aggregate bedgraph keeps being killed

[astrovsky01]

I'm running the command

clodius aggregate bedgraph data/bedgraph_chrx_2e6_5e6.bg.bedgraph.sorted --output-file data/bedgraph_chrx_2e6_5e6.bg.bedgraph.out --chromosome-col 1 --from-pos-col 2 --to-pos-col 3 --value-col 4 --assembly hg19 --nan-value NA --chromsizes-filename negspy/negspy/data/hg19/chromSizes.tsv

and it appears to start up properly every time:

output file: data/bedgraph_chrx_2e6_5e6.bg.bedgraph.out
assembly_size: 3095693983
assembly: hg19
assembly size (max-length) 3095693983
max-width 4294967296
max_zoom: 22
chunk-size: 16777216
chrom-order [b'chr1' b'chr2' b'chr3' b'chr4' b'chr5' b'chr6' b'chr7' b'chr8' b'chr9'
 b'chr10' b'chr11' b'chr12' b'chr13' b'chr14' b'chr15' b'chr16' b'chr17'
 b'chr18' b'chr20' b'chr19' b'chr21' b'chr22' b'chrX' b'chrY' b'chrM']

But then it just returns "killed" and exits. How do I fix this/tell what is going wrong?

[pkerpedjiev]

Hey! clodius aggregate bedgraph will be deprecated shortly. Would you mind trying to create a bigWig instead? See here for instructions: http://docs.higlass.io/data_preparation.html#creating-bigwig-files

[astrovsky01]

I had been having trouble getting bedgraphtobigwig running the container I'm using, so I had fallen back to aggregate bedgraph, but I'll give it another try. Thanks!

[astrovsky01]

@pkerpedjiev just to double check, then, are any other clodius aggregate commands being deprecated?

[pkerpedjiev]

No, that one just has a clear alternative and there's no purpose in maintaining another file format for multi-resolution coverage tracks.

[astrovsky01]

Completely understandable, I just wanted to check, since I'm writing a script that uploads multiple files/filetypes. Thank you!