We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
I'm running bfc on my full set now (1.4 billion reads) and the log is giving me a sequence count that is oscillating. Is this the expected behavior?
[M::bfc_count_cb @4667.7_1946.9%] processed 809616 sequences; # distinct k-mers: 2635769628 [M::bfc_count_cb] read 809443 sequences [M::bfc_count_cb @4670.6_1947.4%] processed 809443 sequences; # distinct k-mers: 2636069642 [M::bfc_count_cb] read 809500 sequences [M::bfc_count_cb @4673.9_1947.7%] processed 809500 sequences; # distinct k-mers: 2636370228 [M::bfc_count_cb] read 809470 sequences [M::bfc_count_cb @4676.6_1948.2%] processed 809470 sequences; # distinct k-mers: 2636673453 [M::bfc_count_cb] read 809400 sequences [M::bfc_count_cb @4679.5*1948.6%] processed 809400 sequences; # distinct k-mers: 2636970314
The text was updated successfully, but these errors were encountered:
This just means that your read file has this oscillation. Nothing wrong with BFC.
Sorry, something went wrong.
Sorry if I'm misunderstanding, does the processed N sequences not refer to the number of reads processed?
Ah, that's reads per chunk, not a running total like the k-mer count.
No branches or pull requests
I'm running bfc on my full set now (1.4 billion reads) and the log is giving me a sequence count that is oscillating. Is this the expected behavior?
bfc -s 2.9g -k 55 -t 31 all_reads.fastq.gz |gzip >all_reads.cor.fastq.gz
[M::bfc_count_cb @4667.7_1946.9%] processed 809616 sequences; # distinct k-mers: 2635769628
[M::bfc_count_cb] read 809443 sequences
[M::bfc_count_cb @4670.6_1947.4%] processed 809443 sequences; # distinct k-mers: 2636069642
[M::bfc_count_cb] read 809500 sequences
[M::bfc_count_cb @4673.9_1947.7%] processed 809500 sequences; # distinct k-mers: 2636370228
[M::bfc_count_cb] read 809470 sequences
[M::bfc_count_cb @4676.6_1948.2%] processed 809470 sequences; # distinct k-mers: 2636673453
[M::bfc_count_cb] read 809400 sequences
[M::bfc_count_cb @4679.5*1948.6%] processed 809400 sequences; # distinct k-mers: 2636970314
The text was updated successfully, but these errors were encountered: