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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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EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt" #87

Open YingYa opened 3 years ago

YingYa commented 3 years ago

Hi

ctat_mutations.v3.0.0.simg used with GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play is giving the EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"

which ctat genome lib should I use with ctat_mutations.v3.0.0.simg

Thanks

joshua-gould commented 3 years ago

STAR version v2.7.2b is included in the image. Either https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.8/ or https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.9/ will work ( https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix ).

On Mon, Mar 29, 2021 at 3:50 AM YingYa @.***> wrote:

Hi

ctat_mutations.v3.0.0.simg used with GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play is giving the EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"

which ctat genome lib should I use with ctat_mutations.v3.0.0.simg

Thanks

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YingYa commented 3 years ago

Could the "ctat_mutations.v3.0.0.simg" image adapt with bam form STAR-Fusion Release v1.10.0 that aligned by STAR 2.7.8a with __genome_libs_StarFv1.10? Or I could replace the STAR v2.7.2b of ctat_mutations.v3.0.0.simg by STAR 2.7.8a to use __genome_libs_StarFv1.10?

joshua-gould commented 3 years ago

If you have an already aligned bam file, then you can use the --bam flag to provide that bam with the updated genome lib.

On Mon, Mar 29, 2021 at 11:13 AM YingYa @.***> wrote:

Could the "ctat_mutations.v3.0.0.simg" image adapt with bam form STAR-Fusion Release v1.10.0 that aligned by STAR 2.7.8a with __genome_libs_StarFv1.10? Or I could replace the STAR v2.7.2b of ctat_mutations.v3.0.0.simg by STAR 2.7.8a to use __genome_libs_StarFv1.10?

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