SRRs = ["SRR11111111","SRR22222222","SRR33333333","SRR44444444","SRR55555555","SRR66666666","SRR77777777" ]rule all: input: expand("../atac_seq/{srr}/{srr}_1.fastq.gz", srr=SRRs), expand("../atac_seq/{srr}/{srr}_2.fastq.gz", srr=SRRs), expand("../atac_seq/{srr}/{srr}_3.fastq.gz", srr=SRRs), expand("../atac_seq/{srr}/{srr}_4.fastq.gz", srr=SRRs)rule fastq_dump: output: "../atac_seq/{n}/{n}_1.fastq.gz","../atac_seq/{n}/{n}_2.fastq.gz","../atac_seq/{n}/{n}_3.fastq.gz","../atac_seq/{n}/{n}_4.fastq.gz" shell:""" fastq-dump --split-files --gzip {wildcards.n}.sra """
Hi all, right now in the directory /atac_seq/{srr}/ there is only a .sra file. I want to expand the .sra file using fastqdump and snakemake, but I get the error: "fastq-dump.3.1.1 err: item not found while constructing within virtual database module - the path 'SRRXXXXX.sra' cannot be opened as database or table".
I've tried using fastq-dump in bash in the individual folders, and it works, but I'm not sure why my script doesn't work.