Open Npaffen opened 1 year ago
Please check that your version of biopython is the most recent. That error usually pops up because of an older version of biopython.
Get BlueMail for Androidhttps://bluemail.me On Jul 12, 2023, at 6:51 PM, Npaffen @.**@.>> wrote:
Describe the bug A clear and concise description of what the bug is.
When I try to run gen_reads.py with a custom vcf for the variants to add to output some golden bam with a reduced coverage the pipeline breaks after reading the vcf.
My pipeline looks like this.
reading input VCF...
found 4128997 valid variants in input vcf.
reading chr1... 175.558 (sec) found 323780 valid variants for chr1 in input VCF... 161 variants skipped...
sampling reads...
[Traceback (most recent call last):
File "neat-genreads-master/gen_reads.py", line 901, in
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I have the most recent biopython version installed. See :
pip install biopython update
Requirement already satisfied: biopython in /home/nils/.local/lib/python3.10/site-packages (1.81)
Requirement already satisfied: update in /home/nils/.local/lib/python3.10/site-packages (0.0.1)
Requirement already satisfied: numpy in /home/nils/.local/lib/python3.10/site-packages (from biopython) (1.23.5)
Requirement already satisfied: style==1.1.0 in /home/nils/.local/lib/python3.10/site-packages (from update) (1.1.0)
(base) nils@Gigapepe2:$ python3 --version
Python 3.10.11
Actually, so what I would recommend is instead of this repo, which is no longer maintained, you check out our newest work on github.com/ncsa/NEAT. If you want to maintain the same functionality as this version, then checkout the latest release of version 3. Otherwise, you can also try version 4, which is different. I believe we've resolved this bug in that more up-to-date repo.
Unless biopython overhauled their mutable sequence code again, in which case I'll have to do some more investigation. Try using the latest and post a bug on that page if it still isn't working. Thanks!
Describe the bug A clear and concise description of what the bug is.
When I try to run
gen_reads.py
with a custom vcf for the variants to add to output some golden bam with a reduced coverage the pipeline breaks after reading the vcf.My pipeline looks like this.