI:

```auto
python3 scripts/sanitize_sequences.py --sequences data/puerto-rico_sequences_2022-12-12.fasta --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_puertorico.txt | nextalign run --jobs=8 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --output-translations results/translations/seqs_puertorico.gene.{gene}.fasta --output-fasta results/aligned_puertorico.fasta --output-insertions results/insertions_puertorico.tsv > logs/align_puertorico.txt 2>&1;
        xz -2 -T 8 results/aligned_puertorico.fasta;
        xz -2 -T 8 results/translations/seqs_puertorico.gene.*.fasta
        
Traceback (most recent call last):
  File "/nextstrain/build/scripts/combine_metadata.py", line 2, in <module>
    from augur.io import open_file, read_metadata
ImportError: cannot import name 'open_file' from 'augur.io' (/nextstrain/augur/augur/io/ __init__.py)
[Wed Dec 14 19:20:53 2022]
Error in rule combine_input_metadata:
    jobid: 65
    output: results/combined_metadata.tsv.xz
    log: logs/combine_input_metadata.txt (check log file(s) for error message)
    shell:
        
        python3 scripts/combine_metadata.py --metadata data/puerto-rico_metadata_2022-12-12.tsv data/hcov_global_metadata_2022-12-12.tsv --origins puertorico globe --output results/combined_metadata.tsv.xz 2>&1 | tee logs/combine_input_metadata.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Dec 14 19:20:53 2022]
Error in rule align:
    jobid: 73
    output: results/aligned_globe.fasta.xz, results/insertions_globe.tsv, results/translations/seqs_globe.gene.ORF1a.fasta.xz, results/translations/seqs_globe.gene.ORF1b.fasta.xz, results/translations/seqs_globe.gene.S.fasta.xz, results/translations/seqs_globe.gene.ORF3a.fasta.xz, results/translations/seqs_globe.gene.E.fasta.xz, results/translations/seqs_globe.gene.M.fasta.xz, results/translations/seqs_globe.gene.ORF6.fasta.xz, results/translations/seqs_globe.gene.ORF7a.fasta.xz, results/translations/seqs_globe.gene.ORF7b.fasta.xz, results/translations/seqs_globe.gene.ORF8.fasta.xz, results/translations/seqs_globe.gene.N.fasta.xz, results/translations/seqs_globe.gene.ORF9b.fasta.xz
    log: logs/align_globe.txt (check log file(s) for error message)
[Wed Dec 14 19:20:53 2022]
    shell:
        
        python3 scripts/sanitize_sequences.py --sequences data/hcov_global_sequences_2022-12-12.fasta --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_globe.txt | nextalign run --jobs=8 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --output-translations results/translations/seqs_globe.gene.{gene}.fasta --output-fasta results/aligned_globe.fasta --output-insertions results/insertions_globe.tsv > logs/align_globe.txt 2>&1;
        xz -2 -T 8 results/aligned_globe.fasta;
        xz -2 -T 8 results/translations/seqs_globe.gene.*.fasta
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Error in rule align:

    jobid: 72
    output: results/aligned_puertorico.fasta.xz, results/insertions_puertorico.tsv, results/translations/seqs_puertorico.gene.ORF1a.fasta.xz, results/translations/seqs_puertorico.gene.ORF1b.fasta.xz, results/translations/seqs_puertorico.gene.S.fasta.xz, results/translations/seqs_puertorico.gene.ORF3a.fasta.xz, results/translations/seqs_puertorico.gene.E.fasta.xz, results/translations/seqs_puertorico.gene.M.fasta.xz, results/translations/seqs_puertorico.gene.ORF6.fasta.xz, results/translations/seqs_puertorico.gene.ORF7a.fasta.xz, results/translations/seqs_puertorico.gene.ORF7b.fasta.xz, results/translations/seqs_puertorico.gene.ORF8.fasta.xz, results/translations/seqs_puertorico.gene.N.fasta.xz, results/translations/seqs_puertorico.gene.ORF9b.fasta.xz
    log: logs/align_puertorico.txt (check log file(s) for error message)
    shell:
        
        python3 scripts/sanitize_sequences.py --sequences data/puerto-rico_sequences_2022-12-12.fasta --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_puertorico.txt | nextalign run --jobs=8 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --output-translations results/translations/seqs_puertorico.gene.{gene}.fasta --output-fasta results/aligned_puertorico.fasta --output-insertions results/insertions_puertorico.tsv > logs/align_puertorico.txt 2>&1;
        xz -2 -T 8 results/aligned_puertorico.fasta;
        xz -2 -T 8 results/translations/seqs_puertorico.gene.*.fasta
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job align since they might be corrupted:
results/insertions_globe.tsv

Removing output files of failed job align since they might be corrupted:
results/insertions_puertorico.tsv
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /nextstrain/build/.snakemake/log/2022-12-14T192051.806843.snakemake.log

```

I think this might be related to the Python Public API as indicated by the most recent Augur [changelog](https://github.com/nextstrain/augur/blob/master/CHANGES.md). Is there a workaround for this issue?

Thanks,  
Arnold.

---

<div class="post-metadata">

**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\
**Post date:** [December 14, 2022, 8:11pm UTC](https://nextstrain.discourse.group/t/broken-workflow-after-updating-runtime-and-cli/1290/2 "2022-12-14T20:11:34Z")

</div>

Indeed, that’s the issue. Thanks for flagging it. We’re addressing this now and will issue a new Augur release (probably 19.1.0).

---

<div class="post-metadata">

**Author:** ![joverlee](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@joverlee](https://nextstrain.discourse.group/u/joverlee)\
**Post date:** [December 15, 2022, 9:22pm UTC](https://nextstrain.discourse.group/t/broken-workflow-after-updating-runtime-and-cli/1290/3 "2022-12-15T21:22:28Z")

</div>

Hi @arodzh,

Augur 19.1.0 has been released. This issue should be resolved if you update your runtime again.

---

<div class="post-metadata">

**Author:** ![arodzh](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/arodzh/32/215_2.png) [@arodzh](https://nextstrain.discourse.group/u/arodzh)\
**Post date:** [December 15, 2022, 10:45pm UTC](https://nextstrain.discourse.group/t/broken-workflow-after-updating-runtime-and-cli/1290/4 "2022-12-15T22:45:32Z")

</div>

Hi @joverlee,

I updated the runtime and everything is working properly. Thanks!