Comments (3)
A workaround (at least for Sunbeam) is to pin to v0.3.4....which already appears to be the case. I guess my local version was behind. Keeping this open for additional testing
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I just now made an empty environment and did conda install -c louiejtaylor -c bioconda grabseqs
and grabseqs and numpy combo I ended up with (versions 0.5.0 and 1.16.2) seem happy, for what that's worth.
from grabseqs.
Thanks for looking at this, Jesse! I thought the issue was related to installing numpy via pip and conda, but it worked fine (conda install -c louiejtaylor -c bioconda grabseqs
installed the same versions you saw and import numpy
threw no errors).
The numpy version installed with Sunbeam is different (1.12.1)--so that might be the source of the problem. I can troubleshoot it later; this is a low-priority problem that will likely only affect me so don't worry about spending more of your valuable time tracking it down!
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Related Issues (20)
- Make --no_SRR_parsing default
- Figure out why iMicrobe breaks on circleCI
- fasterq-dump error: HOT 3
- Add callout to FAQ in main README
- SRA metadata not including BioSample attributes HOT 4
- Refactor code
- Use "conda deactivate" instead of "source deactivate"
- pigz attempting to zip files that don't exist HOT 1
- Check to see whether user has fasterq-dump installed HOT 1
- Dependency check
- Not compatible with Python 3.7? HOT 4
- Allow users to pass custom args to fast(er)q-dump
- grabseqs and geofetch
- error handling when sra accession doesn't exist / doesn't return runs HOT 1
- Add support to download data from EBI HOT 3
- Add support to download data from National Genomics Data Center
- All grabseqs SRA downloads failing HOT 10
- Grabseqs error HOT 9
- 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 HOT 1
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