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[2023-06-04T07:45:16Z INFO coverm::contig] In sample 'cdhit_rep_seq.fna/SRR13083091_1.fq.gz', found 0 reads mapped out of 0 total (NaN%) #169
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Hi, From the timestamps it seems minimap2 finishes instantly, which isn't a good sign. Is something wrong with the input files or minimap2 executable? |
Hello, I was wondering if you have managed to solve this problem. I'm having a similar issue and would greatly appreciate any help you can give me. |
You can just map reads to the contigs by minimap2
before calculating abundance by coverm.
##reference: https://github.com/deng-lab/viroprofiler/blob/main/modules/local/abundance.nf
##[WARNING] For a multi-part index, no @sq lines will be outputted.
Please use --split-prefix. lh3/minimap2#301
##node: One CPUs contains two cores. If threads=4, %CPU will be around 200%.
rule mapping_reads_to_contigs:
input:
r1 = lambda wildcards: sample_reads[wildcards.samp][0],
r2 = lambda wildcards: sample_reads[wildcards.samp][1],
representative_genes = join(outdir,"cdhit_rep_seq.fna")
output:
bam = join(outdir, "bam", "{samp}.bam")
params:
tempdir = join(outdir, "bam", "{samp}_temp_bam")
threads: 4
shell:"""
/home1/jialh/tools/anaconda3/envs/coverm/bin/minimap2 -t {threads} \
-ax sr --split-prefix {params.tempdir}
{input.representative_genes} {input.r1} {input.r2} | \
/home1/jialh/tools/anaconda3/bin/samtools sort --threads
{threads} -o {output.bam}
"""
rule CoverM:
input:
bam = join(outdir, "bam", "{samp}.bam")
output:
gene_abundance = join(outdir, "coverm", "{samp}_gene_abundance.txt")
params:
temp_dir = join(outdir, "coverm", "{samp}_coverm_temp")
threads: 4
conda: "/home1/jialh/brain/pipeline/2020NBTbhattlab/CAGs/scripts/coverm.yaml"
shell: """
/home1/jialh/tools/anaconda3/envs/coverm/bin/coverm contig \
--bam-files {input.bam} -t {threads} --min-read-percent-identity 0.95 \
--output-file {output.gene_abundance}
"""
Wanning888 ***@***.***> 于2023年6月26日周一 11:01写道:
… Hello,
I was wondering if you have managed to solve this problem. I'm having a
similar issue and would greatly appreciate any help you can give me.
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When we run coverm:
We got the next error. The reference file cdhit_rep_seq.fna is from hundreds of samples, which include the sample SRR13083091. Why do we got this error? How to deal with this issue?
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