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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\":\"**_{_{![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 👍 / 👎.\",\"path\":\"pawsey_minion/download_taxon_db.slurm\",\"side\":\"RIGHT\",\"line\":33}{\"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}{\"type\":\"pull_request_comment\",\"body\":\"@codex fix comments\",\"path\":\"pawsey_minion/download_taxon_db.slurm\",\"side\":\"RIGHT\",\"line\":33}","text_elements",[],{"_395":731,"_374":375,"_397":381},{"_398":732,"_400":-5,"_45":-5,"_402":733,"_404":-5,"_100":311,"_96":406},[734],{"_407":381},{"_49":727,"_96":430},{"_395":736,"_374":375,"_397":381},{"_398":737,"_400":-5,"_45":-5,"_402":738,"_404":-5,"_100":311,"_96":406},[739],{"_407":381},{"_49":740,"_96":430},"\n /workspace/atavide_lite\n bash\n 2026-08-03\n Etc/UTC\n /workspace/atavide_lite\n",{"_395":742,"_374":375,"_397":381},{"_398":743,"_400":-5,"_45":-5,"_402":744,"_404":-5,"_100":745,"_96":406},[746],{"_407":381},"developer",{"_49":747,"_96":430},"Do not spawn sub-agents unless the user or applicable AGENTS.md/skill instructions explicitly ask for sub-agents, delegation, or parallel agent work.",{"_395":749,"_374":375,"_397":381},{"_398":750,"_400":-5,"_45":-5,"_402":751,"_404":-5,"_100":745,"_96":406},[752],{"_407":381},{"_49":753,"_96":430},"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.",{"_395":755,"_374":375,"_397":381},{"_398":756,"_400":-5,"_45":-5,"_402":757,"_404":-5,"_100":745,"_96":406},[758,759],{"_407":381},{"_49":761,"_96":430},{"_49":760,"_96":430},"\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",{"_374":375,"_91":764},{"_107":-5,"_45":381,"_382":765,"_384":385,"_386":387,"_388":766},[],"inProgress",{"_388":768,"_374":375},{"_769":770,"_96":771},"activeFlags",[],"active","thread/started",{"_774":775},"thread",{"_776":-5,"_777":-5,"_778":779,"_780":387,"_440":441,"_781":18,"_782":-5,"_783":-5,"_784":-5,"_785":786,"_45":375,"_787":788,"_185":-5,"_789":-5,"_165":790,"_791":203,"_792":387,"_793":375,"_446":794,"_388":795,"_796":-5,"_81":797,"_798":387},"agentNickname","agentRole","cliVersion","0.144.0-alpha.4","createdAt","ephemeral","extra","forkedFromId","gitInfo","historyMode","legacy","modelProvider","openai","parentThreadId","/opt/codex/sessions/2026/08/03/rollout-2026-08-03T10-19-30-019fc722-beca-70f1-b9ad-a8755b239d70.jsonl","preview","recencyAt","sessionId","vscode",{"_96":392},"threadSource",[],"updatedAt",[],"messages",[802],{"_45":803,"_804":805,"_806":807,"_808":807,"_398":809,"_388":810,"_400":-5,"_811":35,"_812":813,"_814":815,"_816":-5},"f85bf82a-4d16-44e7-8792-7988b705910e","author",{"_100":311,"_185":-5,"_812":825},"create_time",1785752370.031017,"update_time",{"_821":49,"_822":823},"finished_successfully","weight","metadata",{"_817":818},"recipient","all","channel","l1239dk1",{"_819":820},"inline_comments",[],"content_type","parts",[824],"@codex fix comments\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.\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

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

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**_{_{![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\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

\n@codex fix comments",{},"created",1785752463.7848954,"Completing the task","event_type","info",{"_96":406,"_100":97,"_398":952},{"_96":859,"_860":861},{"_96":834,"_835":509,"_836":837,"_838":839,"_840":-5},"pr","pr_title","pr_message","### Motivation\n- Address review feedback that taxonomy and human-reference download jobs could report success despite failed or partial transfers. \n- Prevent corrupted or partial files from being accepted as complete databases and avoid needless timestamp updates. \n- Improve robustness by making downloads retry transient failures and clean up temporary artifacts on error. \n\n### Description\n- Enabled fail-fast shell behavior by adding `set -euo pipefail` to the four download scripts (`pawsey_minion/*` and `pawsey_shortread/*`). \n- Made taxonomy downloads extract into a temporary directory created with `mktemp -d`, validated each expected `required_files` is present and non-empty, then `mv`ed validated files into the target directory; added a `trap` to remove the temp dir on exit. \n- Made human-reference downloads atomic by downloading to a `mktemp` temporary file, using `curl --fail --location --retry 3`, verifying the temp file is non-empty, then moving it into place and avoiding `touch` on existing files; switched existence checks to `-s` to ensure non-empty files. \n- Changed downloads to use `curl --fail --location --retry 3` and explicit `--output` paths so HTTP errors and transient problems fail the job instead of producing partial files. \n\n### Testing\n- Ran `git diff --check` which passed with no whitespace errors. \n- Performed shell syntax checks with `bash -n` on the four modified scripts (`pawsey_minion/download_taxon_db.slurm`, `pawsey_shortread/download_taxon_db.slurm`, `pawsey_minion/download_human.slurm`, `pawsey_shortread/download_human.slurm`) which completed successfully. \n- Attempted `shellcheck` but it is not installed in the environment, so static linting was not executed.","output_diff",{"_96":838,"_841":441,"_132":133,"_842":-5,"_310":843,"_844":845,"_846":847,"_848":849,"_850":851,"_852":853,"_854":855},"pre_apply_patch","repo_id","preapply_patch_base_commit_sha","diff --git a/pawsey_minion/download_human.slurm b/pawsey_minion/download_human.slurm\nindex af67df820a41cf1dd3e1742dccce8225689d9ef2..3bae4c9b0be9a65c642e6fd22f554c492793ef59 100644\n--- a/pawsey_minion/download_human.slurm\n+++ b/pawsey_minion/download_human.slurm\n@@ -1,22 +1,30 @@\n #!/bin/bash\n #SBATCH --job-name=human_download\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 DEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human\n+GENOME=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz\n \n-mkdir -p $DEST\n-cd $DEST\n+mkdir -p \"$DEST\"\n+cd \"$DEST\"\n \n-if [[ -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+if [[ -s $GENOME ]]; then\n+\techo \"$GENOME already exists. Nothing to do\"\n \texit 0\n fi\n \n-curl -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\n+temp_file=$(mktemp \"$DEST/.${GENOME}.XXXXXX\")\n+trap 'rm -f \"$temp_file\"' EXIT\n+curl --fail --location --retry 3 \\\n+ --output \"$temp_file\" \\\n+ \"https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/$GENOME\"\n+[[ -s $temp_file ]]\n+mv -f \"$temp_file\" \"$GENOME\"\n echo \"Downloaded human db to $DEST\"\ndiff --git a/pawsey_minion/download_taxon_db.slurm b/pawsey_minion/download_taxon_db.slurm\nindex db3d3d55af616f9e30b58564535f88fa6db1edbb..f6d8550f5baea4efae250b7003e1b21a526b39b6 100644\n--- a/pawsey_minion/download_taxon_db.slurm\n+++ b/pawsey_minion/download_taxon_db.slurm\n@@ -1,38 +1,57 @@\n #!/bin/bash\n #SBATCH --job-name=taxon_dld\n #SBATCH --time=1-0\n #SBATCH --ntasks=1\n #SBATCH --cpus-per-task=1\n #SBATCH --mem=32G\n #SBATCH -o %x-%j.out\n #SBATCH -e %x-%j.err\n \n+set -euo pipefail\n+\n TAXDIR=\"/scratch/$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 echo \"Missing: $file\"\n missing=1\n fi\n done\n \n if [[ $missing -eq 1 ]]; then\n- echo \"One or more files are missing. Downloading taxdump.tar.gz...\"\n- curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n- tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\n+ echo \"One or more files are missing. Downloading taxonomy database...\"\n+ temp_dir=$(mktemp -d \"$TAXDIR/.taxdump.XXXXXX\")\n+ trap 'rm -rf \"$temp_dir\"' EXIT\n+\n+ curl --fail --location --retry 3 \\\n+ --output \"$temp_dir/taxdump.tar.gz\" \\\n+ https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n+ tar -xzf \"$temp_dir/taxdump.tar.gz\" -C \"$temp_dir\"\n+\n+ for file in \"${required_files[@]}\"; do\n+ if [[ ! -s \"$temp_dir/$file\" ]]; then\n+ echo \"Downloaded taxonomy database is missing or has an empty $file\" >&2\n+ exit 1\n+ fi\n+ done\n+\n+ for file in \"$temp_dir\"/*; do\n+ [[ $file == \"$temp_dir/taxdump.tar.gz\" ]] && continue\n+ mv -f \"$file\" \"$TAXDIR/\"\n+ done\n else\n echo \"All required files are present.\"\n fi\n \n echo \"Done\"\ndiff --git a/pawsey_shortread/download_human.slurm b/pawsey_shortread/download_human.slurm\nindex af67df820a41cf1dd3e1742dccce8225689d9ef2..3bae4c9b0be9a65c642e6fd22f554c492793ef59 100644\n--- a/pawsey_shortread/download_human.slurm\n+++ b/pawsey_shortread/download_human.slurm\n@@ -1,22 +1,30 @@\n #!/bin/bash\n #SBATCH --job-name=human_download\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 DEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human\n+GENOME=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz\n \n-mkdir -p $DEST\n-cd $DEST\n+mkdir -p \"$DEST\"\n+cd \"$DEST\"\n \n-if [[ -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+if [[ -s $GENOME ]]; then\n+\techo \"$GENOME already exists. Nothing to do\"\n \texit 0\n fi\n \n-curl -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\n+temp_file=$(mktemp \"$DEST/.${GENOME}.XXXXXX\")\n+trap 'rm -f \"$temp_file\"' EXIT\n+curl --fail --location --retry 3 \\\n+ --output \"$temp_file\" \\\n+ \"https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/$GENOME\"\n+[[ -s $temp_file ]]\n+mv -f \"$temp_file\" \"$GENOME\"\n echo \"Downloaded human db to $DEST\"\ndiff --git a/pawsey_shortread/download_taxon_db.slurm b/pawsey_shortread/download_taxon_db.slurm\nindex db3d3d55af616f9e30b58564535f88fa6db1edbb..f6d8550f5baea4efae250b7003e1b21a526b39b6 100644\n--- a/pawsey_shortread/download_taxon_db.slurm\n+++ b/pawsey_shortread/download_taxon_db.slurm\n@@ -1,38 +1,57 @@\n #!/bin/bash\n #SBATCH --job-name=taxon_dld\n #SBATCH --time=1-0\n #SBATCH --ntasks=1\n #SBATCH --cpus-per-task=1\n #SBATCH --mem=32G\n #SBATCH -o %x-%j.out\n #SBATCH -e %x-%j.err\n \n+set -euo pipefail\n+\n TAXDIR=\"/scratch/$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 echo \"Missing: $file\"\n missing=1\n fi\n done\n \n if [[ $missing -eq 1 ]]; then\n- echo \"One or more files are missing. Downloading taxdump.tar.gz...\"\n- curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n- tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz\n+ echo \"One or more files are missing. Downloading taxonomy database...\"\n+ temp_dir=$(mktemp -d \"$TAXDIR/.taxdump.XXXXXX\")\n+ trap 'rm -rf \"$temp_dir\"' EXIT\n+\n+ curl --fail --location --retry 3 \\\n+ --output \"$temp_dir/taxdump.tar.gz\" \\\n+ https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\n+ tar -xzf \"$temp_dir/taxdump.tar.gz\" -C \"$temp_dir\"\n+\n+ for file in \"${required_files[@]}\"; do\n+ if [[ ! -s \"$temp_dir/$file\" ]]; then\n+ echo \"Downloaded taxonomy database is missing or has an empty $file\" >&2\n+ exit 1\n+ fi\n+ done\n+\n+ for file in \"$temp_dir\"/*; do\n+ [[ $file == \"$temp_dir/taxdump.tar.gz\" ]] && continue\n+ mv -f \"$file\" \"$TAXDIR/\"\n+ done\n else\n echo \"All required files are present.\"\n fi\n \n echo \"Done\"\n","external_storage_diff",{"_856":857,"_858":-5},"files_modified",4,"lines_added",76,"lines_removed",22,"commit_message","Make database downloads fail safely","additional_parent_commit_shas",[],"file_id","file_000000005db081f7967457cd55520703","ttl","partial_repo_snapshot","files",[862,863,864,865],{"_165":948,"_867":-5,"_868":949,"_870":-5},{"_165":907,"_867":-5,"_868":908,"_870":-5},{"_165":903,"_867":-5,"_868":904,"_870":-5},{"_165":866,"_867":-5,"_868":869,"_870":-5},"pawsey_shortread/download_human.slurm","contents","line_range_contents",[871],"missing_reason",{"_872":873,"_874":875,"_398":876,"_877":62},"line_range_start",1,"line_range_end",30,[878,879,880,881,882,883,884,885,203,886,203,887,888,203,889,890,203,891,892,893,894,203,895,896,897,898,899,900,901,902],"contains_end_of_file","#!/bin/bash","#SBATCH --job-name=human_download","#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","DEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human","GENOME=GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz","mkdir -p \"$DEST\"","cd \"$DEST\"","if [[ -s $GENOME ]]; then","\techo \"$GENOME already exists. Nothing to do\"","\texit 0","fi","temp_file=$(mktemp \"$DEST/.${GENOME}.XXXXXX\")","trap 'rm -f \"$temp_file\"' EXIT","curl --fail --location --retry 3 \\"," --output \"$temp_file\" \\"," \"https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/$GENOME\"","[[ -s $temp_file ]]","mv -f \"$temp_file\" \"$GENOME\"","echo \"Downloaded human db to $DEST\"","pawsey_minion/download_human.slurm",[905],{"_872":873,"_874":875,"_398":906,"_877":62},[878,879,880,881,882,883,884,885,203,886,203,887,888,203,889,890,203,891,892,893,894,203,895,896,897,898,899,900,901,902],"pawsey_shortread/download_taxon_db.slurm",[909],{"_872":873,"_874":910,"_398":911,"_877":62},57,[878,912,880,881,882,883,884,885,203,886,203,913,203,914,915,203,916,917,918,919,920,203,921,203,922,923,924,925,926,927,203,928,929,930,931,203,932,933,934,935,203,936,937,938,939,940,941,203,942,943,944,941,945,946,894,203,947],"#SBATCH --job-name=taxon_dld","TAXDIR=\"/scratch/$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 [[ ! -f \"$file\" ]]; then"," echo \"Missing: $file\""," missing=1"," fi","done","if [[ $missing -eq 1 ]]; then"," echo \"One or more files are missing. Downloading taxonomy database...\""," temp_dir=$(mktemp -d \"$TAXDIR/.taxdump.XXXXXX\")"," trap 'rm -rf \"$temp_dir\"' EXIT"," curl --fail --location --retry 3 \\"," --output \"$temp_dir/taxdump.tar.gz\" \\"," https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"," tar -xzf \"$temp_dir/taxdump.tar.gz\" -C \"$temp_dir\""," for file in \"${required_files[@]}\"; do"," if [[ ! -s \"$temp_dir/$file\" ]]; then"," echo \"Downloaded taxonomy database is missing or has an empty $file\" >&2"," exit 1"," fi"," done"," for file in \"$temp_dir\"/*; do"," [[ $file == \"$temp_dir/taxdump.tar.gz\" ]] && continue"," mv -f \"$file\" \"$TAXDIR/\"","else"," echo \"All required files are present.\"","echo \"Done\"","pawsey_minion/download_taxon_db.slurm",[950],{"_872":873,"_874":910,"_398":951,"_877":62},[878,912,880,881,882,883,884,885,203,886,203,913,203,914,915,203,916,917,918,919,920,203,921,203,922,923,924,925,926,927,203,928,929,930,931,203,932,933,934,935,203,936,937,938,939,940,941,203,942,943,944,941,945,946,894,203,947],[953,954,955,956,957,958,959],{"_821":49,"_49":965},{"_821":961,"_165":948,"_872":962,"_874":964},{"_821":961,"_165":907,"_872":962,"_874":964},{"_821":49,"_49":963},{"_821":961,"_165":903,"_872":962,"_874":875},{"_821":961,"_165":866,"_872":962,"_874":875},{"_821":49,"_49":960},"\n* Committed the changes in commit `895373c` (`Make database downloads fail safely`) and created the follow-up pull request titled **“Follow-up: make Pawsey database downloads fail safely.”**\n\n**Testing**\n\n* ✅ `git diff --check`\n* ✅ `bash -n pawsey_minion/download_taxon_db.slurm pawsey_shortread/download_taxon_db.slurm pawsey_minion/download_human.slurm pawsey_shortread/download_human.slurm`\n* ⚠️ `shellcheck pawsey_minion/download_taxon_db.slurm pawsey_shortread/download_taxon_db.slurm pawsey_minion/download_human.slurm pawsey_shortread/download_human.slurm` (ShellCheck is not installed in the environment.)\n* ✅ `git status --short --branch` (working tree clean after commit)","repo_file_citation",10,"\n* Hardened both human-reference download jobs by accepting only non-empty existing references, removing the unnecessary timestamp update, downloading to temporary files, cleaning up failed transfers, and atomically moving successful downloads into place. ",52,"### Summary\n\n* Added fail-fast error handling to the taxonomy download jobs in both Pawsey workflows. Downloads now reject HTTP errors, retry transient failures, extract into temporary directories, validate all required files, and publish files only after successful validation. ",{"_96":311,"_45":88,"_100":311,"_968":969,"_970":971,"_972":973,"_136":-5,"_123":974},[87],"input_items",[992,993,994,995,996,997,998,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,1011,1012,1013,1014,1015,1016,1017,1018,1019],"external_post_config",{"_975":976,"_248":249,"_977":291,"_260":-5,"_841":243,"_978":-5,"_979":-5,"_980":981,"_982":983,"_984":-5,"_985":-5,"_986":987,"_988":18,"_989":62,"_990":57,"_991":18},"user_model_slug","slug",1785752361.829309,"installation_id",105641882,"pr_number","gitlab_service_account_project_id","review_trigger","comment_id",5165115477,"comment_type","issue","pr_write_guard_token","pending_pr_reaction_id","pending_comment_reaction_id",391956596,"comment_if_no_findings","comment_on_error","share_url","is_parallel_review",{"_96":406,"_100":311,"_398":1057},{"_298":299,"_300":301,"_1054":305,"_1055":133,"_307":-5,"_96":1056},{"_96":1020,"_300":1053,"_165":866,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1052,"_165":903,"_1022":1023,"_1024":320},{"_96":1020,"_300":1051,"_165":-5,"_1022":-5,"_1024":-5},{"_96":1020,"_300":1050,"_165":1037,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1049,"_165":1036,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1047,"_165":1031,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1047,"_165":1048,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1047,"_165":907,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1047,"_165":866,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1045,"_165":1046,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1043,"_165":1044,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1042,"_165":948,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1041,"_165":903,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1040,"_165":1033,"_1022":1023,"_1024":1034},{"_96":1020,"_300":1039,"_165":-5,"_1022":-5,"_1024":-5},{"_96":1020,"_300":1038,"_165":-5,"_1022":-5,"_1024":-5},{"_96":1020,"_300":1035,"_165":1037,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1035,"_165":1036,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1032,"_165":1033,"_1022":1023,"_1024":1034},{"_96":1020,"_300":1030,"_165":1031,"_1022":1023,"_1024":-5},{"_96":1020,"_300":1029,"_165":-5,"_1022":-5,"_1024":-5},{"_96":1020,"_300":1028,"_165":-5,"_1022":-5,"_1024":-5},{"_96":1020,"_300":1027,"_165":-5,"_1022":-5,"_1024":-5},{"_96":1020,"_300":1026,"_165":948,"_1022":1023,"_1024":291},{"_96":1020,"_300":1025,"_165":-5,"_1022":-5,"_1024":-5},{"_96":1020,"_300":1021,"_165":948,"_1022":1023,"_1024":291},"pull_request_comment","@codex fix comments","side","RIGHT","line","\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

","**_{_{![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 👍 / 👎.","@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","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.","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_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

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","**_{_{![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 👍 / 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