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Merged
linsalrob merged 3 commits into from
Aug 6, 2026
Merged

renaming and editing #41

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f91b01e
renaming and editing
linsalrob Aug 6, 2026
ca8b45c
Merge remote-tracking branch 'origin/main' into renaming
Copilot Aug 6, 2026
d874d40
docs: use megahit_allreads in quickstart command
Copilot Aug 6, 2026
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2 changes: 1 addition & 1 deletion docs/quickstart.md
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ Assembly can begin from cleaned reads without waiting for read-based taxonomy:
```bash
ASSEMBLY_JOB=$(sbatch --parsable \
--dependency="afterok:${HOST_JOB}" \
"$ATAVIDE_PROFILE/megahit_hostremoved.slurm")
"$ATAVIDE_PROFILE/megahit_allreads.slurm")
```

Prepare FASTA for MMseqs2:
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22 changes: 18 additions & 4 deletions pawsey_shortread/README.md
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Expand Up @@ -135,7 +135,21 @@ We use these assemblies, e.g. for binning with VAMB. The assemblies are not used
to complete before submitting the subsequent jobs.

```
MEGAHITHR=$(sbatch --parsable --dependency=afterok:$HOSTJOB $PAWSEY_SRC/megahit_hostremoved.slurm)
MEGAHITHR=$(sbatch --parsable --dependency=afterok:$HOSTJOB $PAWSEY_SRC/megahit_allreads.slurm)

@chatgpt-codex-connector chatgpt-codex-connector Bot Aug 6, 2026

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P1 Badge Update the quick-start after renaming the assembly script

When users follow docs/quickstart.md with the documented Pawsey profile, step 9 still submits megahit_hostremoved.slurm. This commit removes that path in favor of megahit_allreads.slurm, so the quick-start assembly submission now fails before a job is created; update that command as part of the rename.

Useful? React with 👍 / 👎.

```

### 8b. If you want to do individual assemblies, and then merge them with contigger:

First, do the assemblies separately:

```
MEGAHITJOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 --dependency=afterok:$HOSTJOB $PAWSEY_SRC/megahit.slurm)
```

Then, merge the assemblies with contigger:

```
TBD!
Comment on lines +149 to +152
```

## 9. Convert to fasta.
Expand Down Expand Up @@ -260,8 +274,8 @@ Then we use the usual VAMB approach to bin the contigs.
</summary>


Assemble using the `megahit_hostremoved.slurm` script above. This will take a while to run, so do it early! Also note that `megahit` can continue if it is interuppted. Make sure the `--continue` flag is active
in the `megahit_hostremoved.slurm` script.
Assemble using the `megahit_allreads.slurm` script above. This will take a while to run, so do it early! Also note that `megahit` can continue if it is interuppted. Make sure the `--continue` flag is active
in the `megahit_allreads.slurm` script.

```
VCRJOB=$(sbatch --parsable $PAWSEY_SRC/vamb_concat_crass.slurm samples.tsv)
Expand Down Expand Up @@ -294,7 +308,7 @@ directory to find the error.
```
JOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 $PAWSEY_SRC/fastp.slurm)
HOSTJOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 --dependency=afterok:$JOB $PAWSEY_SRC/host_removal.slurm)
MEGAHITHR=$(sbatch --parsable --dependency=afterok:$HOSTJOB $PAWSEY_SRC/megahit_hostremoved.slurm)
MEGAHITHR=$(sbatch --parsable --dependency=afterok:$HOSTJOB $PAWSEY_SRC/megahit_allreads.slurm)
sbatch --parsable $PAWSEY_SRC/16S_detection_single.slurm
FAJOB=$(sbatch --parsable --dependency=afterok:$HOSTJOB $PAWSEY_SRC/fastq2fasta.slurm)
MMSEQSJOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 --dependency=afterok:$FAJOB $PAWSEY_SRC/mmseqs_easy_taxonomy.slurm)
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4 changes: 2 additions & 2 deletions pawsey_shortread/megahit_hostremoved.slurm → pawsey_shortread/megahit_allreads.slurm
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Expand Up @@ -5,8 +5,8 @@
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=960G
#SBATCH -o slurm_output/megahit_slurm/%x-%j.out
#SBATCH -e slurm_output/megahit_slurm/%x-%j.err
#SBATCH -o slurm_output/%x-%j.out
#SBATCH -e slurm_output/%x-%j.err



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