yarden/rnaseqlib

ERROR 1146:can not download all ucsc header for hg38

HandsYe opened this issue · 0 comments

Fetching tables..
Download UCSC tables...

  • Output dir: /share/home/yh/software/graphviz/yarden-rnaseqlib-269114a/test/pipeline_init/hg38/ucsc
    Downloading all UCSC headers for hg38
  • Output dir: /share/home/yh/software/graphviz/yarden-rnaseqlib-269114a/test/pipeline_init/hg38/ucsc/headers
    Downloading header for knownGene (hg38)
    Downloading header for kgXref (hg38)
    Downloading header for knownToEnsembl (hg38)
    Downloading header for knownAlt (hg38)
    Downloading header for knownIsoforms (hg38)
    Downloading header for ensGene (hg38)
    ERROR: Failed to get header.
    Standard output was:
    Standard error was:
    ERROR 1146 (42S02) at line 1: Table 'hg38.ensGene' doesn't exist
    Traceback (most recent call last):
    File "/share/home/yh/bin/rna_pipeline.py", line 190, in
    main()
    File "/share/home/yh/bin/rna_pipeline.py", line 186, in main
    init_params=init_params)
    File "/share/home/yh/bin/rna_pipeline.py", line 101, in initialize_pipeline
    base_obj.initialize()
    File "/share/apps/python2/python2/lib/python2.7/site-packages/rnaseqlib/RNABase.py", line 213, in initialize
    self.download_tables()
    File "/share/apps/python2/python2/lib/python2.7/site-packages/rnaseqlib/RNABase.py", line 135, in download_tables
    self.output_dir)
    File "/share/apps/python2/python2/lib/python2.7/site-packages/rnaseqlib/tables.py", line 1206, in download_ucsc_tables
    download_all_ucsc_headers(genome, ucsc_tables, output_dir)
    File "/share/apps/python2/python2/lib/python2.7/site-packages/rnaseqlib/tables.py", line 1114, in download_all_ucsc_headers
    header_str = "\t".join(header)
    TypeError: can only join an iterable