picard MarkIlluminaAdapters for Non-Illumina Adapters Error
Hi,
When I try MarkIlluminaAdapters for Non-Illumina Adapters, it gives me below error.....Any help in correct syntax?
a) GATK version used:
4.2.0
Picard Version:2.25.0
b) Exact command used:
picard MarkIlluminaAdapters -I /mnt/d/gen/uAdi.bam -O /mnt/d/gen/uAdi.bam_mark.bam -M /mnt/d/gen/metrics.txt --ADAPTERS null THREE_PRIME_ADAPTER:AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA FIVE_PRIME_ADAPTER:AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG
c) Entire error log:
(base) adi@Khalil-AbuAli:/mnt/d/gen$ picard MarkIlluminaAdapters -I /mnt/d/gen/uAdi.bam -O /mnt/d/gen/uAdi.bam_mark.bam -M /mnt/d/gen/metrics.txt --ADAPTERS null THREE_PRIME_ADAPTER:AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA FIVE_PRIME_ADAPTER:AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG
USAGE: MarkIlluminaAdapters [arguments]
Reads a SAM or BAM file and rewrites it with new adapter-trimming tags. <p>This tool clears any existing
adapter-trimming tags (XT:i:) in the optional tag region of a SAM file. The SAM/BAM file must be sorted by query
name.</p> <p>Outputs a metrics file histogram showing counts of bases_clipped per read.<h4>Usage example:</h4><pre>java
-jar picard.jar MarkIlluminaAdapters \<br /> INPUT=input.sam \<br />METRICS=metrics.txt </pre><hr />
Version:2.25.0
Illegal argument value: Positional arguments were provided ',THREE_PRIME_ADAPTER:AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA{FIVE_PRIME_ADAPTER:AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG}' but no positional argument is defined for this tool.
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Let me give you a small bit of advice. MarkIlluminaAdapters tool with this command line does not completely mark all possible adapter remnants unfortunately. MGI adapters tend to be in different orientations. I would strongly suggest using cutadapt to remove all adapters from MGI data before any other preprocessing steps.
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Just use cutadapt tool to trim all adapters from reads. For fastqc you need to incorporate MGI adapters to the known adapters list or provide those adapters as parameters to fastqc commandline.
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Hi Adi Abuali,
I think there is a typo in your command line, the THREE_PRIME_ADAPTER argument should be given as --THREE_PRIME_ADAPTER with the hyphens. Same with the five prime adapter argument.
You can read more here: https://gatk.broadinstitute.org/hc/en-us/articles/360057439471-MarkIlluminaAdapters-Picard-
Best,
Genevieve
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Hi Genevieve,
Thanks but I tried this before and it gave me different error as below:
picard MarkIlluminaAdapters -I /mnt/d/gen/uAdi.bam -O /mnt/d/gen/uAdi.bam_mark.bam -M /mnt/d/gen/metrics.txt --ADAPTERS null --THREE_PRIME_ADAPTER:AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA --FIVE_PRIME_ADAPTER:AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG
No argument value found for tagged argument: THREE_PRIME_ADAPTER:AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA
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Finally it works with below syntax:
gatk MarkIlluminaAdapters I=/mnt/d/gen/uAdi.bam O=/mnt/d/gen/uAdi.bam_mark.bam M=/mnt/d/gen/metrics.txt ADAPTERS=null FIVE_PRIME_ADAPTER=AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAG
GAGTTG THREE_PRIME_ADAPTER=AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA TMP_DIR=/mnt/d/tmpThanks,
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Thanks for the update and posting your solution Adi Abuali, glad you were able to solve the problem!
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Thank you SkyWarrior...I know it's not GATK tool as well, but if you advice for MGI fastp tool as well for same approach ?
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Thank you for the advise...Appreciated.
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