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

[YingYa]

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]

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 ).

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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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#87>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABH6THZHHXPGUQQHAKYUVZTTGAWNLANCNFSM4Z7CBCWA> .

[YingYa]

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]

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

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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? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#87 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABH6THYX3PXZUBVNHVWZFEDTGCKKZANCNFSM4Z7CBCWA> .