ComputeMatrix is not complete even in 3 days of running

[Aditi Singh]

Dear Deeptools developers,

 

I am finding it difficult to get the output from computeMatrix.

I am running it on HPC at my University and the job is not complete even after 3 days.

Can you please help me about this issue.

Below is my command:

 

python3 computeMatrix scale-regions -R /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR1765727_sort.bed /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR1765728_sort.bed /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR1765729_sort.bed -S /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR*_sort.bw -b 3000 -a 3000 --regionBodyLength 5000 --skipZeros -o /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/1_multipleBW_scaled.gz --outFileNameMatrix /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/1_multipleBW_scaled.tab --outFileSortedRegions /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/1_regions_multipleBW_genes.bed

 

Looking forward to your response!

 

Thanks and regards,

Aditi

[Devon Ryan]

Hi Aditi,

Firstly please use multiple cores, such as by added `-p 20` to your command to use 20 cores. Secondly, perhaps it died or was killed by the cluster for some reason. Please check any relevant cluster logs to find out why. Most likely it needed more RAM than whatever the default on your cluster is.

Devon

--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51

79108 Freiburg

Germany

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[adit...@gmail.com]

Thanks Devon,

I am using 20gb memory and 8 cores. Will increase as suggested.

Thanks for the response!

Best,

Aditi

On Wednesday, 15 January 2020 12:55:51 UTC, Devon Ryan wrote:

Hi Aditi,

Firstly please use multiple cores, such as by added `-p 20` to your command to use 20 cores. Secondly, perhaps it died or was killed by the cluster for some reason. Please check any relevant cluster logs to find out why. Most likely it needed more RAM than whatever the default on your cluster is.

Devon

--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51

79108 Freiburg

Germany

On Wed, Jan 15, 2020 at 1:53 PM Aditi Singh <A.S...@qub.ac.uk> wrote:

Dear Deeptools developers,

 

I am finding it difficult to get the output from computeMatrix.

I am running it on HPC at my University and the job is not complete even after 3 days.

Can you please help me about this issue.

Below is my command:

 

python3 computeMatrix scale-regions -R /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR1765727_sort.bed /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR1765728_sort.bed /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR1765729_sort.bed -S /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/SRR*_sort.bw -b 3000 -a 3000 --regionBodyLength 5000 --skipZeros -o /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/1_multipleBW_scaled.gz --outFileNameMatrix /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/1_multipleBW_scaled.tab --outFileSortedRegions /mnt/scratch/users/3055195/Genevia/NeuroD1-UCSC/1_regions_multipleBW_genes.bed

 

Looking forward to your response!

 

Thanks and regards,

Aditi

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