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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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CTAT-mutation-lib-integration #51

Open ryangimple opened 4 years ago

ryangimple commented 4 years ago

I downloaded the CTAT-mutations package from https://anaconda.org/bioconda/ctat-mutations in a new environment. I downloaded this github package and tried running the "ctat-mutation-lib-integration.py" program but got the message "Set $PICARD_HOME to your picard software". I tried exporting the path to my picard software, but got an error:

subprocess.CalledProcessError: Command '['java', '-jar', '/home/rcgimple/anaconda3/envs/ctat-mutations/bin:/home/rcgimple/anaconda3/condabin:/opt/openmpi/intel/ib/bin:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/bin/intel64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/sdsc/bin:/opt/sdsc/sbin:/opt/gold/bin:/opt/gold/sbin:.:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/home/rcgimple/bin:/home/rcgimple/anaconda3/envs/ctat-mutations/bin/picard:/home/rcgimple/anaconda3/envs/ctat-mutations/bin/picard/picard.jar', 'CreateSequenceDictionary', 'R=', '/home/rcgimple/scratch/STAR-Fusion-Files/GRCh38_gencode_v32_CTAT_lib_Dec062019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa', 'O=', '/home/rcgimple/scratch/STAR-Fusion-Files/GRCh38_gencode_v32_CTAT_lib_Dec062019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.dict', 'VALIDATION_STRINGENCY=LENIENT']' returned non-zero exit status 1.

Could you please suggest a way to fix this? It would be great if the "ctat-mutation-lib-integration.py" script could be included in the Conda package so there wouldn't be issues with file paths or the need to download multiple software components from multiple websites.

Thanks, Ryan

brianjohnhaas commented 4 years ago

hi Ryan,

Can you download the latest code from our release site? Conda packages are built by community volunteers and aren't guaranteed to reflect the latest code.

https://github.com/NCIP/ctat-mutations/releases

latest documentation is available: https://github.com/NCIP/ctat-mutations/wiki

best,

~b

On Thu, Apr 2, 2020 at 7:54 PM ryangimple notifications@github.com wrote:

I downloaded the CTAT-mutations package from https://anaconda.org/bioconda/ctat-mutations in a new environment. I downloaded this github package and tried running the "ctat-mutation-lib-integration.py" program but got the message "Set $PICARD_HOME to your picard software". I tried exporting the path to my picard software, but got an error:

subprocess.CalledProcessError: Command '['java', '-jar', '/home/rcgimple/anaconda3/envs/ctat-mutations/bin:/home/rcgimple/anaconda3/condabin:/opt/openmpi/intel/ib/bin:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/bin/intel64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/sdsc/bin:/opt/sdsc/sbin:/opt/gold/bin:/opt/gold/sbin:.:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/home/rcgimple/bin:/home/rcgimple/anaconda3/envs/ctat-mutations/bin/picard:/home/rcgimple/anaconda3/envs/ctat-mutations/bin/picard/picard.jar', 'CreateSequenceDictionary', 'R=', '/home/rcgimple/scratch/STAR-Fusion-Files/GRCh38_gencode_v32_CTAT_lib_Dec062019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa', 'O=', '/home/rcgimple/scratch/STAR-Fusion-Files/GRCh38_gencode_v32_CTAT_lib_Dec062019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.dict', 'VALIDATION_STRINGENCY=LENIENT']' returned non-zero exit status 1.

Could you please suggest a way to fix this? It would be great if the "ctat-mutation-lib-integration.py" script could be included in the Conda package so there wouldn't be issues with file paths or the need to download multiple software components from multiple websites.

Thanks, Ryan

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ryangimple commented 4 years ago

I am trying to use the program through Singularity, but get the following message: ERROR : Unknown image format/type: ctat_mutations.v2.4.0.simg ABORT : Retval = 255

Could you let me know if there is a good way to fix this? Perhaps I can import from the docker image?

Thanks, Ryan

ryangimple commented 4 years ago

I was able to rebuild the singularity image by importing from docker. For future reference, this may be a useful way to run the CTAT-mutations pipeline: To install using Singularity:

  1. Load the Singularity Module
  2. Use the Pull command to generate a singularity image: "singularity pull docker://trinityctat/ctat_mutations"
  3. Run CTAT-Mutations with the following script: singularity exec -e -B [PATH-TO-YOUR-RAW-DATA] :/data \ -B [PATH-TO-YOUR-CTAT-GENOME-LIBRARY:/ctat_genome_lib_dir:ro \ ctat_mutations.simg \ /usr/local/src/ctat-mutations/ctat_mutations \ --left /data/[NAME-OF-YOUR-FASTQ-1-FILE \ --right /data/[NAME-OF-YOUR-FASTQ-2-FILE \ --out_dir /data/NAME-OF-YOUR-OUTPUT-DIRECTORY \ --threads 10 \ --genome_lib_dir /ctat_genome_lib_dir
brianjohnhaas commented 4 years ago

Thanks for letting us know about the problem. I'm not sure why the image we provide wasn't working for you, but I'm glad you were able to build one directly successfully. I've added a note to our Singularity page now for how you can do this build directly: https://github.com/NCIP/ctat-mutations/wiki/ctat_mutations_docker_singularity

many thx,

~brian

On Fri, Apr 3, 2020 at 3:56 PM ryangimple notifications@github.com wrote:

I was able to rebuild the singularity image by importing from docker. For future reference, this may be a useful way to run the CTAT-mutations pipeline: To install using Singularity:

  1. Load the Singularity Module
  2. Use the Pull command to generate a singularity image: "singularity pull docker://trinityctat/ctat_mutations"
  3. Run CTAT-Mutations with the following script: singularity exec -e -B [PATH-TO-YOUR-RAW-DATA] :/data -B [PATH-TO-YOUR-CTAT-GENOME-LIBRARY:/ctat_genome_lib_dir:ro ctat_mutations.simg /usr/local/src/ctat-mutations/ctat_mutations --left /data/[NAME-OF-YOUR-FASTQ-1-FILE --right /data/[NAME-OF-YOUR-FASTQ-2-FILE --out_dir /data/NAME-OF-YOUR-OUTPUT-DIRECTORY --threads 10 --genome_lib_dir /ctat_genome_lib_dir

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/51#issuecomment-608630019, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXYV22G7RZFI6O3B5YDRKY5O3ANCNFSM4L3DDLUQ .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

ryangimple commented 4 years ago

For the CTAT-mutation-libary-integration script, it is necessary to run the following script, which is different than that shown on the documentation webpage:

singularity exec -e -B [PATH-to-your-ctat_genome_lib_build_dir]:/data [PATH-to-CTAT-Singularity-CTATmutation-Image].simg /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py --genome_lib_dir /data

The important missing part is that the path the the ctat-genome-lib-build directory must be linked to a "data" directory within the Singularity image.

brianjohnhaas commented 4 years ago

Hi,

You'd have to run the integration step somehow.... If you're running it in singularity, you can mount it as any directory name you want (instead of /data) but you have to give the path to it as one of the parameters so it'll find it.

~b

On Sun, Apr 5, 2020 at 1:53 PM ryangimple notifications@github.com wrote:

For the CTAT-mutation-libary-integration script, it is necessary to run the following script, which is different than that shown on the documentation webpage:

singularity exec -e -B [PATH-to-your-ctat_genome_lib_build_dir]:/data [PATH-to-CTAT-Singularity-CTATmutation-Image].simg /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py --genome_lib_dir /data

The important missing part is that the path the the ctat-genome-lib-build directory must be linked to a "data" directory within the Singularity image.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/51#issuecomment-609456055, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3ANRHGBE65HPW3EUDRLDAPZANCNFSM4L3DDLUQ .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas