Open hehouts opened 2 years ago
this is with genome-grist version v0.8.4.dev6+g7590338
and the most .err file is here: /home/hehouts/dynamic-duos-virome/grist/sra5smpl/jobs/sra5.j50895726.err
I tried running SRR3051889 and SRR3051890, and they both had this error
hi @hehouts yay cool new errors 😆
It looks to me like the error is in trim-low-abund,
File "/home/hehouts/dynamic-duos-virome/grist/sra5smpl/.snakemake/conda/9f06064bd6e082e98e81386024b7b271/bin/trim-low-abund.py", line 212, in pass1
for n, is_pair, read1, read2 in reader:
File "/home/hehouts/dynamic-duos-virome/grist/sra5smpl/.snakemake/conda/9f06064bd6e082e98e81386024b7b271/lib/python3.8/site-packages/khmer/utils.py", line 81, in broken_paired_reader
for record in screed_iter:
OSError: Generic StreamReadError error
and it may be in reading from the file.
Can you download one of these files yourself (using SRA toolkit) and take a look at the sequences?
Just ran into this error myself on another workflow. Any further documentation on this issue?
I'm trying to run grist on one sample, using starting with SRA accession numbers (not trying to use local genomes). Im getting a "
OSError: Generic StreamReadError error
" duringrule kmer_trim_reads_wc
config looks like
I requested 66G of memory, and max mem used was only ~ 40 gb. not having enough memory was my best guess at the problem. Not sure what to try next.