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Re: [Samtools-help] Fwd: ERROR: Problem constructing Integer from the string 'RGDT=..
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From: Alec W. <al...@br...> - 2014-04-25 14:51:16
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Hi Monica,
Something very strange is happened with the command-line parsing. The only integer expected on the command line is for the RGPI argument. And stranger still, the string in the error message should be the stuff after the equal sign. So, somehow the command-line parser things that the value passed to RGPI is 'RGDT=2013-12-13'. Try moving RGPI=425 to the end of the command line. I confess that I'm grasping at straws.
-Alec
On Apr 25, 2014, at 9:54 AM, Mónica Fabbro <mc...@gm...> wrote:
> Hi Alec!
> Thank you so much for your answer!
> I try your suggestion but it didn't work.
> Here is the entire output:
>
> ERROR: Problem constructing Integer from the string 'RGDT=2013-12-13'.
>
> Replaces all read groups in the INPUT file with a new read group and assigns all reads to this read group in the OUTPUT BAMVersion: 1.0
>
> Version: 1.112(1930)
>
>
> Options:
>
> --help
> -h Displays options specific to this tool.
>
> --stdhelp
> -H Displays options specific to this tool AND options common to all Picard command line
> tools.
>
> --version Displays program version.
>
> INPUT=File
> I=File Input file (bam or sam). Required.
>
> OUTPUT=File
> O=File Output file (bam or sam). Required.
>
> SORT_ORDER=SortOrder
> SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
> Default value: null. Possible values: {unsorted, queryname, coordinate}
>
> RGID=String
> ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
> value.
>
> RGLB=String
> LB=String Read Group Library Required.
>
> RGPL=String
> PL=String Read Group platform (e.g. illumina, solid) Required.
>
> RGPU=String
> PU=String Read Group platform unit (eg. run barcode) Required.
>
> RGSM=String
> SM=String Read Group sample name Required.
>
> RGCN=String
> CN=String Read Group sequencing center name Default value: null.
>
> RGDS=String
> DS=String Read Group description Default value: null.
>
> RGDT=Iso8601Date
> DT=Iso8601Date Read Group run date Default value: null.
>
> RGPI=Integer
> PI=Integer Read Group predicted insert size Default value: null.
>
> TMP_DIR=File This option may be specified 0 or more times.
>
> VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to
> clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG}
>
> QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option
> can be set to 'null' to clear the default value. Possible values: {true, false}
>
> VALIDATION_STRINGENCY=ValidationStringency
> Validation stringency for all SAM files read by this program. Setting stringency to
> SILENT can improve performance when processing a BAM file in which variable-length data
> (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This
> option can be set to 'null' to clear the default value. Possible values: {STRICT,
> LENIENT, SILENT}
>
> COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and GELI). Default value:
> 5. This option can be set to 'null' to clear the default value.
>
> MAX_RECORDS_IN_RAM=Integer When writing SAM files that need to be sorted, this will specify the number of records
> stored in RAM before spilling to disk. Increasing this number reduces the number of file
> handles needed to sort a SAM file, and increases the amount of RAM needed. Default
> value: 500000. This option can be set to 'null' to clear the default value.
>
> CREATE_INDEX=Boolean Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value:
> false. This option can be set to 'null' to clear the default value. Possible values:
> {true, false}
>
> CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
> false. This option can be set to 'null' to clear the default value. Possible values:
> {true, false}
>
> OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
> options, unrecognized options are ignored. A single-valued option set in an options file
> may be overridden by a subsequent command-line option. A line starting with '#' is
> considered a comment. This option may be specified 0 or more times.
>
>
> The command line was:
>
> java -Xmx16G -jar /opt/picard/AddOrReplaceReadGroups.jar I=pas1.aligned.sorted.dedupped.bam O=pas1.aligned.sorted.dedupped.RG.bam LB=TruSeqDNA PL=Illumina PU=H88U6ADXX SM=pas1 RGID=pas1 RGPI=425 RGDT='2013-12-13' RGCN=Indear CREATE_INDEX=true CREATE_MD5_FILE=true
>
> Thanks in advance!
>
> Mónica
>
>
>
>
>
>
>
>
> 2014-04-24 18:05 GMT-03:00 Alec Wysoker <al...@br...>:
>
> Hi Monica,
>
> You command line looks fine to me. In addition, the error message you report makes me think that there is something strange about whitespace and perhaps quoting arguments in your command line. Could you try this again, retyping the entire command line, and then send me the exact and complete output that the program produces?
>
> Thanks, Alec
>
> On Apr 24, 2014, at 4:14 PM, Mónica Fabbro <mc...@gm...> wrote:
>
> > Hi everyone
> >
> > I'm trying to run the AddorReplaceReadsGroups Picard tool and I get this error message:
> >
> > ERROR: Problem constructing Integer from the string 'RGDT=2013-12-13'
> >
> > The command line is:
> >
> > java -Xmx16G -jar /opt/picard-tools-v1.112/AddOrReplaceReadGroups.jar I=pas1.aligned.sorted.dedupped.bam O=pas1.aligned.sorted.dedupped.RG.bam LB=TruSeqDNA PL=Illumina PU=H88U6ADXX SM=pas1 RGDT=2013-12-13 RGID=pas1 RGPI=425 RGCN=Indear CREATE_INDEX=true CREATE_MD5_FILE=true
> >
> > My java version is: "1.7.0_51"
> >
> > Hope anyone could help me!
> >
> > Thanks in advance
> >
> > Mónica
> >
> >
> >
> >
> >
> >
> >
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>
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