i got this error when i wanted to Evaluate the depth of coverage of the aligned region -- ALL GATK 1.4 tools are deprecated and should be avoided.

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/028/008/28008534/_job_tmp -Xmx7g -Xms256m
[Wed Apr 22 22:21:55 CDT 2020] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/jobdir/028/008/28008534/_job_tmp/tmp-gatk-FCsWXU/gatk_input.fasta OUTPUT=/galaxy-repl/main/jobdir/028/008/28008534/_job_tmp/tmp-gatk-FCsWXU/dict7481932586338388707.tmp    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Apr 22 22:22:04 CDT 2020] Executing as g2main@roundup64 on Linux 3.10.0-1062.18.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057)
[Wed Apr 22 22:22:09 CDT 2020] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.23 minutes.
Runtime.totalMemory()=750256128
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version exported): 
##### 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Badly formed genome loc: Contig chr20 given as location, but this contig isn't present in the Fasta sequence dictionary
##### ERROR ------------------------------------------------------------------------------------------
mv: cannot stat ‘/galaxy-repl/main/files/039/619/dataset_39619384.dat.sample_summary’: No such file or directory
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Have you looked into this part of the message?

1 Like

i didn’t have this error message

That is a part of the message you have posted. I just copied it out.

Hi @Sanae_Borrohou,

@marten is correct, the notes about mismatched data inputs is part of your error message.

I also replied to your bug report.

The problem may be in your data, but you will have problems later on if you continue to use the deprecated GATK 1.4 tools.

For clarification about why to avoid all GATK 1.4 tools, please see: https://github.com/galaxyproject/usegalaxy-playbook/issues/281#issuecomment-618586374

Quoted here:

Note for end-users:

Again, all GATK 1.4 tools are deprecated and should be avoided . Several have known issues unrelated to this particular correction. Your job may not even fail, but instead, produce putatively “successful” results are scientifically incorrect .

It is strongly recommended to use updated variant analysis methods

See the GTN Tutorials: https://training.galaxyproject.org/training-material/topics/variant-analysis/

The ONLY valid and current GATK tool at this time is:

GATK4 Mutect2 - Call somatic SNVs and indels via local assembly of haplotypes (Galaxy Version 4.1.4.0+galaxy2)

Thanks!

Thanks for the help