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How do I reach my data when running GATK in docker?

zsuzsannaHzsuzsannaH HungaryMember
Hi! I would like to try out GATK but I am new to Linux OS, generally I use Windows OS. I installed Ubuntu 18.04.3 LTS through Oracle VirtualBox 6.0 on a laptop running Windows 10. I followed the instructions on the website to install Docker and downloading the GATK container image. When I try to run the FastqToSam tool it looks like this:

[email protected]:~$ sudo docker run -v ~/home/lmi/NGS:/gatk/my_data -it broadinstitute/gatk:
[sudo] password for lmi:
(gatk) [email protected]:/gatk# gatk FastqToSam -F1 F1.fastq -F2 F2.fastq -O uBAM.bam -SM sample001 -RG rg0013
Using GATK jar /gatk/gatk-package-
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/gatk-package- FastqToSam -F1 F1.fastq -F2 F2.fastq -O uBAM.bam -SM sample001 -RG rg0013
09:40:34.696 INFO NativeLibraryLoader - Loading from jar:file:/gatk/gatk-package-!/com/intel/gkl/native/
[Thu Oct 10 09:40:34 UTC 2019] FastqToSam --FASTQ F1.fastq --FASTQ2 F2.fastq --OUTPUT uBAM.bam --READ_GROUP_NAME rg0013 --SAMPLE_NAME sample001 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Oct 10, 2019 9:40:41 AM runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Thu Oct 10 09:40:41 UTC 2019] Executing as [email protected] on Linux 5.0.0-31-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:
[Thu Oct 10 09:40:41 UTC 2019] picard.sam.FastqToSam done. Elapsed time: 0.12 minutes.
To get help, see
htsjdk.samtools.SAMException: Cannot read non-existent file: file:///gatk/F1.fastq
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(
at picard.sam.FastqToSam.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(
at org.broadinstitute.hellbender.Main.runCommandLineProgram(
at org.broadinstitute.hellbender.Main.mainEntry(
at org.broadinstitute.hellbender.Main.main(
(gatk) [email protected]:/gatk#

If I understand it correctly from "Cannot read non-existent file", it can't find the input fastq files I have in my NGS directory. I would like for my working directory to be /home/lmi/NGS. How should I start GATK to resolve this?

Thank you!

Best Answer


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