HiGlass crashes during resize of higlass-transcripts track

pkrisz5 commented 1 year ago

I created a new higlass-transcripts track from GeneCode_M31 in the following way:

cd ../data/ref/GeneCode_M31/higlass
curl https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.primary_assembly.annotation.gtf.gz > gencode.vM31.primary_assembly.annotation.gtf.gz
gzip -d gencode.vM31.primary_assembly.annotation.gtf.gz

FILE=gencode.vM31.primary_assembly.annotation.gtf
BEDDB=gencode.vM31.primary_assembly_transcripts.beddb
PATH_SCRIPT=../../../../tools/higlass/higlass-transcripts # this repo was cloned here
CHRSIZE=mm39.chrom.mod.sizes

python $PATH_SCRIPT/scripts/extract_transcript_data.py --input-filename $FILE --chromsizes-filename $CHRSIZE -o $FILE.txt

clodius aggregate bedfile --max-per-tile 20 --importance-column 5 --chromsizes-filename $CHRSIZE --output-file $BEDDB --delimiter $'\t' $FILE.txt

# Finally I ingested the following way:

docker exec higlass-container python higlass-server/manage.py ingest_tileset --filename /tmp/gencode.vM31.primary_assembly_transcripts.beddb --filetype beddb --datatype gene-annotation --uid transcripts_abcd1234

But when I include this transcript track at the top in HiGlass then it is empty. If I try to modify the size of the track then HiGlass crashes and only a white page appears.

Note: This was the "mm39.chrom.mod.sizes" file:

chr1    195154279
chr2    181755017
chr3    159745316
chr4    156860686
chr5    151758149
chr6    149588044
chr7    144995196
chr8    130127694
chr9    124359700
chr10   130530862
chr11   121973369
chr12   120092757
chr13   120883175
chr14   125139656
chr15   104073951
chr16   98008968
chr17   95294699
chr18   90720763
chr19   61420004
chrX    169476592
chrY    91455967
chrM    16299
GL456210.1  169725
GL456211.1  241735
GL456212.1  153618
GL456219.1  175968
GL456221.1  206961
GL456233.2  559103
GL456239.1  40056
GL456354.1  195993
GL456359.1  22974
GL456360.1  31704
GL456366.1  47073
GL456367.1  42057
GL456368.1  20208
GL456370.1  26764
GL456372.1  28664
GL456378.1  31602
GL456379.1  72385
GL456381.1  25871
GL456382.1  23158
GL456383.1  38659
GL456385.1  35240
GL456387.1  24685
GL456389.1  28772
GL456390.1  24668
GL456392.1  23629
GL456394.1  24323
GL456396.1  21240
JH584295.1  1976
JH584296.1  199368
JH584297.1  205776
JH584298.1  184189
JH584299.1  953012
JH584300.1  182347
JH584301.1  259875
JH584302.1  155838
JH584303.1  158099
JH584304.1  114452
MU069434.1  8412
MU069435.1  31129

alexander-veit commented 1 year ago

Does your $File.txt look good (i.e., not empty)?
Could you try theaggregate_transcripts.py script in the scripts folder instead of clodius aggregate?
Which errors are you seeing in the browser console?

alexander-veit commented 1 year ago

This is the format the lines in $File.txt should have: https://raw.githubusercontent.com/higlass/higlass-transcripts/master/examples/transcripts_test.txt

higlass / higlass-transcripts

HiGlass crashes during resize of higlass-transcripts track #39