ApplyBQSR no positional argument is defined for this tool
Answered
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.2.0.0
b) Exact command used:
gatk ApplyBQSR \
--java-options "-Xmx14G" \
–R GRCh38.dna.primary_assembly/GRCh38.dna.primary_assembly.fa \
–I Sample.SplitNCigarReads.bam \
–bqsr Sample.before.recal_data.table \
–O Sample.recal.bam
c) Entire error log:
A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',–R{GRCh38.dna.primary_assembly/GRCh38.dna.primary_assembly.fa{–I{Sample.SplitNCigarReads.bam{–bqsr{Sample.before.recal_data.table{–O{Sample.recal.bam}' but no positional argument is defined for this tool.
***********************************************************************
org.broadinstitute.barclay.argparser.CommandLineException$BadArgumentValue: Illegal argument value: Positional arguments were provided ',–R{GRCh38.dna.primary_assembly/GRCh38.dna.primary_assembly.fa{–I{Sample.SplitNCigarReads.bam{–bqsr{Sample.before.recal_data.table{–O{Sample.recal.bam}' but no positional argument is defined for this tool.
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.propagateParsedValues(CommandLineArgumentParser.java:507)
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:170)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:233)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:207)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?
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Hi Jose Aragon, check out this post from another user who saw this same error message and see if it can help you solve the issue: https://gatk.broadinstitute.org/hc/en-us/community/posts/360076948391--No-positional-argument-is-defined-Error-in-HaplotypeCaller
It is most likely caused by a typo in your command line.
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Thank you for your response. Yes, I checked this post. It is not solving my problem. My code has no spaces in the tags:
Bad tag:
- RGood tag:
-RCould it be that it is from a different tool? In this case my problem is with ApplyBQSR and not with HaplotypeCaller.
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Hi Jose Aragon, this would not be different between GATK tools. I think you still have a typo because of the error message:
A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',–R{GRCh38.dna.primary_assembly/GRCh38.dna.primary_assembly.fa{–I{Sample.SplitNCigarReads.bam{–bqsr{Sample.before.recal_data.table{–O{Sample.recal.bam}' but no positional argument is defined for this tool.
It looks like there is no space between the R and {GRCh38... which will cause issues in running the command.
Best,
Genevieve
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I checked for any typo and I cannot see anything that can be related to spaces or other type of typos.
I tried another computer and here is the command line:
gatk ApplyBQSR \
--java-options "-Xmx48G" \
–R GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
–I sample1.SplitNCigarReads.bam \
–bqsr sample1.recal_data.table \
–O EL53.1.RecalReads.bamAnd here is the error message when I use -DGATK_STACKTRACE_ON_USER_EXCEPTION=true
gatk ApplyBQSR \
--java-options "-Xmx48G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
–R GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
–I sample1.SplitNCigarReads.bam \
–bqsr sample1.recal_data.table \
–O EL53.1.RecalReads.bam***********************************************************************A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',–R{GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa{–I{sample1.SplitNCigarReads.bam{–bqsr{sample1.recal_data.table{–O{EL53.1.RecalReads.bam}' but no positional argument is defined for this tool.***********************************************************************org.broadinstitute.barclay.argparser.CommandLineException$BadArgumentValue: Illegal argument value: Positional arguments were provided ',–R{GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa{–I{sample1.SplitNCigarReads.bam{–bqsr{sample1.recal_data.table{–O{EL53.1.RecalReads.bam}' but no positional argument is defined for this tool.at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.propagateParsedValues(CommandLineArgumentParser.java:507)at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:170)at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:233)at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:207)at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)at org.broadinstitute.hellbender.Main.main(Main.java:289) -
Hi Jose Aragon, thank you for checking that!
I think I found the source of the issue, the --java-options should be listed before the GATK command ApplyBQSR.
There is more information here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531892-GATK4-command-line-syntax
I hope this solves it!
Genevieve
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Hi
I get this error too
in bqsr
how could i solve it
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It looks like there is an issue with your command line. Could you provide your command line in text for troubleshooting purposes? And also the complete program log.
Here is the tool index page where you can also find example commands for the tool you are using: https://gatk.broadinstitute.org/hc/en-us/articles/4418051394587--Tool-Documentation-Index.
Best,
Genevieve
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