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rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Readme Demo Data Download Fails #182

Open LeeBergstrand opened 1 month ago

LeeBergstrand commented 1 month ago

Problem Description

@jmtsuji This code fails.

# For the long read data, to get the quality scores (i.e., not SRA Lite format), you will need to use the SRA Toolkit
#   available here: https://github.com/ncbi/sra-tools/wiki (accessed 2023.12.20). You can then download the files using:
prefetch SRR21124986 && fasterq-dump -Z SRR21124986 | gzip > sample_fastq_dir/ecoli.fastq.gz
# Otherwise, if you are OK with quality scores stripped out (not what the test was run with), you can just use the following 
#  command to directly output the FastQ file (this command is commented out for clarity):
# wget -O sample_fastq_dir/ecoli.fastq.gz https://www.be-md.ncbi.nlm.nih.gov/Traces/sra-reads-be/fastq?acc=SRR21124986

Error message:

2024-05-31T21:21:05 fasterq-dump.3.1.1 err: directing output to stdout requested.
2024-05-31T21:21:05 fasterq-dump.3.1.1 err: but requested mode ( FASTQ split 3 ) would produce multiple files

It looks like it is failing to write to standard out.

jmtsuji commented 2 weeks ago

Will take a look -- thanks for flagging this.