problem with hicAggragateContacts

[eferreA9]

Version 3.7.2

Good morning, I'm using hicAggregateContacts for creating new plots, I've used this command in previously ocasions and I didn't have any trouble, now I'm using a matrix of 10kb, and different bed files, and it always appears the same message multiple times, is this one:

INFO:hicexplorer.hicAggregateContacts:The given interval exceeds the chromosome range on chr1. It is skipped.
INFO:hicexplorer.hicAggregateContacts:The given interval exceeds the chromosome range on chr1. It is skipped.
INFO:hicexplorer.hicAggregateContacts:The given interval exceeds the chromosome range on chr1. It is skipped.
INFO:hicexplorer.hicAggregateContacts:The given interval exceeds the chromosome range on chr1. It is skipped.

And the job stops due the time limit that in this case was 24 hours.

This is my command:

hicAggregateContacts -m hicMatrix_trunc/HiC_UT_100kb.Corrected_KR.h5
--outFileName AggregateContacts/AP_HiC_UT_Het_test.pdf
--BED bed_files/Het_fibro.bed
--numberOfBins 51
--range 300000:1000000
--vMin 0.6 --vMax 1.8
--largeRegionsOperation center
--transform obs/exp
--chromosomes chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX --operationType mean --transform obs/exp --mode all

Thanks,

Estel

[davidecarnevali]

Hi,
same problem here with version 3.7.2

My command is:
hicAggregateContacts --matrix sample1_40K_norm.KR.h5 --BED merged_T0_specific.bed --outFileName sample1_40k_merged_T60_specific.png --numberOfBins 80 --operationType mean --vMin 0.0 --vMax 1.6 --range 500000:10000000 --transform obs/exp --mode intra-chr

The h5 matrix comes from converting the hicPro raw matrix to h5 then hicNormalize and then hicCorrectMatrix

The job is finally killed for unknown reason after roughly 30/40 mins ....

Any hint?

Thank you