From f91b01ec4a9d8470009305935285a753356a4b2f Mon Sep 17 00:00:00 2001 From: linsalrob Date: Thu, 6 Aug 2026 09:54:27 +0800 Subject: [PATCH 1/2] renaming and editing --- pawsey_shortread/README.md | 22 +++++++++++++++---- ...stremoved.slurm => megahit_allreads.slurm} | 4 ++-- 2 files changed, 20 insertions(+), 6 deletions(-) rename pawsey_shortread/{megahit_hostremoved.slurm => megahit_allreads.slurm} (94%) diff --git a/pawsey_shortread/README.md b/pawsey_shortread/README.md index a236c5a..b0dbba1 100644 --- a/pawsey_shortread/README.md +++ b/pawsey_shortread/README.md @@ -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 $PAWSEY_SRC/megahit_allreads.slurm) +``` + +### 8b. If you want to do individual assemblies, and then merge them with contigger: + +First, do the assemblies separately: + +``` +MEGAHITJOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 --dependency=afterok:$HOSTJOB $PAWSEY_SRC/megahit.slurm) +``` + +Then, merge the assemblies with contigger: + +``` +TBD! ``` ## 9. Convert to fasta. @@ -260,8 +274,8 @@ Then we use the usual VAMB approach to bin the contigs. -Assemble using the `megahit_hostremoved.slurm` script above. This will take a while to run, so do it early! Also note that `megahit` can continue if it is interuppted. Make sure the `--continue` flag is active -in the `megahit_hostremoved.slurm` script. +Assemble using the `megahit_allreads.slurm` script above. This will take a while to run, so do it early! Also note that `megahit` can continue if it is interuppted. Make sure the `--continue` flag is active +in the `megahit_allreads.slurm` script. ``` VCRJOB=$(sbatch --parsable $PAWSEY_SRC/vamb_concat_crass.slurm samples.tsv) @@ -294,7 +308,7 @@ directory to find the error. ``` JOB=$(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 $PAWSEY_SRC/mmseqs_easy_taxonomy.slurm) diff --git a/pawsey_shortread/megahit_hostremoved.slurm b/pawsey_shortread/megahit_allreads.slurm similarity index 94% rename from pawsey_shortread/megahit_hostremoved.slurm rename to pawsey_shortread/megahit_allreads.slurm index 6a7df15..a9ceb9d 100644 --- a/pawsey_shortread/megahit_hostremoved.slurm +++ b/pawsey_shortread/megahit_allreads.slurm @@ -5,8 +5,8 @@ #SBATCH --ntasks=1 #SBATCH --cpus-per-task=1 #SBATCH --mem=960G -#SBATCH -o slurm_output/megahit_slurm/%x-%j.out -#SBATCH -e slurm_output/megahit_slurm/%x-%j.err +#SBATCH -o slurm_output/%x-%j.out +#SBATCH -e slurm_output/%x-%j.err From d874d40378ed667e49dfcc2222b61bb9587ef664 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 6 Aug 2026 02:05:37 +0000 Subject: [PATCH 2/2] docs: use megahit_allreads in quickstart command Co-authored-by: linsalrob <836231+linsalrob@users.noreply.github.com> --- docs/quickstart.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/quickstart.md b/docs/quickstart.md index 422f1c2..8e89925 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -111,7 +111,7 @@ Assembly can begin from cleaned reads without waiting for read-based taxonomy: ```bash ASSEMBLY_JOB=$(sbatch --parsable \ --dependency="afterok:${HOST_JOB}" \ - "$ATAVIDE_PROFILE/megahit_hostremoved.slurm") + "$ATAVIDE_PROFILE/megahit_allreads.slurm") ``` Prepare FASTA for MMseqs2: