ERROR 1146:can not download all ucsc header for hg38
HandsYe opened this issue · 0 comments
HandsYe commented
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