Hello everyone,
I started a scRNA-seq project recently.
I wrote a snakemake script for the mapping part with STARsolo.
SAMPLES, = glob_wildcards("Data/Raw/{sample}_L001_R1.fastq.gz")
rule StarSolo:
input:
R1L1 = "Data/Raw/{sample}_L001_R1.fastq.gz",
R1L2 = "Data/Raw/{sample}_L002_R1.fastq.gz",
R2L1 = "Data/Raw/{sample}_L001_R2.fastq.gz",
R2L2 = "Data/Raw/{sample}_L002_R2.fastq.gz"
threads:
8
shell:
'STAR --runThreadN {threads} '
'--genomeDir /Genome/Human/GRCh38/ '
'--readFilesIn {input.R1L1},{input.R1L2} {input.R2L1},{input.R2L2} '
'--readFilesCommand gunzip -c '
'--soloType CB_UMI_Simple '
'--soloCBwhitelist 3M-february-2018.txt '
'--soloCBlen 16 '
'--soloUMIstart 17 '
'--soloUMIlen 12 '
I obtained this error message:
Building DAG of jobs...
WildcardError in line 11 of /script/Snakefile4:
Wildcards in input files cannot be determined from output files:
'sample'
Where is the problem ? Line 11 is rule StarSolo.
Thank you for your help.
•
written
by
wanaga3166 •
snakefiles should be composed as such: 1) write implicit rules that connect input and output using wildcards 2) write target rules that list files you want produced as input
Thank you, that the problems, I don't know the output for Starsolo. I think I will have 6 files:
But I don't know the names. So it's difficult to write the output.
one of them is {sample}.Aligned.out.sam. Start by creating a target variable that point to the sam files you want produced
SAMPLES = ['foo','bar'] #or from your glob
SAMS = ["{0}.Aligned.out.sam".format(sample) for sample in SAMPLES]
rule all:
input: SAMS
Thank Jeremy and Ram for your help. I made some modification in my snakefile.
SAMPLES, = glob_wildcards("Data/Raw/{sample}_L001_R1.fastq.gz")
#SAMPLES = ["Sample_S1_L001_R1_001.fastq.gz", "Sample_S1_L001_R2_001.fastq.gz"]
SAMS = ["{0}.Aligned.out.sam".format(sample) for sample in SAMPLES]
rule all:
input:
SAMS
rule StarSolo:
input:
R1L1 = "Data/Raw/{sample}_L001_R1.fastq.gz",
R1L2 = "Data/Raw/{sample}_L002_R1.fastq.gz",
R2L1 = "Data/Raw/{sample}_L001_R2.fastq.gz",
R2L2 = "Data/Raw/{sample}_L002_R2.fastq.gz"
output:
"{0}.Aligned.out.sam"
threads:
8
shell:
'STAR --runThreadN {threads} '
'--genomeDir /Genome/Human/GRCh38/ '
'--readFilesIn {input.R2L1},{input.R2L2} {input.R1L1},{input.R1L2} '
'--readFilesCommand gunzip -c '
'--soloType CB_UMI_Simple '
'--soloCBwhitelist 3M-february-2018.txt '
'--soloCBlen 16 '
'--soloUMIstart 17 '
'--soloUMIlen 12 '
It's work better, but STARsolo didn't start its analyze.
Below the snakemake return:
(snakemake) -bash-4.2$ snakemake --cluster "qsub -N STAR_scRNA -l hostname=Node1 -b y" -s Snakefile4 -j 8 -n
Building DAG of jobs...
Job counts:
count jobs
1 all
1
[Sat May 15 22:52:56 2021]
localrule all:
jobid: 0
Job counts:
count jobs
1 all
1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
Where I did a mistake ?
{0} is not a Snakemake wildcard, it's only for string placeholders in Python, so use
output:
"{sample}.Aligned.out.sam"
Thank you for your help. I solved the problem :-)
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How are you running snakemake? Show us that command as well, please. Also, what is the purpose of the
,inSAMPLES ,= glob...? And is that line supposed to be outside of a rule?I used this command line.
Yes, this line is outside the rule.
Follow Jeremy's advice. Your Snakefile is badly formed and the line outside the rule breaks everything.
i think
SAMPLES ,= glob_wildcardsis valid but i do prefer to know what I am trying to make rather than let a directory run the show https://snakemake.readthedocs.io/en/stable/project_info/faq.html#id13I stand corrected. I just noticed that OP is trying to run Snakemake without specifying a target.
Small comment: for
shell:, you just need: