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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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FileNotFoundError: [Errno 2] No such file or directory: 'refFlat.txt' #507

Closed moldach closed 4 years ago

moldach commented 4 years ago

I'm trying to use this tool for WGS data on C. elegans so I'm using the -m wgs flag. Furthermore, I have no normal samples to use for the reference so I use the -n flag without specifying any additional BAM files but I'm getting an error:


[moldach@cdr767 first_batch]$ cnvkit.py batch N2_trim_bwaMEM_sort_dedupped.bam -n -m wgs -f /scratch/moldach/data/references/c_elegans.PRJNA13758.WS265.genomic.fa --annotate refFlat.txt
CNVkit 0.9.7.b1
I: Scanning for accessible regions
        Accessible region I:0-15072434 (size 15072434)
II: Scanning for accessible regions
        Accessible region II:0-15279421 (size 15279421)
III: Scanning for accessible regions
        Accessible region III:0-13783801 (size 13783801)
IV: Scanning for accessible regions
        Accessible region IV:0-17493829 (size 17493829)
V: Scanning for accessible regions
        Accessible region V:0-20924180 (size 20924180)
X: Scanning for accessible regions
        Accessible region X:0-17718942 (size 17718942)
MtDNA: Scanning for accessible regions
        Accessible region MtDNA:0-13794 (size 13794)
I: Joining over small gaps
II: Joining over small gaps
III: Joining over small gaps
IV: Joining over small gaps
V: Joining over small gaps
X: Joining over small gaps
MtDNA: Joining over small gaps
Wrote c_elegans.PRJNA13758.WS265.genomic.bed with 7 regions
Detected file format: bed
Splitting large targets
Applying annotations as target names
Traceback (most recent call last):
  File "/scratch/moldach/bin/cnvkit/.venv/bin/cnvkit.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/scratch/moldach/bin/cnvkit/cnvkit.py", line 9, in <module>
    args.func(args)
  File "/scratch/moldach/bin/cnvkit/cnvlib/commands.py", line 110, in _cmd_batch
    args.reference, args.targets, args.antitargets = batch.batch_make_reference(
  File "/scratch/moldach/bin/cnvkit/cnvlib/batch.py", line 89, in batch_make_reference
    target_arr = target.do_target(bait_arr, annotate, short_names, True,
  File "/scratch/moldach/bin/cnvkit/cnvlib/target.py", line 20, in do_target
    annotation = tabio.read_auto(annotate)
  File "/scratch/moldach/bin/cnvkit/skgenome/tabio/__init__.py", line 102, in read_auto
    fmt = sniff_region_format(infile)
  File "/scratch/moldach/bin/cnvkit/skgenome/tabio/__init__.py", line 224, in sniff_region_format
    with as_handle(infile, 'rU') as handle:
  File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.8.0/lib/python3.8/contextlib.py", line 113, in __enter__
    return next(self.gen)
  File "/scratch/moldach/bin/cnvkit/.venv/lib/python3.8/site-packages/Bio/File.py", line 120, in as_handle
    with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'refFlat.txt'

I thought this command should create the "flat"reference for me? What's going on here?

etal commented 4 years ago

It should work if you leave off the --annotate refFlat.txt part. The --annotate option is for providing gene labels, and the argument is a tabular file downloaded from the UCSC Genome Browser FTP site (or another annotation source, as long as it's in GFF, UCSC BED, or UCSC RefGene format.)

moldach commented 4 years ago

Hi @etal leaving off --annotate refFlat.txt worked fine.

I'm just looking through the results now and have noticed an issue.

In the files produced I'm not seeing the LOH column. Any idea why?