wwood
[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%)
When we run coverm:
/home1/jialh/anaconda3/envs/MAG/bin/coverm contig \
-t 8 -r /home1/jialh/brain/CAGs/CAGs/cdhit_rep_seq.fna \
-1 /home1/jialh/brain/JPN/preprocessing/01_processing/05_sync/SRR13083091_1.fq.gz \
-2 /home1/jialh/brain/JPN/preprocessing/01_processing/05_sync/SRR13083091_2.fq.gz \
--bam-file-cache-directory /home1/jialh/brain/CAGs/CAGs/coverm/SRR13083091_coverm_temp \
--output-file /home1/jialh/brain/CAGs/CAGs/coverm/SRR13083091_gene_abundance.txt
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?
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. https://github.com/lh3/minimap2/issues/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.
— Reply to this email directly, view it on GitHub https://github.com/wwood/CoverM/issues/169#issuecomment-1606520397, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHXJVDKLQGXLW3KXIF6EM5LXND3QPANCNFSM6AAAAAAYZY7MFQ . You are receiving this because you authored the thread.Message ID: @.***>