Comments (1)
Unfortunately, I can't exactly recreate this issue but have been hearing of this curl to the NCBI FTP being variable as of late. If you run the individual lines from the get_data_dependencies.sh
but with added verbose flags:
curl -s --verbose "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz" > ./GRC38_no_alt_analysis_set.fna.gz
gunzip --verbose ./GRC38_no_alt_analysis_set.fna.gz
And come across specific errors, please let me know here so I can try and pinpoint a resolution. You can run the lines above as is, without the actual get_data_dependencies.sh
script.
The inconsistency of the error may be attributed to curl itself or NCBI and its FTP server, but I need more information.
from covid-19-signal.
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