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gatk 4.4 docker image missing dependancies

booby35booby35 canadaMember

Hi there,

I am trying to perform Base recalibration using the docker image of gatk 4.4. (I used 3.6 before but a dependency problem with R pointed me to the latest version, in which the problem should be fixed according to the GATK forum) - but here I am with v4.4 and a similar error message "Error in library("reshape") : there is no package called 'reshape'" (see full message at the bottom of the message).

The library is indeed not installed in R.
Is there a repo having a container will all depencies installed? or is it just like v3.6 and running script "manually" is required? What am I missing to perform this step correctly?

thanks in advance for your answer.

Best,

B.

`
[email protected]$ docker run --mount type=bind,source="$ld",target=/data/ --mount type=bind,source=/media/b35/DATA/genomic/reference_genomes/,target=/ref/ broadinstitute/gatk:latest sh -c "gatk AnalyzeCovariates -bqsr /data/data/recal.table${i} -plots /data/data/AnalyzeCovariates${i}.pdf"
19:36:17.277 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/build/libs/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
19:36:17.414 INFO AnalyzeCovariates - ------------------------------------------------------------
19:36:17.415 INFO AnalyzeCovariates - The Genome Analysis Toolkit (GATK) v4.0.4.0
19:36:17.415 INFO AnalyzeCovariates - For support and documentation go to https://software.broadinstitute.org/gatk/
19:36:17.415 INFO AnalyzeCovariates - Executing as [email protected] on Linux v4.13.0-43-generic amd64
19:36:17.415 INFO AnalyzeCovariates - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11
19:36:17.415 INFO AnalyzeCovariates - Start Date/Time: May 28, 2018 7:36:17 PM UTC
19:36:17.415 INFO AnalyzeCovariates - ------------------------------------------------------------
19:36:17.415 INFO AnalyzeCovariates - ------------------------------------------------------------
19:36:17.416 INFO AnalyzeCovariates - HTSJDK Version: 2.14.3
19:36:17.416 INFO AnalyzeCovariates - Picard Version: 2.18.2
19:36:17.416 INFO AnalyzeCovariates - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:36:17.416 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:36:17.416 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:36:17.416 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:36:17.416 INFO AnalyzeCovariates - Deflater: IntelDeflater
19:36:17.416 INFO AnalyzeCovariates - Inflater: IntelInflater
19:36:17.416 INFO AnalyzeCovariates - GCS max retries/reopens: 20
19:36:17.417 INFO AnalyzeCovariates - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
19:36:17.417 INFO AnalyzeCovariates - Initializing engine
19:36:17.417 INFO AnalyzeCovariates - Done initializing engine
19:36:17.731 INFO AnalyzeCovariates - Generating csv file '/tmp/root/AnalyzeCovariates2520511082455841657.csv'
19:36:17.789 INFO AnalyzeCovariates - Generating plots file '/data/data/AnalyzeCovariates1.pdf'
19:36:18.255 INFO AnalyzeCovariates - Shutting down engine
[May 28, 2018 7:36:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=320864256
org.broadinstitute.hellbender.utils.R.RScriptExecutorException:
Rscript exited with 1
Command Line: Rscript -e tempLibDir = '/tmp/root/Rlib.7509374791326779134';source('/tmp/root/BQSR.8897197604108889283.R'); /tmp/root/AnalyzeCovariates2520511082455841657.csv /data/data/recal.table1 /data/data/AnalyzeCovariates1.pdf
Stdout:
Stderr:
Attaching package: 'gplots'

The following object is masked from 'package:stats':

lowess

Error in library("reshape") : there is no package called 'reshape'
Calls: source -> withVisible -> eval -> eval -> library
Execution halted

at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:80)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:19)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:126)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.exec(RScriptExecutor.java:131)
at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.generatePlots(RecalUtils.java:360)
at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:329)
at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.doWork(AnalyzeCovariates.java:341)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
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)

Using GATK jar /gatk/build/libs/gatk-package-4.0.4.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/build/libs/gatk-package-4.0.4.0-local.jar AnalyzeCovariates -bqsr /data/data/recal.table1 -plots /data/data/AnalyzeCovariates1.pdf
`

Issue · Github
by Sheila

Issue Number
3104
State
open
Last Updated
Assignee
Array

Best Answer

  • booby35booby35 canada
    edited May 2018 Accepted Answer

    I added the library to the dockerfile, this seems to have solved the problem:

    from broadinstitute/gatk:latest
    
    RUN R -e "install.packages('reshape', repos = 'http://cran.us.r-project.org')"
    

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