hicPlotTADs gives ValueError: negative dimensions are not allowed on release 2.2

[gundalav]

I have the the hic file downloadable here (1.2Gb).

What I did is to convert this file into .cool format and then .h5 format. The over all code is this:

#!/bin/bash
export LC_ALL=C

HIC_FILE=test.hic
OUTDIR_HIC=$(dirname "${HIC_FILE}")
TMPBASE=${HIC_FILE##*/}
HIC_BASENAME=${TMPBASE%.*}
OUTFILE_HIC_H5=${OUTDIR_HIC}/${HIC_BASENAME}.hicexplorer.h5
OUTFILE_HIC_COOL=${OUTDIR_HIC}/${HIC_BASENAME}.hicexplorer.cool
OUTFILE_HIC_COOL_BIN=${OUTDIR_HIC}/${HIC_BASENAME}.hicexplorer_250000.cool
OUTFILE_H5_TADS_PREFIX=${OUTDIR_HIC}/${HIC_BASENAME}.hicexplorer.tads
echo $OUTFILE_HIC_H5
echo $OUTFILE_HIC_COOL
echo $OUTFILE_HIC_COOL_BIN
echo $OUTFILE_H5_TADS_PREFIX

### File type conversion
hicConvertFormat -m $HIC_FILE --outFileName $OUTFILE_HIC_COOL --inputFormat hic --outputFormat cool --resolution 250000
hicConvertFormat -m $OUTFILE_HIC_COOL_BIN --outFileName $OUTFILE_HIC_H5 --inputFormat cool --outputFormat h5

### Find TAD
hicFindTADs --correctForMultipleTesting fdr -m $OUTFILE_HIC_H5 --outPrefix $OUTFILE_H5_TADS_PREFIX --numberOfProcessors 16

### Plot tad
hicPlotTADs --tracks tracks.ini --region chr2:151001514-163998482 -t 'CTCF.HIC' -o tads.pdf

All the steps works fine except when hicPlotTADs being executed. It gives me this error

ValueError: negative dimensions are not allowed

How can I resolve this?

My tracks.ini looks like this:

[hic matrix]
file = test.hicexplorer.h5
title = Hi-C data
# depth is the maximum distance plotted in bp. In Hi-C tracks
# the height of the track is calculated based on the depth such
# that the matrix does not look deformed
depth = 300000
transform = log1p
file_type = hic_matrix

[tads]
file = test.hicexplorer.tads_domains.bed
file_type = domains
border color = black
color = none
# the tads are overlay over the hic-matrix
# the share-y options sets the y-axis to be shared
# between the Hi-C matrix and the TADs.
overlay previous = share-y

I'm using latest version of HiCExplorer v.2.2 and numpy version 1.16.0

Thanks and hope to hear from you again.

G.V.

[gtrichard]

Do you have more specific error messages coming before this one?

ValueError: negative dimensions are not allowed

[joachimwolff]

Any update here?

[joachimwolff]

No more feedback provided, closing this issue. In case you want to reopen: Please test the newest release we have published in the meantime.