CHM13_v1 mappability

[Gilad Evrony]

Hi,

Is it possible to make a Umap annotation (multi-map 24, 50, 100) for the new telomere-to-telomere CHM13_v1 human genome?

I don't have access to a SGE, so it would be complicated to get Umap to work.

https://s3.amazonaws.com/nanopore-human-wgs/chm13/assemblies/chm13.draft_v1.0.fasta.gz

https://github.com/nanopore-wgs-consortium/CHM13

Thanks.

[Mehran Karimzadeh]

So in summary umap uses job arrays.

In SGE, job arrays are in this format

qsub -q <queuename> -t <startid>-<endid> -hold_jid <jobid to wait before running> -e <path to error> -o <path to log> -b y <path to executable .sh file>

This will run the script after -b y N times, each time specifying SGE_TASK_ID to a number between <startid>-<endid>

In slurm, the name of this variable is SLURM_ARRAY_TASK_ID

So you can run ubismap.py and specify -var_id SLURM_ARRAY_TASK_ID as one of the parameters

Since it doesn't support SGE, it will still generate a .sh file with qsub commands.

You can replace the qsub commands to sbatch as:

sbatch -p <partition name> --array=<startid>-<endid> --dependency=afterany:<jobid to wait for before running> -e <path to error> -o <path to log> <path to executable .sh file>

One example:

In SGE you can do:

qsub -q hoffmangroup -N $JOBNAME -e Logs/$JOBNAME.ERR -t 1-30 -o Logs/$JOBNAME.LOG -cwd -b y python uint8_to_bed_parallel.py $INDIR $OUTDIR C2T-Converted -chrsize_path $MAINDIR/$GENOME/chrsize.tsv -C2T -WriteUnique -kmers 24 36 50 100

In Slurm:

1. You create .sh file with the command

echo -e '#!/bin/sh' > myScript.sh

echo "python uint8_to_bed_parallel.py $INDIR $OUTDIR C2T-Converted -chrsize_path $MAINDIR/$GENOME/chrsize.tsv -C2T -WriteUnique -kmers 24 36 50 100 -varid SLURM_ARRAY_TASK_ID" >> myScript.sh

sbatch -c 1 -p hoffmangroup --mem=8G -t 12:00:00 --array=1-30 -e Logs/$JOBNAME.ERR -o Logs/$JOBNAME.LOG myScript.sh

Hope this helps!

M

On Thu, Oct 22, 2020 at 10:41 AM gevrony <g.ev...@gmail.com> wrote:

Perfect! Yes we have slurm. Can you send me this?

 

From: Mehran Karimzadeh <mehran.k...@gmail.com>
Date: Thursday, October 22, 2020 at 10:23 AM
To: Gilad Evrony <g.ev...@gmail.com>
Subject: Re: CHM13_v1 mappability

 

Hi Gilad,

 

What type of HPC do you have access to? If it's slurm, I have scripts that make Umap work on slurm smoothly.

 

Thanks,

Mehran

 

--
You received this message because you are subscribed to the Google Groups "Ubismap" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ubismap+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ubismap/bad29b03-43e1-4cd4-a8e6-d73aa10a2db7n%40googlegroups.com.