GATK error: no positional argument is defined for this tool.

Question

[kamanovae]

Hi!

I am trying to run a pipeline GATK using the Snakemake. When I form the pipeline gradually, add one rule to the snakemake and the input/otput data are formed in stages, then such a problem does not arise.

But when I run this pipeline, I get the error:

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',out_GatherBQSRReports/NSK9.normal.GatherBQSRReports.txt}' but no positional argument is defined for this tool.

and such snakemake error:

/gatk-4.1.9.0/gatk --java-options -Xmx7680m GatherBQSRReports -I -O out_GatherBQSRReports/NSK9.normal.GatherBQSRReports.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

import glob

SAMPLES = glob_wildcards("input_bam/{sample}.bam")
INTERVALS = glob_wildcards("intervals/{interval}.bed")
all_samples_BaseRecalibrator = glob.glob("out_BaseRecalibrator/*-scattered.txt")

rule all:
        input: expand("out/{sample}.AddOrReplaceReadGroups.bam", sample = SAMPLES.sample), 
                expand("out/{sample}.MarkDuplicates.txt", sample = SAMPLES.sample), 
                expand("out/{sample}.MarkDuplicates.bam", sample = SAMPLES.sample), 
                expand("out_BaseRecalibrator/{sample}.BaseRecalibrator.{interval}.txt", interval=INTERVALS.interval, sample=SAMPLES.sample),
                expand("out_GatherBQSRReports/{sample}.GatherBQSRReports.txt", sample=SAMPLES.sample)
rule gatk_AddOrReplaceReadGroups:
        input: "input_bam/{sample}.bam"
        output: "out/{sample}.AddOrReplaceReadGroups.bam"
        shell: "./gatk-4.1.9.0/gatk --java-options ""-Xmx30g""  AddOrReplaceReadGroups -I {input}  -O {output} -ID group1 -SM NORMAL -PL illumina -LB lib1 -PU unit1"

rule gatk_MarkDuplicates:
        input: rules.gatk_AddOrReplaceReadGroups.output
        output: output1="out/{sample}.MarkDuplicates.bam", output2="out/{sample}.MarkDuplicates.txt"
        shell: "./gatk-4.1.9.0/gatk --java-options  ""-Xmx4g""  MarkDuplicates  -I {input}  -O {output.output1} -M {output.output2} --CREATE_INDEX true"

rule bedtools_genomecov:
        input: "input_bam/{sample}.bam"
        output: output1="out/{sample}.bedtools_genomecov.genome.covered.bed"
        shell: "bedtools genomecov -ibam -I {input} -bg > -O {output.output1}"

rule gatk_BaseRecalibrator:
        input: input1="intervals/{interval}.bed", input2="out/{sample}.MarkDuplicates.bam", input3='ref/ref.fa', input4="dbsnp/dbsnp_150.hg38.vcf.gz"
        output: "out_BaseRecalibrator/{sample}.BaseRecalibrator.{interval}.txt",
        shell: "./gatk-4.1.9.0/gatk --java-options ""-Xmx7680m""  BaseRecalibrator -L {input.input1} -I {input.input2} -O {output} -R {input.input3} --known-sites {input.input4}"

rule gatk_GatherBQSRReports:
    input: all_samples_BaseRecalibrator
    output: "out_GatherBQSRReports/{sample}.GatherBQSRReports.txt"
    params: all_samples_BaseRecalibrator='-I'.join(all_samples_BaseRecalibrator)
        shell: "./gatk-4.1.9.0/gatk --java-options  ""-Xmx7680m"" GatherBQSRReports -I {params.all_samples_BaseRecalibrator}  -O {output}"

[Pierre Lindenbaum]

the value of all_samples_BaseRecalibrator is empty. Furthermore, why do you have two -I in this command ?

[kamanovae]

Sorry, I tried to fix the error and added an extra input. However, nothing changes even if the last rule looks like this:

rule gatk_GatherBQSRReports:
        input: all_samples_BaseRecalibrator
        output: "out_GatherBQSRReports/{sample}.GatherBQSRReports.txt"
        params: all_samples_BaseRecalibrator=' -I '.join(all_samples_BaseRecalibrator)
        shell: "./gatk-4.1.9.0/gatk --java-options  ""-Xmx7680m"" GatherBQSRReports -I {params.all_samples_BaseRecalibrator}  -O {output}"

It seems to me that the reason for the error in the snakemake. Because the gatk_GatherBQSRReports works successfully if the folder already contains the results of the previous rules.