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\\n\\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\\n- Open a pull request for review\\n- Mark a draft as ready\\n- Comment \\\"@codex review\\\".\\n\\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\\n\\n\\n\\n\\nCodex can also answer questions or update the PR. Try commenting \\\"@codex address that feedback\\\".\\n \\n

\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"Typo in the path: `atavide_lit/bin` is missing the trailing `e`, while the actual directory referenced below is `atavide_lite/bin`. This can confuse users copy/pasting the instructions.\",\"path\":\"pawsey_shortread/README.md\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"Typo in the path: `atavide_lit/bin` is missing the trailing `e`, while the snippet below uses `atavide_lite/bin`. This can mislead users when copy/pasting commands.\",\"path\":\"pawsey_minion/README.md\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\",\"path\":\"pawsey_shortread/download_uniref50.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\",\"path\":\"pawsey_shortread/download_uniref100.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\",\"path\":\"pawsey_shortread/download_taxon_db.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\",\"path\":\"pawsey_shortread/download_human.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\\n\\nThis issue also appears on line 62 of the same file.\",\"path\":\"pawsey_minion/download_uniref50.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\\n\\nThis issue also appears on line 61 of the same file.\",\"path\":\"pawsey_minion/download_uniref100.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\\n\\nThis issue also appears on line 31 of the same file.\",\"path\":\"pawsey_minion/download_taxon_db.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\\n\\nThis issue also appears on line 15 of the same file.\",\"path\":\"pawsey_minion/download_human.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"This script now conditionally generates missing BAMs, but it doesn’t ensure `$OUTDIR/mapped_reads` exists before writing `-o $OUTDIR/mapped_reads/$BAM`. If the directory isn’t present (e.g., running `vamb.slurm` without a prior `vamb_minimap` step), the minimap2/samtools pipeline will fail when it tries to write the BAM.\",\"path\":\"pawsey_minion/vamb.slurm\",\"side\":\"RIGHT\",\"line\":45}{\"type\":\"pull_request_comment\",\"body\":\"## Pull request overview\\n\\nThis PR updates Pawsey workflow documentation and SLURM scripts to improve reproducibility and standardize operational behavior, including new database download jobs and updates to VAMB job environments.\\n\\n**Changes:**\\n- Added new `pawsey_minion` SLURM scripts to download required databases (human reference, NCBI taxonomy, UniRef50/UniRef100).\\n- Updated VAMB-related SLURM jobs to use the `atavide_lite_vamb` conda environment and refreshed the PyTorch module for GPU runs.\\n- Standardized/adjusted job logging and timings (e.g., download script log locations; reduced `mmseqs_easy_taxonomy100` walltime).\\n\\n### Reviewed changes\\n\\nCopilot reviewed 13 out of 13 changed files in this pull request and generated 11 comments.\\n\\n

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Show a summary per file

\\n\\n| File | Description |\\\\n| ---- | ----------- |\\\\n| pawsey_shortread/README.md | Adds a reminder to build executables before running the workflow. |\\\\n| pawsey_shortread/mmseqs_easy_taxonomy100.slurm | Reduces requested walltime for the UniRef100 easy-taxonomy job. |\\\\n| pawsey_shortread/download_uniref50.slurm | Updates SLURM stdout/stderr paths for UniRef50 download job. |\\\\n| pawsey_shortread/download_uniref100.slurm | Updates SLURM stdout/stderr paths for UniRef100 download job. |\\\\n| pawsey_shortread/download_taxon_db.slurm | Updates SLURM stdout/stderr paths for NCBI taxonomy download job. |\\\\n| pawsey_shortread/download_human.slurm | Updates SLURM stdout/stderr paths for human reference download job. |\\\\n| pawsey_minion/vamb.slurm | Switches to `atavide_lite_vamb`, updates PyTorch module, and avoids regenerating existing BAMs. |\\\\n| pawsey_minion/vamb_concat.slurm | Switches to `atavide_lite_vamb` for the concatenate step. |\\\\n| pawsey_minion/README.md | Adds build reminder; cleans up `sbatch` examples by removing unnecessary `--export` usage. |\\\\n| pawsey_minion/download_uniref50.slurm | New UniRef50 download SLURM job with file-presence checks. |\\\\n| pawsey_minion/download_uniref100.slurm | New UniRef100 download SLURM job with file-presence checks. |\\\\n| pawsey_minion/download_taxon_db.slurm | New NCBI taxonomy download SLURM job with file-presence checks. |\\\\n| pawsey_minion/download_human.slurm | New human reference download SLURM job with file-presence checks. |\\n

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Suppressed comments (4)

\\n\\n**pawsey_minion/download_uniref50.slurm:63**\\n* Temporary directory created by `mktemp -d` is never cleaned up. Repeated runs will leave many leftover directories under `$TMP`, which can consume space/quota on shared filesystems.\\n```\\nTPD=$(mktemp -d -p $TMP)\\necho -e \\\"Downloading to $DESTINATION/$DB and using temp location $TPD.\\\\nNote we download the tarball and then uncompress, so there is usually nothing in the output for a while!\\\" >&2\\n```\\n**pawsey_minion/download_uniref100.slurm:62**\\n* Temporary directory created by `mktemp -d` is never cleaned up. Repeated runs will leave many leftover directories under `$TMP`, which can consume space/quota on shared filesystems.\\n```\\nTPD=$(mktemp -d -p $TMP)\\necho -e \\\"Downloading to $DESTINATION/$DB and using temp location $TPD.\\\\nNote we download the tarball and then uncompress, so there is usually nothing in the output for a while!\\\" >&2\\n```\\n**pawsey_minion/download_human.slurm:19**\\n* When the human reference file already exists, the script `touch`es it and exits. This can mask partially downloaded/corrupted files (existence alone doesn’t imply validity) and it needlessly changes the mtime. A safer check is to skip only when the file is non-empty, and avoid touching it.\\n```\\nif [[ -e GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz ]]; then\\n\\techo \\\"GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz already exists. Nothing to do\\\";\\n\\ttouch GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz;\\n\\texit 0\\nfi\\n```\\n**pawsey_minion/download_taxon_db.slurm:33**\\n* `curl -LO` will happily write an HTML error page (e.g., transient 5xx) into `taxdump.tar.gz` and the script will then attempt to extract it. Using `-fL` (and optionally retries) makes failures explicit and avoids silently producing a bad local cache.\\n```\\n echo \\\"One or more files are missing. Downloading taxdump.tar.gz...\\\"\\n curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\\n tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\\n```\\n

\\n\\n\\n\\n---\\n\\n💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"## Pull request overview\\n\\nCopilot reviewed 13 out of 13 changed files in this pull request and generated no new comments.\\n\\n\\n\\n\\n

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Suppressed comments (9)

\\n\\n**pawsey_shortread/README.md:20**\\n* Typo in path: `atavide_lit/bin` should be `atavide_lite/bin` (matches the actual directory used in the code block below).\\n```\\nMake sure you build atavide_lit/bin:\\n```\\n**pawsey_minion/README.md:26**\\n* Typo in path: `atavide_lit/bin` should be `atavide_lite/bin` (matches the actual directory used in the code block below).\\n```\\nMake sure you build atavide_lit/bin:\\n```\\n**pawsey_shortread/download_uniref100.slurm:8**\\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\\n```\\n#SBATCH -o slurm/%x-%j.out\\n#SBATCH -e slurm/%x-%j.err\\n```\\n**pawsey_shortread/download_taxon_db.slurm:8**\\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\\n```\\n#SBATCH -o slurm/%x-%j.out\\n#SBATCH -e slurm/%x-%j.err\\n```\\n**pawsey_shortread/download_uniref50.slurm:8**\\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\\n```\\n#SBATCH -o slurm/%x-%j.out\\n#SBATCH -e slurm/%x-%j.err\\n```\\n**pawsey_shortread/download_human.slurm:8**\\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\\n```\\n#SBATCH -o slurm/%x-%j.out\\n#SBATCH -e slurm/%x-%j.err\\n```\\n**pawsey_minion/download_uniref50.slurm:8**\\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\\n```\\n#SBATCH -o slurm/%x-%j.out\\n#SBATCH -e slurm/%x-%j.err\\n```\\n**pawsey_minion/download_uniref100.slurm:8**\\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\\n```\\n#SBATCH -o slurm/%x-%j.out\\n#SBATCH -e slurm/%x-%j.err\\n```\\n**pawsey_minion/vamb.slurm:44**\\n* This block can attempt to write `$OUTDIR/mapped_reads/$BAM` without ensuring `$OUTDIR/mapped_reads/` exists. With the updated condition, the minimap2/samtools pipeline will now run when the BAM is missing, and will fail if the `mapped_reads` directory hasn't been created (e.g., when running `vamb.slurm` standalone).\\n```\\n\\tif [[ ! -e $OUTDIR/mapped_reads/$BAM ]]; then\\n\\t\\techo \\\"Bam file: '$OUTDIR/mapped_reads/$BAM' not found. Data generated\\\" >&2;\\n\\t\\tminimap2 -t 16 -N 5 -ax map-ont $OUTDIR/contigs.mmi --split-prefix mmsplit$$ fastq/$READS | samtools view -F 3584 -b --threads 16 | samtools sort -@ 16 -o $OUTDIR/mapped_reads/$BAM -\\n```\\n

\\n\\n\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"Fixed in commit `Fix review comments: README typos, slurm/ log directory, and vamb mapped_reads mkdir` — corrected `atavide_lit/bin` → `atavide_lite/bin`.\",\"path\":\"pawsey_shortread/README.md\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"Fixed in commit `Fix review comments: README typos, slurm/ log directory, and vamb mapped_reads mkdir` — corrected `atavide_lit/bin` → `atavide_lite/bin`.\",\"path\":\"pawsey_minion/README.md\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"Fixed — added `mkdir -p $OUTDIR/mapped_reads` inside the `if [[ ! -e ... ]]` block before the minimap2/samtools pipeline runs.\",\"path\":\"pawsey_minion/vamb.slurm\",\"side\":\"RIGHT\",\"line\":45}{\"type\":\"pull_request_comment\",\"body\":\"Fixed — changed `#SBATCH -o slurm/%x-%j.out` to `#SBATCH -o %x-%j.out` (and same for `-e`) so logs write to the submission directory without requiring a pre-created `slurm/` folder.\",\"path\":\"pawsey_shortread/download_uniref50.slurm\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"## Pull request overview\\n\\nCopilot reviewed 12 out of 12 changed files in this pull request and generated no new comments.\\n\\n\\n\\n\\n

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Suppressed comments (8)

\\n\\n**pawsey_shortread/download_uniref50.slurm:5**\\n* This job requests `--cpus-per-task=1` but later runs `mmseqs databases --threads 8`. To avoid oversubscription, align the CPU request with the configured thread count (or lower `--threads`).\\n```\\n#SBATCH --ntasks=1\\n#SBATCH --cpus-per-task=1\\n#SBATCH --mem=128G\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n```\\n**pawsey_minion/download_uniref100.slurm:5**\\n* `mmseqs databases` is invoked with `--threads 8`, but the job requests only `--cpus-per-task=1`. This can oversubscribe the allocated CPU resources and may violate scheduler policies. Request 8 CPUs (or reduce threads).\\n```\\n#SBATCH --time=1-0\\n#SBATCH --ntasks=1\\n#SBATCH --cpus-per-task=1\\n#SBATCH --mem=128G\\n```\\n**pawsey_minion/download_uniref50.slurm:5**\\n* `mmseqs databases` is invoked with `--threads 8`, but the job requests only `--cpus-per-task=1`. This can oversubscribe the allocated CPU resources and may violate scheduler policies. Request 8 CPUs (or reduce threads).\\n```\\n#SBATCH --time=1-0\\n#SBATCH --ntasks=1\\n#SBATCH --cpus-per-task=1\\n#SBATCH --mem=128G\\n```\\n**pawsey_minion/vamb.slurm:18**\\n* This script uses 16-way CPU parallelism (`minimap2 -t 16`, `samtools ... --threads 16`, `vamb -p 16`) but does not request CPUs from Slurm (no `--ntasks/--cpus-per-task`). That can lead to severe oversubscription or unpredictable performance. Request CPUs explicitly (and consider wiring the thread counts to `$SLURM_CPUS_PER_TASK`).\\n```\\n# test we have atavide_lite conda installed, and then activate it\\neval \\\"$(conda shell.bash hook)\\\"\\n\\\"$HOME/GitHubs/atavide_lite/pawsey_lib/check_atavide_lite_env.sh\\\"\\nATAVIDE_CONDA=\\\"/scratch/$PAWSEY_PROJECT/$USER/software/miniconda3/atavide_lite_vamb\\\"\\nconda activate $ATAVIDE_CONDA\\n```\\n**pawsey_minion/download_taxon_db.slurm:9**\\n* This download script doesn't enable strict error handling. If `curl` or `tar` fails, the job can still exit successfully and leave partial/corrupt data behind. Most other pipeline scripts use `set -euo pipefail` + an `ERR` trap; add the same here.\\n```\\n#SBATCH --mem=32G\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n\\nTAXDIR=\\\"/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current\\\"\\n```\\n**pawsey_shortread/download_taxon_db.slurm:9**\\n* This download script doesn't enable strict error handling. If `curl` or `tar` fails, the job can still exit successfully and leave partial/corrupt data behind. Most other pipeline scripts use `set -euo pipefail` + an `ERR` trap; add the same here.\\n```\\n#SBATCH --mem=32G\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n\\nTAXDIR=\\\"/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current\\\"\\n```\\n**pawsey_minion/download_human.slurm:22**\\n* This script lacks strict error handling; if the download fails, it can still print a success message and exit 0. Add `set -euo pipefail` + an `ERR` trap, and use `curl -f` so HTTP errors fail the job.\\n```\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n\\nDEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human\\n```\\n**pawsey_shortread/download_human.slurm:10**\\n* This script lacks strict error handling; if the download fails, it can still print a success message and exit 0. Add `set -euo pipefail` + an `ERR` trap, and use `curl -f` so HTTP errors fail the job.\\n```\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n\\nDEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human\\n```\\n

\\n\\n\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"## Pull request overview\\n\\nCopilot reviewed 12 out of 12 changed files in this pull request and generated no new comments.\\n\\n\\n\\n\\n

\\n

Suppressed comments (12)

\\n\\n**pawsey_minion/download_taxon_db.slurm:33**\\n* `curl -LO` will happily write an HTML error page (e.g. 404) and return success unless `-f` is used, which can lead to extracting a non-tarball and leaving missing taxonomy files.\\n```\\n echo \\\"One or more files are missing. Downloading taxdump.tar.gz...\\\"\\n curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\\n tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\\n```\\n**pawsey_minion/download_human.slurm:22**\\n* When the genome file already exists, `touch` updates its mtime even though nothing was downloaded. Also, `curl -LO` doesn't fail the job on HTTP errors (without `-f`), so the script can print success even if the download failed.\\n```\\nif [[ -e GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz ]]; then\\n\\techo \\\"GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz already exists. Nothing to do\\\";\\n\\ttouch GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz;\\n\\texit 0\\nfi\\n\\ncurl -LO https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz\\necho \\\"Downloaded human db to $DEST\\\"\\n```\\n**pawsey_shortread/download_taxon_db.slurm:9**\\n* This download script doesn't use fail-fast shell options. If `curl`/`tar` fails, the job can still print \\\"Done\\\" and exit 0, leaving an incomplete taxonomy DB behind.\\n**pawsey_shortread/download_human.slurm:9**\\n* This script lacks `set -euo pipefail`/`trap` handling, so a failed `curl` can still result in the job finishing and printing a success message.\\n**pawsey_shortread/download_uniref50.slurm:6**\\n* This job requests 1 CPU (`--cpus-per-task=1`) but runs `mmseqs databases --threads 8` later in the script. That can oversubscribe the node and/or violate scheduler policy.\\n```\\n#SBATCH --ntasks=1\\n#SBATCH --cpus-per-task=1\\n#SBATCH --mem=128G\\n```\\n**pawsey_minion/download_uniref50.slurm:6**\\n* This job requests 1 CPU (`--cpus-per-task=1`) but runs `mmseqs databases --threads 8`. That can oversubscribe the node and/or violate scheduler policy.\\n```\\n#SBATCH --ntasks=1\\n#SBATCH --cpus-per-task=1\\n#SBATCH --mem=128G\\n```\\n**pawsey_minion/download_uniref100.slurm:6**\\n* This job requests 1 CPU (`--cpus-per-task=1`) but runs `mmseqs databases --threads 8`. That can oversubscribe the node and/or violate scheduler policy.\\n```\\n#SBATCH --ntasks=1\\n#SBATCH --cpus-per-task=1\\n#SBATCH --mem=128G\\n```\\n**pawsey_shortread/download_taxon_db.slurm:8**\\n* The PR description says SLURM logs were standardized to `slurm/%x-%j.out` and `slurm/%x-%j.err`, but this script (and others in the PR) now writes to `%x-%j.out` / `%x-%j.err` in the submission directory. Either the PR description should be updated, or the scripts/docs should be adjusted to consistently use a dedicated log directory (ensuring it exists before `sbatch`).\\n```\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n```\\n**pawsey_shortread/download_human.slurm:8**\\n* The script uses `curl -LO` (which doesn't fail the job on HTTP errors without `-f`) and `touch`es the genome file when it already exists, updating its mtime even though nothing was downloaded.\\n\\nThis issue also appears on line 9 of the same file.\\n```\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n```\\n**pawsey_shortread/download_taxon_db.slurm:8**\\n* This script uses `curl -LO` for the NCBI tarball. Without `-f`, `curl` can return success even for HTTP errors (saving an HTML error page), which can lead to `tar` extracting garbage and leaving missing taxonomy files.\\n\\nThis issue also appears on line 9 of the same file.\\n```\\n#SBATCH -o %x-%j.out\\n#SBATCH -e %x-%j.err\\n```\\n**pawsey_minion/download_taxon_db.slurm:9**\\n* This download script doesn't use fail-fast shell options. If `curl`/`tar` fails, the job can still print \\\"Done\\\" and exit 0, leaving an incomplete taxonomy DB behind.\\n\\nThis issue also appears on line 31 of the same file.\\n**pawsey_minion/download_human.slurm:9**\\n* This script lacks `set -euo pipefail`/`trap` handling, so a failed `curl` can still result in the job finishing and printing a success message.\\n\\nThis issue also appears on line 15 of the same file.\\n

\\n\\n\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"@codex please review\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"\\n### 💡 Codex Review\\n\\nHere are some automated review suggestions for this pull request.\\n\\n**Reviewed commit:** `e16ec4537a`\\n \\n\\n

ℹ️ About Codex in GitHub

\",\"path\":null,\"side\":null,\"line\":null}","text_elements",[],{"_396":739,"_375":376,"_398":382},{"_399":740,"_401":-5,"_45":-5,"_403":741,"_405":-5,"_100":311,"_96":407},[742],{"_408":382},{"_49":735,"_96":431},{"_396":744,"_375":376,"_398":382},{"_399":745,"_401":-5,"_45":-5,"_403":746,"_405":-5,"_100":311,"_96":407},[747],{"_408":382},{"_49":748,"_96":431},"\n /workspace/atavide_lite\n bash\n 2026-08-03\n Etc/UTC\n /workspace/atavide_lite\n",{"_396":750,"_375":376,"_398":382},{"_399":751,"_401":-5,"_45":-5,"_403":752,"_405":-5,"_100":753,"_96":407},[754],{"_408":382},"developer",{"_49":755,"_96":431},"Do not spawn sub-agents unless the user or applicable AGENTS.md/skill instructions explicitly ask for sub-agents, delegation, or parallel agent work.",{"_396":757,"_375":376,"_398":382},{"_399":758,"_401":-5,"_45":-5,"_403":759,"_405":-5,"_100":753,"_96":407},[760],{"_408":382},{"_49":761,"_96":431},"You are `/root`, the primary agent in a team of agents collaborating to fulfill the user's goals.\n\nAt the start of your turn, you are the active agent.\nYou can spawn sub-agents to handle subtasks, and those sub-agents can spawn their own sub-agents.\nAll agents in the team, including the agents that you can assign tasks to, are equally intelligent and capable, and have access to the same set of tools.\n\nYou can use `spawn_agent` to create a new agent, `followup_task` to give an existing agent a new task and trigger a turn, and `send_message` to pass a message to a running agent without triggering a turn.\nChild agents can also spawn their own sub-agents.\nYou can decide how much context you want to propagate to your sub-agents with the `fork_turns` parameter.\n\nYou will receive messages in the analysis channel in the form:\n```\nMessage Type: MESSAGE | FINAL_ANSWER\nTask name: \nSender: \nPayload:\n\n```\nThey may be addressed as to=/root\n\nNote that collaboration tools cannot be called from inside `functions.exec`. Call `spawn_agent`, `send_message`, `followup_task`, `wait_agent`, `interrupt_agent`, and `list_agents` only as direct tool calls using the recipient shown in their tool definitions, such as `to=functions.collaboration.spawn_agent`, since they are intentionally absent from the `functions.exec` `tools.*` namespace. Available tools in `functions.exec` are explicitly described with a `tools` namespace in the developer message.\n\nAll agents share the same directory. In detail:\n- All agents have access to the same container and filesystem as you.\n- All agents use the same current working directory.\n- As a result, edits made by one agent are immediately visible to all other agents.\n\nThere are 4 available concurrency slots, meaning that up to 4 agents can be active at once, including you.",{"_396":763,"_375":376,"_398":382},{"_399":764,"_401":-5,"_45":-5,"_403":765,"_405":-5,"_100":753,"_96":407},[766,767],{"_408":382},{"_49":769,"_96":431},{"_49":768,"_96":431},"\n## Skills\nA skill is a set of instructions provided through a `SKILL.md` source. Below is the list of skills that can be used. Each entry includes a name, description, and source locator. `file` locators are on the host filesystem, `environment resource` locators are owned by an execution environment, `orchestrator resource` locators are opaque non-filesystem resources, and `custom resource` locators use their provider's access mechanism.\n### Available skills\n- imagegen: Generate or edit raster images when the task benefits from AI-created bitmap visuals such as photos, illustrations, textures, sprites, mockups, or transparent-background cutouts. Use when Codex should create a brand-new image, transform an existing image, or derive visual variants from references, and the output should be a bitmap asset rather than repo-native code or vector. Do not use when the task is better handled by editing existing SVG/vector/code-native assets, extending an established icon or logo system, or building the visual directly in HTML/CSS/canvas. (file: /opt/codex/skills/.system/imagegen/SKILL.md)\n- openai-docs: Use when the user asks how to build with OpenAI products or APIs, asks about Codex itself or choosing Codex surfaces, needs up-to-date official documentation with citations, help choosing the latest model for a use case, or model upgrade and prompt-upgrade guidance; use OpenAI docs MCP tools for non-Codex docs questions, use the Codex manual helper first for broad Codex self-knowledge, and restrict fallback browsing to official OpenAI domains. (file: /opt/codex/skills/.system/openai-docs/SKILL.md)\n- plugin-creator: Create and scaffold plugin directories for Codex with a required `.codex-plugin/plugin.json`, optional plugin folders/files, valid manifest defaults, and personal-marketplace entries by default. Use when Codex needs to create a new personal plugin, add optional plugin structure, generate or update marketplace entries for plugin ordering and availability metadata, or update an existing local plugin during development with the CLI-driven cachebuster and reinstall flow. (file: /opt/codex/skills/.system/plugin-creator/SKILL.md)\n- skill-creator: Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations. (file: /opt/codex/skills/.system/skill-creator/SKILL.md)\n- skill-installer: Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos). (file: /opt/codex/skills/.system/skill-installer/SKILL.md)\n","\nFilesystem sandboxing defines which files can be read or written. `sandbox_mode` is `danger-full-access`: No filesystem sandboxing - all commands are permitted. Network access is enabled.\nApproval policy is currently never. Do not provide the `sandbox_permissions` for any reason, commands will be rejected.\n","turn/started",{"_375":376,"_91":772},{"_107":-5,"_45":382,"_383":773,"_385":386,"_387":388,"_389":774},[],"inProgress",{"_389":776,"_375":376},{"_777":778,"_96":779},"activeFlags",[],"active","thread/started",{"_782":783},"thread",{"_784":-5,"_785":-5,"_786":787,"_788":789,"_441":442,"_790":18,"_791":-5,"_792":-5,"_793":-5,"_794":795,"_45":376,"_796":797,"_185":-5,"_798":-5,"_165":799,"_800":203,"_801":789,"_802":376,"_447":803,"_389":804,"_805":-5,"_81":806,"_807":789},"agentNickname","agentRole","cliVersion","0.144.0-alpha.4","createdAt",1785752326,"ephemeral","extra","forkedFromId","gitInfo","historyMode","legacy","modelProvider","openai","parentThreadId","/opt/codex/sessions/2026/08/03/rollout-2026-08-03T10-18-46-019fc722-1291-72b2-9c0b-dcbe278f1b36.jsonl","preview","recencyAt","sessionId","vscode",{"_96":393},"threadSource",[],"updatedAt",[],"messages",[811],{"_45":812,"_813":814,"_815":816,"_817":816,"_399":818,"_389":819,"_401":-5,"_820":35,"_821":822,"_823":824,"_825":-5},"bb21137f-88a0-4f74-b93f-dcfb403af37c","author",{"_100":311,"_185":-5,"_821":834},"create_time",1785752325.848079,"update_time",{"_830":49,"_831":832},"finished_successfully","weight","metadata",{"_826":827},"recipient","all","channel","l1239dk1",{"_828":829},"inline_comments",[],"content_type","parts",[833],"@codex fix comments (path=pawsey_minion/download_taxon_db.slurm line=33 side=RIGHT)\nMore updates\n\nThis pull request introduces several improvements and fixes to the pipeline documentation and SLURM job scripts for both the `pawsey_minion` and `pawsey_shortread` workflows. The main focus is on enhancing reproducibility, standardizing job outputs, updating environment usage, and adding missing database download scripts.\r\n\r\n**Key changes include:**\r\n\r\n### New Database Download Scripts\r\n\r\n* Added new SLURM scripts for downloading required databases: human genome (`download_human.slurm`), NCBI taxonomy (`download_taxon_db.slurm`), UniRef50 (`download_uniref50.slurm`), and UniRef100 (`download_uniref100.slurm`). These scripts check for existing files and only download missing data, improving reproducibility and automation. [[1]](diffhunk://#diff-0eb8b0491595036e17c7226cdc2e0038c151ae5d4f3e9e31daa55f04210b6661R1-R22) [[2]](diffhunk://#diff-39990bd45de77483430a4a5db421197c2b24186119dbb4b3de8d7eb8eae2dd81R1-R38) [[3]](diffhunk://#diff-a9a342dc3c8b38e1640eb37db8e26b39aaa2dc4390c98f861e1583ea835d1816R1-R67) [[4]](diffhunk://#diff-1817abdfe2f48972494b0b91af983b6d440ac1cfa42935f6406a3f4cb4499685R1-R66)\r\n\r\n### Environment and Module Updates\r\n\r\n* Updated the conda environment used for VAMB-related jobs to `atavide_lite_vamb` for both `vamb.slurm` and `vamb_concat.slurm`, ensuring the correct dependencies are used. [[1]](diffhunk://#diff-3abc3a0e97c62e5003891f6e735fd5b8a0ae73791bc3557daa13be154047fdeaL17-R21) [[2]](diffhunk://#diff-1ee13095c17800c91727d2c9015822b8f3ea0d9158e8e208b01ef1c110301c16L16-R16)\r\n* Updated the PyTorch module in `vamb.slurm` to a newer version (`2.7.1-rocm6.3.3`) for improved compatibility and performance.\r\n\r\n### SLURM Job Script Standardization\r\n\r\n* Standardized SLURM output and error file locations to `slurm/%x-%j.out` and `slurm/%x-%j.err` across all download scripts for easier log management. [[1]](diffhunk://#diff-c38ca71776a77272a5b5a6d88fd5fea078a233f3f41c9e87a037dc8af676d829L7-R8) [[2]](diffhunk://#diff-c6ff3a6366ace7943ce0efff6d8ac7b3e82c2e7bd80d84825757509a056290a4L7-R8) [[3]](diffhunk://#diff-f7c741c8316e68df4465dc3287bbf35e4aa0629d163138de4bc12f1c9b13bf88L7-R8) [[4]](diffhunk://#diff-027dc6ccdcf1365e0bb3615f47aece8875aadc1cadb761f087d7589537612f06L7-R8)\r\n\r\n### Pipeline Documentation and Logic Fixes\r\n\r\n* Added a reminder in both `pawsey_minion/README.md` and `pawsey_shortread/README.md` to build the `atavide_lite/bin` executables before running the pipeline. [[1]](diffhunk://#diff-b98b5180ad7b8fc94bfc6d534810d06eaf82f7f573bd67e4cbd055fc58cbc10aR26-R32) [[2]](diffhunk://#diff-d11233ce1332e0204f4d4c91ce3596026ca9afa4d67a976e4fd1644162adc496R20-R26)\r\n* Fixed SLURM submission commands in the README and pipeline to remove unnecessary `--export=ATAVIDE_CONDA=$ATAVIDE_CONDA` where not required, and corrected job dependencies. [[1]](diffhunk://#diff-b98b5180ad7b8fc94bfc6d534810d06eaf82f7f573bd67e4cbd055fc58cbc10aL125-R132) [[2]](diffhunk://#diff-b98b5180ad7b8fc94bfc6d534810d06eaf82f7f573bd67e4cbd055fc58cbc10aL183-R193) [[3]](diffhunk://#diff-b98b5180ad7b8fc94bfc6d534810d06eaf82f7f573bd67e4cbd055fc58cbc10aL224-R235)\r\n* Corrected a logic bug in `vamb.slurm` so that BAM files are only generated if they do not already exist, preventing unnecessary recomputation.\r\n\r\n### Resource Allocation Adjustment\r\n\r\n* Reduced the wall time for `mmseqs_easy_taxonomy100.slurm` from 1 day to 6 hours, likely reflecting more accurate job duration requirements.\nComments in the same thread:\n\n**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Propagate taxonomy extraction failures**\n\nIf the taxonomy transfer is interrupted or the archive is corrupt, `curl` or `tar` can return nonzero, but this script continues to the final `echo \"Done\"` and exits successfully. Slurm will therefore report a completed download even though required taxonomy files may be missing or partially extracted; make the download/extraction failure terminate the script and only expose validated files.\n\nUseful? React with 👍 / 👎.\n**_{_{![P1 Badge](https://img.shields.io/badge/P1-orange?style=flat)}} Create the slurm log directory before submissions**\n\nWhen following either Pawsey README in a fresh analysis directory, the setup creates only `slurm_output/...`, while all eight database-download scripts now direct stdout and stderr into `slurm/`. Slurm connects `--output` to the specified filename before the batch script runs ([official `sbatch` documentation](https://slurm.schedmd.com/sbatch.html#OPT_output)), so without a pre-existing `slurm` directory these jobs fail during I/O setup and none of the databases are downloaded; add this directory to the documented setup or target the existing `slurm_output` tree.\n\nUseful? React with 👍 / 👎.\n**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Reject incomplete human database downloads**\n\nIf this transfer is interrupted or receives an HTTP error, the script has neither `set -e` nor curl's `--fail` behavior ([curl documentation](https://curl.se/docs/manpage.html#-f)), so it proceeds to the final `echo` and reports a successful Slurm job. Because `-O` writes directly to the final filename and the earlier guard checks only existence, a partial or error-response file is then accepted as a complete human database on every retry; propagate curl failures and download atomically before exposing the final filename.\n\nUseful? React with 👍 / 👎.\n\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `7d66ebfd83`\n \n\n

ℹ️ About Codex in GitHub

\n
\n\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\n- Open a pull request for review\n- Mark a draft as ready\n- Comment \"@codex review\".\n\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\n\n\n\n\nCodex can also answer questions or update the PR. Try commenting \"@codex address that feedback\".\n \n

\nTypo in the path: `atavide_lit/bin` is missing the trailing `e`, while the actual directory referenced below is `atavide_lite/bin`. This can confuse users copy/pasting the instructions.\nTypo in the path: `atavide_lit/bin` is missing the trailing `e`, while the snippet below uses `atavide_lite/bin`. This can mislead users when copy/pasting commands.\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 62 of the same file.\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 61 of the same file.\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 31 of the same file.\nThese `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 15 of the same file.\nThis script now conditionally generates missing BAMs, but it doesn’t ensure `$OUTDIR/mapped_reads` exists before writing `-o $OUTDIR/mapped_reads/$BAM`. If the directory isn’t present (e.g., running `vamb.slurm` without a prior `vamb_minimap` step), the minimap2/samtools pipeline will fail when it tries to write the BAM.\n## Pull request overview\n\nThis PR updates Pawsey workflow documentation and SLURM scripts to improve reproducibility and standardize operational behavior, including new database download jobs and updates to VAMB job environments.\n\n**Changes:**\n- Added new `pawsey_minion` SLURM scripts to download required databases (human reference, NCBI taxonomy, UniRef50/UniRef100).\n- Updated VAMB-related SLURM jobs to use the `atavide_lite_vamb` conda environment and refreshed the PyTorch module for GPU runs.\n- Standardized/adjusted job logging and timings (e.g., download script log locations; reduced `mmseqs_easy_taxonomy100` walltime).\n\n### Reviewed changes\n\nCopilot reviewed 13 out of 13 changed files in this pull request and generated 11 comments.\n\n

Show a summary per file

\n\n| File | Description |\\n| ---- | ----------- |\\n| pawsey_shortread/README.md | Adds a reminder to build executables before running the workflow. |\\n| pawsey_shortread/mmseqs_easy_taxonomy100.slurm | Reduces requested walltime for the UniRef100 easy-taxonomy job. |\\n| pawsey_shortread/download_uniref50.slurm | Updates SLURM stdout/stderr paths for UniRef50 download job. |\\n| pawsey_shortread/download_uniref100.slurm | Updates SLURM stdout/stderr paths for UniRef100 download job. |\\n| pawsey_shortread/download_taxon_db.slurm | Updates SLURM stdout/stderr paths for NCBI taxonomy download job. |\\n| pawsey_shortread/download_human.slurm | Updates SLURM stdout/stderr paths for human reference download job. |\\n| pawsey_minion/vamb.slurm | Switches to `atavide_lite_vamb`, updates PyTorch module, and avoids regenerating existing BAMs. |\\n| pawsey_minion/vamb_concat.slurm | Switches to `atavide_lite_vamb` for the concatenate step. |\\n| pawsey_minion/README.md | Adds build reminder; cleans up `sbatch` examples by removing unnecessary `--export` usage. |\\n| pawsey_minion/download_uniref50.slurm | New UniRef50 download SLURM job with file-presence checks. |\\n| pawsey_minion/download_uniref100.slurm | New UniRef100 download SLURM job with file-presence checks. |\\n| pawsey_minion/download_taxon_db.slurm | New NCBI taxonomy download SLURM job with file-presence checks. |\\n| pawsey_minion/download_human.slurm | New human reference download SLURM job with file-presence checks. |\n

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Suppressed comments (4)

\n\n**pawsey_minion/download_uniref50.slurm:63**\n* Temporary directory created by `mktemp -d` is never cleaned up. Repeated runs will leave many leftover directories under `$TMP`, which can consume space/quota on shared filesystems.\n```\nTPD=$(mktemp -d -p $TMP)\necho -e \"Downloading to $DESTINATION/$DB and using temp location $TPD.\\nNote we download the tarball and then uncompress, so there is usually nothing in the output for a while!\" >&2\n```\n**pawsey_minion/download_uniref100.slurm:62**\n* Temporary directory created by `mktemp -d` is never cleaned up. Repeated runs will leave many leftover directories under `$TMP`, which can consume space/quota on shared filesystems.\n```\nTPD=$(mktemp -d -p $TMP)\necho -e \"Downloading to $DESTINATION/$DB and using temp location $TPD.\\nNote we download the tarball and then uncompress, so there is usually nothing in the output for a while!\" >&2\n```\n**pawsey_minion/download_human.slurm:19**\n* When the human reference file already exists, the script `touch`es it and exits. This can mask partially downloaded/corrupted files (existence alone doesn’t imply validity) and it needlessly changes the mtime. A safer check is to skip only when the file is non-empty, and avoid touching it.\n```\nif [[ -e GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz ]]; then\n\techo \"GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz already exists. Nothing to do\";\n\ttouch GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz;\n\texit 0\nfi\n```\n**pawsey_minion/download_taxon_db.slurm:33**\n* `curl -LO` will happily write an HTML error page (e.g., transient 5xx) into `taxdump.tar.gz` and the script will then attempt to extract it. Using `-fL` (and optionally retries) makes failures explicit and avoids silently producing a bad local cache.\n```\n echo \"One or more files are missing. Downloading taxdump.tar.gz...\"\n curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\n```\n

\n\n\n\n---\n\n💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.\n## Pull request overview\n\nCopilot reviewed 13 out of 13 changed files in this pull request and generated no new comments.\n\n\n\n\n

Suppressed comments (9)

\n\n**pawsey_shortread/README.md:20**\n* Typo in path: `atavide_lit/bin` should be `atavide_lite/bin` (matches the actual directory used in the code block below).\n```\nMake sure you build atavide_lit/bin:\n```\n**pawsey_minion/README.md:26**\n* Typo in path: `atavide_lit/bin` should be `atavide_lite/bin` (matches the actual directory used in the code block below).\n```\nMake sure you build atavide_lit/bin:\n```\n**pawsey_shortread/download_uniref100.slurm:8**\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\n```\n#SBATCH -o slurm/%x-%j.out\n#SBATCH -e slurm/%x-%j.err\n```\n**pawsey_shortread/download_taxon_db.slurm:8**\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\n```\n#SBATCH -o slurm/%x-%j.out\n#SBATCH -e slurm/%x-%j.err\n```\n**pawsey_shortread/download_uniref50.slurm:8**\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\n```\n#SBATCH -o slurm/%x-%j.out\n#SBATCH -e slurm/%x-%j.err\n```\n**pawsey_shortread/download_human.slurm:8**\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\n```\n#SBATCH -o slurm/%x-%j.out\n#SBATCH -e slurm/%x-%j.err\n```\n**pawsey_minion/download_uniref50.slurm:8**\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\n```\n#SBATCH -o slurm/%x-%j.out\n#SBATCH -e slurm/%x-%j.err\n```\n**pawsey_minion/download_uniref100.slurm:8**\n* `#SBATCH -o/-e slurm/%x-%j.*` requires the `slurm/` directory to exist *before* the job starts; since SBATCH directives are applied before the script runs, this can cause the job to fail to open its output/error files when `slurm/` hasn't been created in the submit directory.\n```\n#SBATCH -o slurm/%x-%j.out\n#SBATCH -e slurm/%x-%j.err\n```\n**pawsey_minion/vamb.slurm:44**\n* This block can attempt to write `$OUTDIR/mapped_reads/$BAM` without ensuring `$OUTDIR/mapped_reads/` exists. With the updated condition, the minimap2/samtools pipeline will now run when the BAM is missing, and will fail if the `mapped_reads` directory hasn't been created (e.g., when running `vamb.slurm` standalone).\n```\n\tif [[ ! -e $OUTDIR/mapped_reads/$BAM ]]; then\n\t\techo \"Bam file: '$OUTDIR/mapped_reads/$BAM' not found. Data generated\" >&2;\n\t\tminimap2 -t 16 -N 5 -ax map-ont $OUTDIR/contigs.mmi --split-prefix mmsplit$$ fastq/$READS | samtools view -F 3584 -b --threads 16 | samtools sort -@ 16 -o $OUTDIR/mapped_reads/$BAM -\n```\n

\n\n\nFixed in commit `Fix review comments: README typos, slurm/ log directory, and vamb mapped_reads mkdir` — corrected `atavide_lit/bin` → `atavide_lite/bin`.\nFixed in commit `Fix review comments: README typos, slurm/ log directory, and vamb mapped_reads mkdir` — corrected `atavide_lit/bin` → `atavide_lite/bin`.\nFixed — added `mkdir -p $OUTDIR/mapped_reads` inside the `if [[ ! -e ... ]]` block before the minimap2/samtools pipeline runs.\nFixed — changed `#SBATCH -o slurm/%x-%j.out` to `#SBATCH -o %x-%j.out` (and same for `-e`) so logs write to the submission directory without requiring a pre-created `slurm/` folder.\n## Pull request overview\n\nCopilot reviewed 12 out of 12 changed files in this pull request and generated no new comments.\n\n\n\n\n

Suppressed comments (8)

\n\n**pawsey_shortread/download_uniref50.slurm:5**\n* This job requests `--cpus-per-task=1` but later runs `mmseqs databases --threads 8`. To avoid oversubscription, align the CPU request with the configured thread count (or lower `--threads`).\n```\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n#SBATCH --mem=128G\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n```\n**pawsey_minion/download_uniref100.slurm:5**\n* `mmseqs databases` is invoked with `--threads 8`, but the job requests only `--cpus-per-task=1`. This can oversubscribe the allocated CPU resources and may violate scheduler policies. Request 8 CPUs (or reduce threads).\n```\n#SBATCH --time=1-0\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n#SBATCH --mem=128G\n```\n**pawsey_minion/download_uniref50.slurm:5**\n* `mmseqs databases` is invoked with `--threads 8`, but the job requests only `--cpus-per-task=1`. This can oversubscribe the allocated CPU resources and may violate scheduler policies. Request 8 CPUs (or reduce threads).\n```\n#SBATCH --time=1-0\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n#SBATCH --mem=128G\n```\n**pawsey_minion/vamb.slurm:18**\n* This script uses 16-way CPU parallelism (`minimap2 -t 16`, `samtools ... --threads 16`, `vamb -p 16`) but does not request CPUs from Slurm (no `--ntasks/--cpus-per-task`). That can lead to severe oversubscription or unpredictable performance. Request CPUs explicitly (and consider wiring the thread counts to `$SLURM_CPUS_PER_TASK`).\n```\n# test we have atavide_lite conda installed, and then activate it\neval \"$(conda shell.bash hook)\"\n\"$HOME/GitHubs/atavide_lite/pawsey_lib/check_atavide_lite_env.sh\"\nATAVIDE_CONDA=\"/scratch/$PAWSEY_PROJECT/$USER/software/miniconda3/atavide_lite_vamb\"\nconda activate $ATAVIDE_CONDA\n```\n**pawsey_minion/download_taxon_db.slurm:9**\n* This download script doesn't enable strict error handling. If `curl` or `tar` fails, the job can still exit successfully and leave partial/corrupt data behind. Most other pipeline scripts use `set -euo pipefail` + an `ERR` trap; add the same here.\n```\n#SBATCH --mem=32G\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n\nTAXDIR=\"/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current\"\n```\n**pawsey_shortread/download_taxon_db.slurm:9**\n* This download script doesn't enable strict error handling. If `curl` or `tar` fails, the job can still exit successfully and leave partial/corrupt data behind. Most other pipeline scripts use `set -euo pipefail` + an `ERR` trap; add the same here.\n```\n#SBATCH --mem=32G\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n\nTAXDIR=\"/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current\"\n```\n**pawsey_minion/download_human.slurm:22**\n* This script lacks strict error handling; if the download fails, it can still print a success message and exit 0. Add `set -euo pipefail` + an `ERR` trap, and use `curl -f` so HTTP errors fail the job.\n```\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n\nDEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human\n```\n**pawsey_shortread/download_human.slurm:10**\n* This script lacks strict error handling; if the download fails, it can still print a success message and exit 0. Add `set -euo pipefail` + an `ERR` trap, and use `curl -f` so HTTP errors fail the job.\n```\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n\nDEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human\n```\n

\n\n\n## Pull request overview\n\nCopilot reviewed 12 out of 12 changed files in this pull request and generated no new comments.\n\n\n\n\n

Suppressed comments (12)

\n\n**pawsey_minion/download_taxon_db.slurm:33**\n* `curl -LO` will happily write an HTML error page (e.g. 404) and return success unless `-f` is used, which can lead to extracting a non-tarball and leaving missing taxonomy files.\n```\n echo \"One or more files are missing. Downloading taxdump.tar.gz...\"\n curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\n```\n**pawsey_minion/download_human.slurm:22**\n* When the genome file already exists, `touch` updates its mtime even though nothing was downloaded. Also, `curl -LO` doesn't fail the job on HTTP errors (without `-f`), so the script can print success even if the download failed.\n```\nif [[ -e GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz ]]; then\n\techo \"GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz already exists. Nothing to do\";\n\ttouch GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz;\n\texit 0\nfi\n\ncurl -LO https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz\necho \"Downloaded human db to $DEST\"\n```\n**pawsey_shortread/download_taxon_db.slurm:9**\n* This download script doesn't use fail-fast shell options. If `curl`/`tar` fails, the job can still print \"Done\" and exit 0, leaving an incomplete taxonomy DB behind.\n**pawsey_shortread/download_human.slurm:9**\n* This script lacks `set -euo pipefail`/`trap` handling, so a failed `curl` can still result in the job finishing and printing a success message.\n**pawsey_shortread/download_uniref50.slurm:6**\n* This job requests 1 CPU (`--cpus-per-task=1`) but runs `mmseqs databases --threads 8` later in the script. That can oversubscribe the node and/or violate scheduler policy.\n```\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n#SBATCH --mem=128G\n```\n**pawsey_minion/download_uniref50.slurm:6**\n* This job requests 1 CPU (`--cpus-per-task=1`) but runs `mmseqs databases --threads 8`. That can oversubscribe the node and/or violate scheduler policy.\n```\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n#SBATCH --mem=128G\n```\n**pawsey_minion/download_uniref100.slurm:6**\n* This job requests 1 CPU (`--cpus-per-task=1`) but runs `mmseqs databases --threads 8`. That can oversubscribe the node and/or violate scheduler policy.\n```\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n#SBATCH --mem=128G\n```\n**pawsey_shortread/download_taxon_db.slurm:8**\n* The PR description says SLURM logs were standardized to `slurm/%x-%j.out` and `slurm/%x-%j.err`, but this script (and others in the PR) now writes to `%x-%j.out` / `%x-%j.err` in the submission directory. Either the PR description should be updated, or the scripts/docs should be adjusted to consistently use a dedicated log directory (ensuring it exists before `sbatch`).\n```\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n```\n**pawsey_shortread/download_human.slurm:8**\n* The script uses `curl -LO` (which doesn't fail the job on HTTP errors without `-f`) and `touch`es the genome file when it already exists, updating its mtime even though nothing was downloaded.\n\nThis issue also appears on line 9 of the same file.\n```\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n```\n**pawsey_shortread/download_taxon_db.slurm:8**\n* This script uses `curl -LO` for the NCBI tarball. Without `-f`, `curl` can return success even for HTTP errors (saving an HTML error page), which can lead to `tar` extracting garbage and leaving missing taxonomy files.\n\nThis issue also appears on line 9 of the same file.\n```\n#SBATCH -o %x-%j.out\n#SBATCH -e %x-%j.err\n```\n**pawsey_minion/download_taxon_db.slurm:9**\n* This download script doesn't use fail-fast shell options. If `curl`/`tar` fails, the job can still print \"Done\" and exit 0, leaving an incomplete taxonomy DB behind.\n\nThis issue also appears on line 31 of the same file.\n**pawsey_minion/download_human.slurm:9**\n* This script lacks `set -euo pipefail`/`trap` handling, so a failed `curl` can still result in the job finishing and printing a success message.\n\nThis issue also appears on line 15 of the same file.\n

\n\n\n@codex please review\n\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `e16ec4537a`\n \n\n

ℹ️ About Codex in GitHub

",{},"created",1785752406.048567,"Completing the task","event_type","info",{"_96":407,"_100":97,"_399":933},{"_96":865,"_866":867},{"_96":843,"_844":508,"_845":846,"_847":848,"_849":-5},"pr","pr_title","pr_message","### Motivation\n\n- The existing taxonomy download jobs could succeed even when `curl` or `tar` failed or produced partial files, leaving an incomplete taxonomy DB behind. \n- File-existence checks accepted empty or partial files and paths were not always safely quoted, which risks data corruption or script errors on retry. \n\n### Description\n\n- Enable fail-fast shell behavior with `set -euo pipefail` and safely quote `TAXDIR` usage in both `pawsey_minion/download_taxon_db.slurm` and `pawsey_shortread/download_taxon_db.slurm`. \n- Treat files as missing if empty by switching checks from `-f` to `-s` and report missing files before attempting download. \n- Download into a temporary staging area created by `mktemp -d`, use `curl --fail --location --retry 3 --output` to fail on HTTP errors and retry transient failures, extract into the staging dir, validate each expected file is non-empty, then atomically move validated files into the live `TAXDIR`, and ensure staging cleanup with a `trap`. \n\n### Testing\n\n- Ran `bash -n pawsey_minion/download_taxon_db.slurm pawsey_shortread/download_taxon_db.slurm` (shell syntax check) which passed. \n- Ran `git diff --check` which reported no whitespace/format errors. \n- `shellcheck` was not available in the environment so static linting with ShellCheck was not executed.","output_diff",{"_96":847,"_850":442,"_132":133,"_851":-5,"_310":852,"_853":854,"_855":703,"_856":857,"_858":316,"_859":508,"_860":861},"pre_apply_patch","repo_id","preapply_patch_base_commit_sha","diff --git a/pawsey_minion/download_taxon_db.slurm b/pawsey_minion/download_taxon_db.slurm\nindex db3d3d55af616f9e30b58564535f88fa6db1edbb..c359f8e36a6a2b189b1353b242e488c0dcd7d381 100644\n--- a/pawsey_minion/download_taxon_db.slurm\n+++ b/pawsey_minion/download_taxon_db.slurm\n@@ -1,38 +1,58 @@\n #!/bin/bash\n #SBATCH --job-name=taxon_dld\n #SBATCH --time=1-0\n #SBATCH --ntasks=1\n #SBATCH --cpus-per-task=1\n #SBATCH --mem=32G\n #SBATCH -o %x-%j.out\n #SBATCH -e %x-%j.err\n \n+set -euo pipefail\n+\n TAXDIR=\"/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current\"\n \n-mkdir -p $TAXDIR\n-cd $TAXDIR;\n+mkdir -p \"$TAXDIR\"\n+cd \"$TAXDIR\"\n \n required_files=(\n citations.dmp delnodes.dmp division.dmp gc.prt\n gencode.dmp images.dmp merged.dmp names.dmp\n nodes.dmp readme.txt\n )\n \n missing=0\n \n for file in \"${required_files[@]}\"; do\n- if [[ ! -f \"$file\" ]]; then\n+ if [[ ! -s \"$file\" ]]; then\n echo \"Missing: $file\"\n missing=1\n fi\n done\n \n if [[ $missing -eq 1 ]]; then\n- echo \"One or more files are missing. Downloading taxdump.tar.gz...\"\n- curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n- tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\n+ echo \"One or more files are missing or empty. Downloading taxdump.tar.gz...\"\n+ temp_dir=$(mktemp -d \"$TAXDIR/.taxdump.XXXXXX\")\n+ trap 'rm -rf \"$temp_dir\"' EXIT\n+\n+ curl --fail --location --retry 3 \\\n+ --output \"$temp_dir/taxdump.tar.gz\" \\\n+ https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n+ mkdir \"$temp_dir/extracted\"\n+ tar -xzf \"$temp_dir/taxdump.tar.gz\" -C \"$temp_dir/extracted\"\n+\n+ for file in \"${required_files[@]}\"; do\n+ if [[ ! -s \"$temp_dir/extracted/$file\" ]]; then\n+ echo \"Downloaded taxonomy archive is missing a valid $file\" >&2\n+ exit 1\n+ fi\n+ done\n+\n+ find \"$temp_dir/extracted\" -mindepth 1 -maxdepth 1 \\\n+ -exec mv -t \"$TAXDIR\" -- {} +\n+ rm -rf \"$temp_dir\"\n+ trap - EXIT\n else\n echo \"All required files are present.\"\n fi\n \n echo \"Done\"\ndiff --git a/pawsey_shortread/download_taxon_db.slurm b/pawsey_shortread/download_taxon_db.slurm\nindex db3d3d55af616f9e30b58564535f88fa6db1edbb..c359f8e36a6a2b189b1353b242e488c0dcd7d381 100644\n--- a/pawsey_shortread/download_taxon_db.slurm\n+++ b/pawsey_shortread/download_taxon_db.slurm\n@@ -1,38 +1,58 @@\n #!/bin/bash\n #SBATCH --job-name=taxon_dld\n #SBATCH --time=1-0\n #SBATCH --ntasks=1\n #SBATCH --cpus-per-task=1\n #SBATCH --mem=32G\n #SBATCH -o %x-%j.out\n #SBATCH -e %x-%j.err\n \n+set -euo pipefail\n+\n TAXDIR=\"/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current\"\n \n-mkdir -p $TAXDIR\n-cd $TAXDIR;\n+mkdir -p \"$TAXDIR\"\n+cd \"$TAXDIR\"\n \n required_files=(\n citations.dmp delnodes.dmp division.dmp gc.prt\n gencode.dmp images.dmp merged.dmp names.dmp\n nodes.dmp readme.txt\n )\n \n missing=0\n \n for file in \"${required_files[@]}\"; do\n- if [[ ! -f \"$file\" ]]; then\n+ if [[ ! -s \"$file\" ]]; then\n echo \"Missing: $file\"\n missing=1\n fi\n done\n \n if [[ $missing -eq 1 ]]; then\n- echo \"One or more files are missing. Downloading taxdump.tar.gz...\"\n- curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n- tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\n+ echo \"One or more files are missing or empty. Downloading taxdump.tar.gz...\"\n+ temp_dir=$(mktemp -d \"$TAXDIR/.taxdump.XXXXXX\")\n+ trap 'rm -rf \"$temp_dir\"' EXIT\n+\n+ curl --fail --location --retry 3 \\\n+ --output \"$temp_dir/taxdump.tar.gz\" \\\n+ https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n+ mkdir \"$temp_dir/extracted\"\n+ tar -xzf \"$temp_dir/taxdump.tar.gz\" -C \"$temp_dir/extracted\"\n+\n+ for file in \"${required_files[@]}\"; do\n+ if [[ ! -s \"$temp_dir/extracted/$file\" ]]; then\n+ echo \"Downloaded taxonomy archive is missing a valid $file\" >&2\n+ exit 1\n+ fi\n+ done\n+\n+ find \"$temp_dir/extracted\" -mindepth 1 -maxdepth 1 \\\n+ -exec mv -t \"$TAXDIR\" -- {} +\n+ rm -rf \"$temp_dir\"\n+ trap - EXIT\n else\n echo \"All required files are present.\"\n fi\n \n echo \"Done\"\n","external_storage_diff",{"_862":863,"_864":-5},"files_modified","lines_added",52,"lines_removed","commit_message","additional_parent_commit_shas",[],"file_id","file_0000000073d481f6a79b86c854ed9cf1","ttl","partial_repo_snapshot","files",[868,869],{"_165":929,"_871":-5,"_872":930,"_874":-5},{"_165":870,"_871":-5,"_872":873,"_874":-5},"pawsey_shortread/download_taxon_db.slurm","contents","line_range_contents",[875],"missing_reason",{"_876":877,"_878":879,"_399":880,"_881":62},"line_range_start",1,"line_range_end",58,[882,883,884,885,886,887,888,889,203,890,203,891,203,892,893,203,894,895,896,897,898,203,899,203,900,901,902,903,904,905,203,906,907,908,909,203,910,911,912,913,914,203,915,916,917,918,919,920,203,921,922,923,924,925,926,927,203,928],"contains_end_of_file","#!/bin/bash","#SBATCH --job-name=taxon_dld","#SBATCH --time=1-0","#SBATCH --ntasks=1","#SBATCH --cpus-per-task=1","#SBATCH --mem=32G","#SBATCH -o %x-%j.out","#SBATCH -e %x-%j.err","set -euo pipefail","TAXDIR=\"/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current\"","mkdir -p \"$TAXDIR\"","cd \"$TAXDIR\"","required_files=("," citations.dmp delnodes.dmp division.dmp gc.prt"," gencode.dmp images.dmp merged.dmp names.dmp"," nodes.dmp readme.txt",")","missing=0","for file in \"${required_files[@]}\"; do"," if [[ ! -s \"$file\" ]]; then"," echo \"Missing: $file\""," missing=1"," fi","done","if [[ $missing -eq 1 ]]; then"," echo \"One or more files are missing or empty. Downloading taxdump.tar.gz...\""," temp_dir=$(mktemp -d \"$TAXDIR/.taxdump.XXXXXX\")"," trap 'rm -rf \"$temp_dir\"' EXIT"," curl --fail --location --retry 3 \\"," --output \"$temp_dir/taxdump.tar.gz\" \\"," https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"," mkdir \"$temp_dir/extracted\""," tar -xzf \"$temp_dir/taxdump.tar.gz\" -C \"$temp_dir/extracted\""," for file in \"${required_files[@]}\"; do"," if [[ ! -s \"$temp_dir/extracted/$file\" ]]; then"," echo \"Downloaded taxonomy archive is missing a valid $file\" >&2"," exit 1"," fi"," done"," find \"$temp_dir/extracted\" -mindepth 1 -maxdepth 1 \\"," -exec mv -t \"$TAXDIR\" -- {} +"," rm -rf \"$temp_dir\""," trap - EXIT","else"," echo \"All required files are present.\"","fi","echo \"Done\"","pawsey_minion/download_taxon_db.slurm",[931],{"_876":877,"_878":879,"_399":932,"_881":62},[882,883,884,885,886,887,888,889,203,890,203,891,203,892,893,203,894,895,896,897,898,203,899,203,900,901,902,903,904,905,203,906,907,908,909,203,910,911,912,913,914,203,915,916,917,918,919,920,203,921,922,923,924,925,926,927,203,928],[934,935,936,937,938,939,940,941,942,943,944,945,946],{"_830":49,"_49":959},{"_830":948,"_165":929,"_876":958,"_878":224},{"_830":948,"_165":870,"_876":958,"_878":224},{"_830":49,"_49":957},{"_830":948,"_165":929,"_876":955,"_878":956},{"_830":948,"_165":870,"_876":955,"_878":956},{"_830":49,"_49":954},{"_830":948,"_165":929,"_876":952,"_878":953},{"_830":948,"_165":870,"_876":952,"_878":953},{"_830":49,"_49":951},{"_830":948,"_165":929,"_876":949,"_878":950},{"_830":948,"_165":870,"_876":949,"_878":950},{"_830":49,"_49":947},"\n* Committed the changes as `71381f8` (`Harden taxonomy database downloads`) and created the follow-up pull request titled **Harden taxonomy database downloads**.\n\n**Testing**\n\n* ✅ `git diff --check`\n* ✅ `bash -n pawsey_minion/download_taxon_db.slurm pawsey_shortread/download_taxon_db.slurm`\n* ⚠️ `shellcheck pawsey_minion/download_taxon_db.slurm pawsey_shortread/download_taxon_db.slurm` (ShellCheck is not installed in the environment.)\n* ✅ `git status --porcelain` (working tree clean after commit)","repo_file_citation",43,53,"\n* Added validation of every required extracted file before publishing the downloaded database into its final location. ",32,41,"\n* Made taxonomy downloads fail on HTTP errors, retry transient failures, and extract into a temporary staging directory with automatic cleanup. ",23,30,"\n* Updated existing-file checks to reject missing or empty taxonomy files. ",10,"### Summary\n\n* Added fail-fast shell behavior and safely quoted taxonomy database paths in both Pawsey workflows. ",{"_96":311,"_45":88,"_100":311,"_962":963,"_964":965,"_966":967,"_136":-5,"_123":968},[87],"input_items",[985,986,987,988,989,990,991,992,993,994,995,996,997,998,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,1011],"external_post_config",{"_969":970,"_248":249,"_971":291,"_260":-5,"_850":243,"_972":-5,"_973":-5,"_974":975,"_976":843,"_977":-5,"_978":-5,"_979":980,"_981":18,"_982":62,"_983":57,"_984":18},"user_model_slug","slug",1785752317.799948,"installation_id",105641882,"pr_number","gitlab_service_account_project_id","review_trigger","comment_id",3702973975,"comment_type","pr_write_guard_token","pending_pr_reaction_id","pending_comment_reaction_id",419912750,"comment_if_no_findings","comment_on_error","share_url","is_parallel_review",{"_96":407,"_100":311,"_399":1050},{"_298":299,"_300":301,"_1047":305,"_1048":133,"_307":-5,"_96":1049},{"_96":1012,"_300":1046,"_165":929,"_1014":1021,"_1015":291},{"_96":1012,"_300":1045,"_165":1039,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1044,"_165":1032,"_1014":1021,"_1015":320},{"_96":1012,"_300":1043,"_165":-5,"_1014":-5,"_1015":-5},{"_96":1012,"_300":1042,"_165":1027,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1041,"_165":1026,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1038,"_165":1020,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1038,"_165":1040,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1038,"_165":870,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1038,"_165":1039,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1036,"_165":1037,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1034,"_165":1035,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1033,"_165":929,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1031,"_165":1032,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1030,"_165":1023,"_1014":1021,"_1015":1024},{"_96":1012,"_300":1029,"_165":-5,"_1014":-5,"_1015":-5},{"_96":1012,"_300":1028,"_165":-5,"_1014":-5,"_1015":-5},{"_96":1012,"_300":1025,"_165":1027,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1025,"_165":1026,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1022,"_165":1023,"_1014":1021,"_1015":1024},{"_96":1012,"_300":1019,"_165":1020,"_1014":1021,"_1015":-5},{"_96":1012,"_300":1018,"_165":-5,"_1014":-5,"_1015":-5},{"_96":1012,"_300":1017,"_165":-5,"_1014":-5,"_1015":-5},{"_96":1012,"_300":1016,"_165":-5,"_1014":-5,"_1015":-5},{"_96":1012,"_300":1013,"_165":-5,"_1014":-5,"_1015":-5},"pull_request_comment","\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `e16ec4537a`\n \n\n

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","side","line","@codex please review","## Pull request overview\n\nCopilot reviewed 12 out of 12 changed files in this pull request and generated no new comments.\n\n\n\n\n

Suppressed comments (12)

\n\n","## Pull request overview\n\nCopilot reviewed 12 out of 12 changed files in this pull request and generated no new comments.\n\n\n\n\n

Suppressed comments (8)

\n\n","Fixed — changed `#SBATCH -o slurm/%x-%j.out` to `#SBATCH -o %x-%j.out` (and same for `-e`) so logs write to the submission directory without requiring a pre-created `slurm/` folder.","pawsey_shortread/download_uniref50.slurm","RIGHT","Fixed — added `mkdir -p $OUTDIR/mapped_reads` inside the `if [[ ! -e ... ]]` block before the minimap2/samtools pipeline runs.","pawsey_minion/vamb.slurm",45,"Fixed in commit `Fix review comments: README typos, slurm/ log directory, and vamb mapped_reads mkdir` — corrected `atavide_lit/bin` → `atavide_lite/bin`.","pawsey_minion/README.md","pawsey_shortread/README.md","## Pull request overview\n\nCopilot reviewed 13 out of 13 changed files in this pull request and generated no new comments.\n\n\n\n\n

Suppressed comments (9)

\n\n","## Pull request overview\n\nThis PR updates Pawsey workflow documentation and SLURM scripts to improve reproducibility and standardize operational behavior, including new database download jobs and updates to VAMB job environments.\n\n**Changes:**\n- Added new `pawsey_minion` SLURM scripts to download required databases (human reference, NCBI taxonomy, UniRef50/UniRef100).\n- Updated VAMB-related SLURM jobs to use the `atavide_lite_vamb` conda environment and refreshed the PyTorch module for GPU runs.\n- Standardized/adjusted job logging and timings (e.g., download script log locations; reduced `mmseqs_easy_taxonomy100` walltime).\n\n### Reviewed changes\n\nCopilot reviewed 13 out of 13 changed files in this pull request and generated 11 comments.\n\n

Show a summary per file

\n\n\n\n\n\n

Suppressed comments (4)

\n\n\n\n---\n\n💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.","This script now conditionally generates missing BAMs, but it doesn’t ensure `$OUTDIR/mapped_reads` exists before writing `-o $OUTDIR/mapped_reads/$BAM`. If the directory isn’t present (e.g., running `vamb.slurm` without a prior `vamb_minimap` step), the minimap2/samtools pipeline will fail when it tries to write the BAM.","These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 15 of the same file.","pawsey_minion/download_human.slurm","These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 31 of the same file.","These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 61 of the same file.","pawsey_minion/download_uniref100.slurm","These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).\n\nThis issue also appears on line 62 of the same file.","pawsey_minion/download_uniref50.slurm","These `--output/--error` paths write into a relative `slurm/` directory. Slurm requires the directory to exist when the job starts; if `slurm/` hasn’t been created, the job can fail to launch or logs may not be written. Prefer writing to the submission directory without requiring a pre-created folder (or update docs/wrappers to create it).","pawsey_shortread/download_human.slurm","pawsey_shortread/download_uniref100.slurm","Typo in the path: `atavide_lit/bin` is missing the trailing `e`, while the snippet below uses `atavide_lite/bin`. This can mislead users when copy/pasting commands.","Typo in the path: `atavide_lit/bin` is missing the trailing `e`, while the actual directory referenced below is `atavide_lite/bin`. This can confuse users copy/pasting the instructions.","\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `7d66ebfd83`\n \n\n

ℹ️ About Codex in GitHub

","**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Reject incomplete human database downloads**\n\nIf this transfer is interrupted or receives an HTTP error, the script has neither `set -e` nor curl's `--fail` behavior ([curl documentation](https://curl.se/docs/manpage.html#-f)), so it proceeds to the final `echo` and reports a successful Slurm job. Because `-O` writes directly to the final filename and the earlier guard checks only existence, a partial or error-response file is then accepted as a complete human database on every retry; propagate curl failures and download atomically before exposing the final filename.\n\nUseful? React with 👍 / 👎.","**_{_{![P1 Badge](https://img.shields.io/badge/P1-orange?style=flat)}} Create the slurm log directory before submissions**\n\nWhen following either Pawsey README in a fresh analysis directory, the setup creates only `slurm_output/...`, while all eight database-download scripts now direct stdout and stderr into `slurm/`. Slurm connects `--output` to the specified filename before the batch script runs ([official `sbatch` documentation](https://slurm.schedmd.com/sbatch.html#OPT_output)), so without a pre-existing `slurm` directory these jobs fail during I/O setup and none of the databases are downloaded; add this directory to the documented setup or target the existing `slurm_output` tree.\n\nUseful? React with 👍 / 👎.","Comments in the same thread:\n\n**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Propagate taxonomy extraction failures**\n\nIf the taxonomy transfer is interrupted or the archive is corrupt, `curl` or `tar` can return nonzero, but this script continues to the final `echo \"Done\"` and exits successfully. Slurm will therefore report a completed download even though required taxonomy files may be missing or partially extracted; make the download/extraction failure terminate the script and only expose validated files.\n\nUseful? 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