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hartleys / QoRTs

Quality of RNA-Seq Toolset
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Exception: SYNTAX ERROR! #80

Closed IlariaPalmi closed 4 years ago

IlariaPalmi commented 4 years ago

Dear all I am runnnig a QC on some bam files and I get some error CAn you please help me? thanks

java -Xmx4G -jar $RDS/home/anaconda3/pkgs/qorts-1.3.6-0/share/qorts-1.3.6-0/QoRTs.jar QC \ --generatePlots \ --genomeFA $RDS/projects/sequ/live/Genecode/mouseannotation/GRCm38.primary_assembly.genome.fa \ $RDS/projects/sequ/live/mapped/Genecodesecondpass/EE_Sample_SDG1Aligned.sortedByCoord.out.bam \ $RDS/projects/sequ/live/Genecode/mouseannotatio/gencode.vM25.primary_assembly.annotation.gtf \ $RDS/projects/sequ/live/mapped/QoRT_QC/ \ --readGroup

and I get the following message: INPUT_COMMAND(QC) INPUT_ARG(infile)=/rds/general/user/ipalmisa/projects/sequ/live/Genecode/mouseannotatio/gencode.vM25.primary_assembly.annotation.gtf INPUT_ARG(gtffile)=/rds/general/user/ipalmisa/projects/sequ/live/mapped/QoRT_QC/ INPUT_ARG(outdir)=--readGroup INPUT_ARG(generatePlots)=true INPUT_ARG(genomeFA)=Some(List(/rds/general/user/ipalmisa/projects/sequ/live/Genecode/mouseannotation/GRCm38.primary_assembly.genome.fa)) <====== FATAL ERROR! ======>

 Error message: "SYNTAX ERROR! Unrecognized Argument: /rds/general/user/ipalmisa/projects/sequ/live/mapped/Genecodesecondpass/EE_Sample_SDG1Aligned.sortedByCoord.out.bam"
 Stack Trace:
    java.base/java.lang.Thread.getStackTrace(Thread.java:1606)
    internalUtils.Reporter$.error(Reporter.scala:331)
    internalUtils.commandLineUI$.internalUtils$commandLineUI$$throwSyntaxErrorMessage(commandLineUI.scala:328)
    internalUtils.commandLineUI$CommandLineArgParser.parseParamArgs(commandLineUI.scala:314)
    internalUtils.commandLineUI$CommandLineArgParser.parseArgs_master(commandLineUI.scala:287)
    internalUtils.commandLineUI$CommandLineArgParser.parseArguments(commandLineUI.scala:152)
    qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:631)
    runner.runner$.main(runner.scala:98)
    runner.runner.main(runner.scala)

<==========================> Exception in thread "main" java.lang.Exception: SYNTAX ERROR! Unrecognized Argument: /rds/general/user/ipalmisa/projects/sequ/live/mapped/Genecodesecondpass/EE_Sample_SDG1Aligned.sortedByCoord.out.bam at internalUtils.Reporter$.error(Reporter.scala:336) at internalUtils.commandLineUI$.internalUtils$commandLineUI$$throwSyntaxErrorMessage(commandLineUI.scala:328) at internalUtils.commandLineUI$CommandLineArgParser.parseParamArgs(commandLineUI.scala:314) at internalUtils.commandLineUI$CommandLineArgParser.parseArgs_master(commandLineUI.scala:287) at internalUtils.commandLineUI$CommandLineArgParser.parseArguments(commandLineUI.scala:152) at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:631) at runner.runner$.main(runner.scala:98) at runner.runner.main(runner.scala)

IlariaPalmi commented 4 years ago

sorry, I had closed it by mistake

IlariaPalmi commented 4 years ago

I understood that the --readGroup option was the problem (it runs fine if I don't use this option). can you please explain me how to use it properly? The bam file has been generate via STAR using different fastq files Thanks

sparthib commented 9 months ago

Hi @IlariaPalmi, this is probably too too late, but I ran into the same issue and I think all the file arguments have to be at the end, so, if you rewrote your code as 

java -Xmx4G -jar $RDS/home/anaconda3/pkgs/qorts-1.3.6-0/share/qorts-1.3.6-0/QoRTs.jar QC
--generatePlots \
--readGroup \
--genomeFA $RDS/projects/sequ/live/Genecode/mouseannotation/GRCm38.primary_assembly.genome.fa \
$RDS/projects/sequ/live/mapped/Genecodesecondpass/EE_Sample_SDG1Aligned.sortedByCoord.out.bam \
$RDS/projects/sequ/live/Genecode/mouseannotatio/gencode.vM25.primary_assembly.annotation.gtf \
$RDS/projects/sequ/live/mapped/QoRT_QC/

it should run