OSError: ["Can't find mysql at path mysql", "Can't find path to fetchChromsizes"]

[konradtaube]

Hello,

I am trying to run DAStk and am finding an issue with process_atac. When I try the following command:

process_atac -e 01intersected.bedgraph -m /scratch/avasemag1/taubekon/ATACseq/FASTQ_ATAC_43955/sortedbams/peaks/motifs/01motifs/knownResults -g GCF_010015445.1 -o /scratch/avasemag1/taubekon/ATACseq/FASTQ_ATAC_43955/sortedbams/DAStk

And then I get the following errors:

Traceback (most recent call last):
  File "/usr/local/lib/python3.10/site-packages/pybedtools/helpers.py", line 896, in chromsizes
    return getattr(genome_registry, genome)
AttributeError: module 'pybedtools.genome_registry' has no attribute 'GCF_010015445.1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/scratch/avasemag1/taubekon/ATACseq/dastk-1.0.1/bin/process_atac", line 10, in <module>
    sys.exit(process_atac())
  File "/usr/local/lib/python3.10/site-packages/DAStk/__init__.py", line 9, in process_atac
    p.main()
  File "/usr/local/lib/python3.10/site-packages/DAStk/process_atac.py", line 211, in main
    chr_size_file = pybedtools.chromsizes(args.genome)
  File "/usr/local/lib/python3.10/site-packages/pybedtools/helpers.py", line 900, in chromsizes
    return get_chromsizes_from_ucsc(genome)
  File "/usr/local/lib/python3.10/site-packages/pybedtools/helpers.py", line 797, in get_chromsizes_from_ucsc
    raise OSError(failures)
OSError: ["Can't find mysql at path mysql", "Can't find path to fetchChromsizes"]

So my guess is that this has something to do with an issue with my genome file. I got my genome file -g GCF_010015445.1 from the UCSC site:

But perhaps there is a step I am missing before I can use this? My bedgraph file looks something like this:

head 01intersected.bedgraph track type=bedGraph CM020909.1 74576 74578 1 CM020909.1 74578 74580 2 CM020909.1 74580 74585 8 CM020909.1 74585 74587 10 CM020909.1 74587 74588 13 CM020909.1 74588 74590 14 CM020909.1 74590 74592 15 CM020909.1 74592 74594 17 CM020909.1 74594 74595 19

Thank you in advance!

[ignaciot]

Hey there,

Sorry it took a bit to get back. It looks like the helper code to retrieve the chromosome sizes is expecting the mysql command-line client to be installed. If you haven't already, could you test this and let us know if the issue persists?

You can find instructions to install the mysql client for your platform here. Also make sure the command-line client executable is in your system path. Next time feel free to nudge if you haven't heard back earlier!