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Malformed walker argument using MarkDuplicatesSpark

I am creating my own NGS pipeline from illumina-fastq file to vcf. This is for pure learning purposes.

When I run the following code everything is ok

java -Xmx4000m "$javatmp" -jar "$picardpath" SortSam \
    INPUT=/home/mdb1c20/my_onw_NGS_pipeline/files/sam/1.sam \
    OUTPUT=/home/mdb1c20/my_onw_NGS_pipeline/files/bam/1_sorted.bam \
    SORT_ORDER=coordinate \
    COMPRESSION_LEVEL=5


java -Xmx4000m "$javatmp" -jar "$picardpath" MarkDuplicates \
    INPUT=/home/mdb1c20/my_onw_NGS_pipeline/files/bam/1_sorted.bam \
    OUTPUT=/home/mdb1c20/my_onw_NGS_pipeline/files/bam/1_sorted_rmdupli.bam \
    METRICS_FILE=/home/mdb1c20/my_onw_NGS_pipeline/files/metrics_files/dupMetrics.txt \

However, when I tried this one (see below), I got an error (also show after code).

java -Xmx4000m "$javatmp" -jar "$gatkpath" \
         -T MarkDuplicatesSpark \
         -I /home/mdb1c20/my_onw_NGS_pipeline/files/sam/1.sam \
         -O /home/mdb1c20/my_onw_NGS_pipeline/files/bam/marked_duplicates.bam \
         -M /home/mdb1c20/my_onw_NGS_pipeline/files/metrics_files/spark_marked_dup_metrics.txt

Error message:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: MarkDuplicatesSpark
##### ERROR ------------------------------------------------------------------------------------------

What I am doing wrong?? I have tried everything and the same error message appears. I have read the documentation and I can find what is wrong

ngs
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by ManuelDB ManuelDB

1 answer 

##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):

there is no MarkDuplicatesSpark before gatk4.*

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written by Pierre Lindenbaum Pierre Lindenbaum

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