GATK-usage-ERROR-Helpreg

[vishnuamaram]

Hi Seqanswers community,


I am doing human whole genome sequence analysis, of the data obtained Illumina Hiseq 2000.

This is the pipeline i followed & get errors in using GATK


a) BWA ------> SAM output
b) samtools ---> sortedindexedbamoutput
c) picard ------> for readgroup replacement & removing duplicates
d) GATK ----> for indelrealignment, BQSR, variant calling.


when i give the following command for GATK-indel realignment, i get the error.

U]cd used:-[/U]

java -Xmx30g -jar GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -T IndelRealigner \ -R INDEX_REF_GENOME_HG19/hg19.fa \ -I WG_PBMC_SAM9_CORDSORT_RMDUP.BAM -targetintervals intervalListFromRTC.intervals \ -o WG_PBMC_SAM9_coordsort_realigned.bam


the errors are :-


##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Argument with name '--targetIntervals' (-targetIntervals) is missing.
##### ERROR ------------------------------------------------------------------------------------------



kindly give me solutions, will be very thankful to you.

Please do let me know the proper usage of GATK.

Thanking you all,

Vishnu.

[sheenams]

targetintervals intervalListFromRTC.intervals

needs to be:

targetIntervals intervalListFromRTC.intervals

[vishnuamaram]

Hi sheenams,

Thank you very much.

I had tried using targetIntervals, but stil again it throws error as follows

##### ERROR MESSAGE: Couldn't read file Sample_WG-9/RAWFASTQ_CAT_FILES/intervalListFromRTC.intervals because The interval file does not exist.


How should i proceed exactly with GATK .

Guys and all members, i request all to help me using GATK with proper commands for indel realignment, BQSR and variant calling.

Thank you,
Vishnu.

[whataBamBam]

Hi Vishnu.. looks like the same error you had on the other thread.. sorry, I thought I'd replied to that but my post didn't register, internet here is quite flaky.

so you tried with relative pathname (i.e. just the file name) and it crashed with

##### ERROR MESSAGE: Couldn't read file Sample_WG-9/RAWFASTQ_CAT_FILES/intervalListFromRTC.intervals because The interval file does not exist.

It's looking in the current working directory for the file and finding it doesn't exist.

And you tried (from other thread) full path

and got

##### ERROR MESSAGE: Couldn't read file /data/odity/Project_Blood-GNPC-464/Sample_WG-9/RAWFASTQ_CAT_FILES/intervalListFromRTC.intervals because The interval file does not exist

so maybe the path is wrong..

what happens when you type

ls /data/odity/Project_Blood-GNPC-464/Sample_WG-9/RAWFASTQ_CAT_FILES/intervalListFromRTC.intervals

at the command line

if it says..

ls: cannot access /data/odity/Project_Blood-GNPC-464/Sample_WG-9/RAWFASTQ_CAT_FILES/intervalListFromRTC.intervals: No such file or directory

then your path is wrong.

And you can find the right one by doing..

/data [HIT TAB KEY]

/data/o [HIT TAB KEY]

/data/odity/P [HIT TAB KEY]

etc.. unix will tab complete the paths for you and you get the path correct.

[vishnuamaram]

Hey whataBamBam,

I had got your responses on other thread too.

Actually, i didnt generate interval file,

My question is how to generate an interval file.

Kindly help me in generating an interval file by giving a proper command usage.

Thank you in tons,
Vishnu.

[dpryan]

Hey whataBamBam,

I had got your responses on other thread too.

Actually, i didnt generate interval file,

My question is how to generate an interval file.

Kindly help me in generating an interval file by giving a proper command usage.

Thank you in tons,
Vishnu.

Did you read my reply to the same question in the other thread? If the RealignerTargetCreator command is itself giving errors, then you should just post those.

[harryzs]

Hi Seqanswers community,


I am doing human whole genome sequence analysis, of the data obtained Illumina Hiseq 2000.

This is the pipeline i followed & get errors in using GATK


a) BWA ------> SAM output
b) samtools ---> sortedindexedbamoutput
c) picard ------> for readgroup replacement & removing duplicates
d) GATK ----> for indelrealignment, BQSR, variant calling.


when i give the following command for GATK-indel realignment, i get the error.

U]cd used:-[/U]

java -Xmx30g -jar GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -T IndelRealigner \ -R INDEX_REF_GENOME_HG19/hg19.fa \ -I WG_PBMC_SAM9_CORDSORT_RMDUP.BAM -targetintervals intervalListFromRTC.intervals \ -o WG_PBMC_SAM9_coordsort_realigned.bam


the errors are :-


##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.6-5-gba531bd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Argument with name '--targetIntervals' (-targetIntervals) is missing.
##### ERROR ------------------------------------------------------------------------------------------



kindly give me solutions, will be very thankful to you.

Please do let me know the proper usage of GATK.

Thanking you all,

Vishnu.

You may follow this

http://www.broadinstitute.org/gatk/guide/topic?name=tutorials

[harryzs]

You may follow this
http://www.broadinstitute.org/gatk/g...name=tutorials

-->(howto) Perform local realignment around indels

[dpryan]

The informative line of that error message is:

##### ERROR MESSAGE: Argument with name '--targetIntervals' (-targetIntervals) is missing.

Your command used "--targetintervals" (note the capital "I" in the error message).