Open linfanxiao opened 3 months ago
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?
Hi developers,
I meet an issue with the output of the de novo motif step. I get the endless run like this
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?