Many meme files in the de novo motif step
linfanxiao opened this issue · comments
linfanxiao commented
Hi developers,
I meet an issue with the output of the de novo motif step. I get the endless run like this
[1] "Sampling 2000 (th: 13.9) peaks over 1014329 possible ones."
Writing results to output directory 'motif_detection/meme_EX51VSST51/meme_76'.
Initializing the motif probability tables for 2 to 1997 sites...
nsites = 1980
Done initializing.
SEEDS: highwater mark: seq 1996 pos 22
BALANCE: samples 1997 residues 43934 nodes 60 residues/node 732
seqs= 1997, min= 22, max= 22, total= 43934
motif=1
SEED WIDTHS: 4 6 8 11 14
em: w= 4, psites= 2, iter= 40
motif=2
SEED WIDTHS: 4 6 8 11 14
em: w= 4, psites= 2, iter= 40
motif=3
SEED WIDTHS: 4 6 8 11 14
em: w= 4, psites= 2, iter= 40
motif=4
SEED WIDTHS: 4 6 8 11 14
em: w= 4, psites= 2, iter= 40
motif=5
SEED WIDTHS: 4 6 8 11 14
em: w= 4, psites= 2, iter= 40
[2024-06-11 19:32:09] Potentials motifs:.
[2024-06-11 19:32:09] Discovered motifs: CCWGG.
Do you want to continue the research for motifs? (Y/N)
Y
[2024-06-11 19:32:15] Removing explained peaks.
[1] "Sampling 2000 (th: 13.9) peaks over 1014329 possible ones."
Writing results to output directory 'motif_detection/meme_EX51VSST51/meme_77'.
Initializing the motif probability tables for 2 to 1997 sites...
nsites = 1980
all motif is CCWGG
when i use parameters "-a" only output a file named "MEME_1"
This is my command:
singularity run --no-home -w nd_example --writable
nanodisco motif -p 60 -b EX51VSST51 -d EX51VSST51_merged/EX51VSST51_difference.RDS -o EX51VSST51_motif -r ncbi_dataset/data/GCF_000401755.1/GCF_000401755.1_Escherichia_coli_ATCC_25922_genomic.fasta
Do I only need the first meme file?