Clodius aggregate with new assembly

[gibcus]

Hi all,
I'm trying to use clodius aggregate bedgraph to generate TADs.

sudo docker exec gibcus-chicken2.0-higlass clodius aggregate bedgraph \
> /tmp/WT-G2-S4-R5.insulation.boundaries.bed \
> --output-file /tmp/WT-G2-S4-R5.insulation.boundaries.bed2ddb \
> --chromosome-col 1 \
> --from-pos-col 2 \
> --to-pos-col 3 \
> --value-col 6 \
> --assembly galGal6 \
> --nan-value NA \
> --has-header

Clodius does not have the galGal6 assembly, so I get this error:

Error: Invalid value for "--assembly" / "-a": invalid choice: galGal6. (choose from b37, mm9, GCF_000005845.2_ASM584v2_genomic, test, dm3, dm6, grch37, GCA_000001215.4_Release_6_plus_ISO1_MT_genomic, GCA_000001405.15_GRCh38_genomic, grch37-lite, test3chroms, mm10, danRer10, hg19, hg38)

I recently added galGal6 to negspy, but it seems that Clodius has a different source for its assemblies. Is there a way (for me) to add galGal6 to Clodius?

[pkerpedjiev]

Can you try using --chromsizes-filename and then point to the chromsizes file for galGal6 (https://github.com/pkerpedjiev/negspy/blob/master/negspy/data/galGal6/chromInfo.txt)? I suspected that Docker container is woefully out of date.

[gibcus]

At first, I thought it worked, because the script started running.

output file: /tmp/WT-G2-S4-R5.insulation.boundaries.bed2ddb
assembly_size: 1050156607
assembly: hg19
assembly size (max-length) 1050156607
max-width 1073741824
max_zoom: 20
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'chr19' b'chr20' b'chr21' b'chr22' b'chr23' b'chr24' b'chr25'
 b'chr26' b'chr27' b'chr28' b'chr30' b'chr31' b'chr32' b'chr33' b'chrM'
 b'chrW' b'chrZ']

But it gave an error after running for a while:

traceback (most recent call last):
  File "/opt/conda/bin/clodius", line 11, in <module>
    sys.exit(cli())
  File "/opt/conda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/opt/conda/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/opt/conda/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/conda/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/conda/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/conda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/opt/conda/lib/python3.6/site-packages/clodius/cli/aggregate.py", line 1322, in bedgraph
    chromsizes_filename, zoom_step)
  File "/opt/conda/lib/python3.6/site-packages/clodius/cli/aggregate.py", line 888, in _bedgraph
    chrom_info.cum_chrom_lengths[parts[chrom_col-1]] +
IndexError: list index out of range

I guess this must be because galGal6 has more chromosomes than hg19?

[pkerpedjiev]

Hmm, would you be willing to send me the file you're trying to aggregate so that I can try it at home? It looks like it can't find the chromosome column in one of the lines on the bedGraph file? Would you be willing to share the file you're trying to aggregate and I can see what's going wrong?