# computeMatrix takes long to run

**URL:** <https://help.galaxyproject.org/t/computematrix-takes-long-to-run/3070>\
**Category:** Uncategorized\
**Tags:** gtn-tutorial, workflow, galaxy-local, macs2\
**Created:** [February 26, 2020, 10:54pm UTC](https://help.galaxyproject.org/t/computematrix-takes-long-to-run/3070 "2020-02-26T22:54:30Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![MzwaneleN](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mzwanelen/32/1859_2.png) [@MzwaneleN](https://help.galaxyproject.org/u/MzwaneleN)\
**Post date:** [February 26, 2020, 10:54pm UTC](https://help.galaxyproject.org/t/computematrix-takes-long-to-run/3070/1 "2020-02-26T22:54:30Z")

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I am going through the ATAC seq data analysis training and trying to generate a matrix using computeMatrix but it is taking way too long to run - it looks like I am plotting the matrix for the whole human genome.

Can you please have a look at my command liine (please see below) and see if I made a mistake? I did specify, “chr22 genes” as the “Region to plot” but I see “SortBed… ENCFF933NTR.bed.gz” as the “Region to plot” in the tool parameters. Is this where the mistake lies?strong text

Command line:  
ln -f -s ‘/data/dnb02/galaxy\_db/files/013/749/dataset\_13749886.dat’ ‘MACS2 bigwig\_0.bw’ && ln -f -s ‘/data/dnb02/galaxy\_db/files/013/749/dataset\_13749887.dat’ ‘Genrich bigwig\_1.bw’ && ln -f -s ‘/data/dnb02/galaxy\_db/files/013/750/dataset\_13750071.dat’ ‘SortBed on https\_\_\_www\_encodeproject\_org\_files\_ENCFF933NTR\_\_\_download\_ENCFF933NTR\_bed\_gz\_0.bed’ && computeMatrix reference-point --regionsFileName ‘SortBed on https\_\_\_www\_encodeproject\_org\_files\_ENCFF933NTR\_\_\_download\_ENCFF933NTR\_bed\_gz\_0.bed’ --scoreFileName ‘MACS2 bigwig\_0.bw’ ‘Genrich bigwig\_1.bw’ --outFileName ‘/data/dnb02/galaxy\_db/job\_working\_directory/007/118/7118718/galaxy\_dataset\_14989742.dat’ --numberOfProcessors “${GALAXY\_SLOTS:-4}” --referencePoint TSS --beforeRegionStartLength 1000 --afterRegionStartLength 1000 --sortRegions ‘keep’ --sortUsing ‘mean’ --averageTypeBins ‘mean’ --missingDataAsZero --binSize 50 --transcriptID transcript --exonID exon --transcript\_id\_designator transcript\_id