admin管理员组文章数量:1356237
samples = ["DM8909"]
rule all:
input:
"/home/huangqiang/whole_genome_pipline/temp/seqkit/second_sequence_statistics.txt"
rule fastp_map:
input:
r1 = "seq/{sample}_1.fastq.gz",
r2 = "seq/{sample}_2.fastq.gz"
output:
r1_clean = "temp/fastp_output/{sample}_R1_clean.fastq.gz",
r2_clean = "temp/fastp_output/{sample}_R2_clean.fastq.gz",
html_report = "temp/fastp_output/{sample}_fastp.html",
json_stats = "temp/fastp_output/{sample}_fastp.json"
shell:
"fastp \
-i {input.r1} \
-I {input.r2} \
-o {output.r1_clean} \
-O {output.r2_clean} \
-h {output.html_report} \
-j {output.json_stats} \
-q 15 -u 40 -l 50 --dedup"
rule mkdir_seqkit:
output:
"temp/seqkit"
shell:
"mkdir -p {output}"
rule second_sequence_statistics:
input:
expand("/home/huangqiang/whole_genome_pipline/temp/fastp_output/{sample}_{pair}_clean.fastq.gz", sample=samples, pair=["R2","R1"])
output:
"/home/huangqiang/whole_genome_pipline/temp/seqkit/second_sequence_statistics.txt"
shell:
"seqkit \
stats -aT -i {input} > {output}"
the result showed R1 has a result but R2 missed
file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%) sum_n
/home/huangqiang/whole_genome_pipline/temp/fastp_output/DM8909_R1_clean.fastq.gz FASTQ DNA 4121308 618107404 50 150.0 150 150.0 150.0 150.0 0 150 1 98.24 94.91 27.70 49.67 9786
samples = ["DM8909"]
rule all:
input:
"/home/huangqiang/whole_genome_pipline/temp/seqkit/second_sequence_statistics.txt"
rule fastp_map:
input:
r1 = "seq/{sample}_1.fastq.gz",
r2 = "seq/{sample}_2.fastq.gz"
output:
r1_clean = "temp/fastp_output/{sample}_R1_clean.fastq.gz",
r2_clean = "temp/fastp_output/{sample}_R2_clean.fastq.gz",
html_report = "temp/fastp_output/{sample}_fastp.html",
json_stats = "temp/fastp_output/{sample}_fastp.json"
shell:
"fastp \
-i {input.r1} \
-I {input.r2} \
-o {output.r1_clean} \
-O {output.r2_clean} \
-h {output.html_report} \
-j {output.json_stats} \
-q 15 -u 40 -l 50 --dedup"
rule mkdir_seqkit:
output:
"temp/seqkit"
shell:
"mkdir -p {output}"
rule second_sequence_statistics:
input:
expand("/home/huangqiang/whole_genome_pipline/temp/fastp_output/{sample}_{pair}_clean.fastq.gz", sample=samples, pair=["R2","R1"])
output:
"/home/huangqiang/whole_genome_pipline/temp/seqkit/second_sequence_statistics.txt"
shell:
"seqkit \
stats -aT -i {input} > {output}"
the result showed R1 has a result but R2 missed
file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%) sum_n
/home/huangqiang/whole_genome_pipline/temp/fastp_output/DM8909_R1_clean.fastq.gz FASTQ DNA 4121308 618107404 50 150.0 150 150.0 150.0 150.0 0 150 1 98.24 94.91 27.70 49.67 9786
1 Answer
Reset to default 0I am not sure this solves your problem, but three things come to mind while looking at your code. A) You should stay consistent with absolute and relative paths (I would say, only use absolute paths if really necessary). B) You do not need to create folders, snakemake does this for you. C) Use triple quotes for multi line code blocks
This will results in:
samples = ["DM8909"]
rule all:
input:
"temp/seqkit/second_sequence_statistics.txt"
rule fastp_map:
input:
r1 = "seq/{sample}_1.fastq.gz",
r2 = "seq/{sample}_2.fastq.gz"
output:
r1_clean = "temp/fastp_output/{sample}_R1_clean.fastq.gz",
r2_clean = "temp/fastp_output/{sample}_R2_clean.fastq.gz",
html_report = "temp/fastp_output/{sample}_fastp.html",
json_stats = "temp/fastp_output/{sample}_fastp.json"
shell:
"""
fastp \
-i {input.r1} \
-I {input.r2} \
-o {output.r1_clean} \
-O {output.r2_clean} \
-h {output.html_report} \
-j {output.json_stats} \
-q 15 -u 40 -l 50 --dedup
"""
rule second_sequence_statistics:
input:
expand("temp/fastp_output/{sample}_{pair}_clean.fastq.gz", sample=samples, pair=["R2","R1"])
output:
"temp/seqkit/second_sequence_statistics.txt"
shell:
"""
seqkit \
stats -aT -i {input} > {output}
"""
I don't know the syntax for seqkit and fastp, but this will run the following commands:
fastp -i seq/DM8909_1.fastq.gz -I seq/DM8909_2.fastq.gz -o temp/fastp_output/DM8909_R1_clean.fastq.gz -O temp/fastp_output/DM8909_R2_clean.fastq.gz -h temp/fastp_output/DM8909_fastp.html -j temp/fastp_output/DM8909_fastp.json -q 15 -u 40 -l 50 --dedup
seqkit stats -aT -i temp/fastp_output/DM8909_R2_clean.fastq.gz temp/fastp_output/DM8909_R1_clean.fastq.gz > temp/seqkit/second_sequence_statistics.txt
本文标签：
版权声明：本文标题：snakemake - I use seqkit to statistic my sequences' information, but only DM8909_R1_clean.fastq.gz has a result and DM89 内容由网友自发贡献，该文观点仅代表作者本人， 转载请联系作者并注明出处：http://www.betaflare.com/web/1743999348a2573571.html， 本站仅提供信息存储空间服务，不拥有所有权，不承担相关法律责任。如发现本站有涉嫌抄袭侵权/违法违规的内容，一经查实，本站将立刻删除。
发表评论