louiejtaylor / grabseqs

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

louiejtaylor/grabseqs Issues

All grabseqs SRA downloads failing
Updated 5 months ago10
Grabseqs error
Updated 8 months ago9
grabseqs sra -l PRJDB5400 pigz not found, using gzip Traceback (most recent call last): File "/home/tools/anaconda3/bin/grabseqs", line 8, in <module> sys.exit(main()) File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/__init__.py", line 58, in main metadata_agg = process_sra(args, zip_func) File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/sra.py", line 27, in process_sra acclist, metadata_agg = get_sra_acc_metadata(sra_identifier, File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/sra.py", line 97, in get_sra_acc_metadata run_col = lines[0].index("Run") ValueError: 'Run' is not in list
Updated a year ago1
Add support to download data from EBI
Updated 4 years ago3
Add support to download data from National Genomics Data Center
Updated 4 years ago
error handling when sra accession doesn't exist / doesn't return runs
Closed 5 years ago1
Allow users to pass custom args to fast(er)q-dump
Closed 5 years ago
grabseqs and geofetch
Updated 5 years ago
Refactor code
Closed 5 years ago
More intelligently handle HTTP errors in downloading MG-RAST files
Updated 5 years ago1
pigz attempting to zip files that don't exist
Closed 5 years ago1
Warn the user if the SRA metadata "paired/unpaired" information does not match which reads come down
Closed 5 years ago1
Dependency check
Closed 5 years ago
Not compatible with Python 3.7?
Closed 5 years ago4
Check to see whether user has fasterq-dump installed
Closed 5 years ago1
Use "conda deactivate" instead of "source deactivate"
Closed 5 years ago
Version 0.5.0 breaks numpy
Closed 5 years ago3
Add tests for iMicrobe
Closed 6 years ago
SRA metadata not including BioSample attributes
Updated 5 years ago4
For SRA downloading, make sure pigz zips only the correct sequence files
Closed 5 years ago1
Add callout to FAQ in main README
Closed 5 years ago
Add documentation/FAQs for all subparsers
Closed 5 years ago
Figure out why iMicrobe breaks on circleCI
Closed 5 years ago
Nicely format SRA, MG-RAST, and iMicrobe metadata
Closed 5 years ago3
fasterq-dump error:
Closed 5 years ago3
Make --no_SRR_parsing default
Closed 5 years ago
Look into downloading from iMicrobe
Closed 6 years ago
Filter output from `-l` to conform with expected result from `--no_parsing` flag
Closed 6 years ago
Add tests for not clobbering already-downloaded samples
Closed 6 years ago1
Allow the user to use `fastq-dump` instead of `fasterq-dump` if they want
Closed 6 years ago
Abstract metadata-parsing and downloading functions to separate modules
Closed 6 years ago
Migrate tests to be platform-independent
Closed 6 years ago
Running with previously downloaded file prints hundreds of thousands of "helpful" messages
Closed 6 years ago
Add integration tests for a few (very small) .fastq files
Closed 6 years ago
Add a -l option for MG-RAST
Closed 6 years ago
Retries parameter should be improved
Closed 6 years ago
allow restarting if download fails
Closed 6 years ago
download a list of SRR
Closed 6 years ago4
gzip fasterq-dump output
Closed 6 years ago