ataqc module fails

[nicolerg]

After implementing the change in #64, call-ataqc fails with the following error:

Traceback (most recent call last):
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/encode_ataqc.py", line 355, in <module>
    ataqc()
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/encode_ataqc.py", line 186, in ataqc
    read_len)
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/run_ataqc.py", line 438, in make_tss_plot
    processes=processes, stranded=True)
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/lib/python2.7/site-packages/metaseq/_genomic_signal.py", line 122, in array
    chunksize=chunksize, **kwargs)
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/lib/python2.7/site-packages/metaseq/array_helpers.py", line 383, in _array_parallel
    itertools.repeat(kwargs)))
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/lib/python2.7/multiprocessing/pool.py", line 253, in map
    return self.map_async(func, iterable, chunksize).get()
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/lib/python2.7/multiprocessing/pool.py", line 572, in get
    raise self._value
ValueError: invalid reference `chr1`

This might be related to non-standard chromosome names. I am using the "atac.keep_irregular_chr_in_bfilt_peak" : false option.

OS/Platform and dependencies

• OS or Platform: Ubuntu 16.04.4 (durga)
• Cromwell/dxWDL version: cromwell 34-unknown-SNAP
• Conda version: conda 4.5.11

debug_65.tar.gz

[nicolerg]

The tar file should be named debug_66.tar.gz

[leepc12]

Can you upload your genome TSV file and two files (tss_enrich and chrsz) in it?

[nicolerg]

The genome is the hard-masked version from the most recent Ensembl rat build: ftp://ftp.ensembl.org/pub/release-94/fasta/rattus_norvegicus/dna/

tss.rn6.bed.gz
rn6_masked.chrom.sizes.txt
rn6_masked.txt

[leepc12]

This will be fixed in the next release v1.1.4. It will be released soon (this week).

[leepc12]

Closing this. Duplicate of #69.