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

[jbeane0428]

Hi, I'm using ctat_mutations.v3.0.0.simg and GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play and I get the following error: EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"

Can you please tell me how to fix this issue? Thank you.

[brianjohnhaas]

Hi,

Because of the timing of the release, v3.0.0 works with the earlier version of the ctat genome lib here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.9/

we added a note in the release page for it: https://github.com/NCIP/ctat-mutations/releases/tag/v3.0.0

best,

~b

On Wed, May 19, 2021 at 10:28 AM jbeanelab @.***> wrote:

Hi, I'm using ctat_mutations.v3.0.0.simg and GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play and I get the following error: EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"

Can you please tell me how to fix this issue? Thank you.

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[ConcettaDe4]

Hi! I had the same error using the singularity image ctat_mutations.v3.0.1.simg and the genome folder GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play. The error is the following:

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"
SOLUTION: use correct parameter name (check the manual)

May 24 14:44:09 ...... FATAL ERROR, exiting

Can you please help me to fix this issue?

Thank you.

Concetta

[brianjohnhaas]

Hi Concetta,

Because of the timing of the release, it uses the earlier version of the ctat genome lib. Please see info here: https://github.com/NCIP/ctat-mutations/releases/tag/v3.0.0

best,

~b

On Mon, May 24, 2021 at 10:49 AM ConcettaDe4 @.***> wrote:

Hi! I had the same error using the singularity image ctat_mutations.v3.0.1.simg and the genome folder GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play. The error is the following:

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt" SOLUTION: use correct parameter name (check the manual)

May 24 14:44:09 ...... FATAL ERROR, exiting

Can you please help me to fix this issue?

Thank you.

Concetta

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[ConcettaDe4]

Hi, Thank you. I am downloading the GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play.tar.gz file. Is that correct? I have already run STAR-Fusion using the GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play, do you suggest to re-run with the new genome folder?

In addition, which the differences between the two genome version?

[brianjohnhaas]

The main difference here just has to do with the version of STAR that the different singularity images are configured for. It's fine to use one for STAR-F and the other for CTAT Mutations for the moment.

In the future, we'll try to better synchronize the various releases to avoid this issue.

best,

~b

On Mon, May 24, 2021 at 11:15 AM ConcettaDe4 @.***> wrote:

Hi, Thank you. I am downloading the GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play.tar.gz file. Is that correct? I have already run STAR-Fusion using the GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play, do you suggest to re-run with the new genome folder?

In addition, which the differences between the two genome version?

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[ConcettaDe4]

OK! I have one more question, it seems that the GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play.tar.gz library have the latest genome release, that is gencode version 33 compared to the other library. It is right? If yes, it is the same also for the fusion_annot_lib.gz?

[brianjohnhaas]

I don't think the fusion_annot_lib has changed in a while. I might update it in the next release.

Note, the latest genome annotations are always supported when we make the release, but our routine use is with hg19/gencodev19 and hg38/gencodev22 - and I'd recommend using one of these for your routine use unless you absolutely need to have the latest annotations.

best,

~b

On Mon, May 24, 2021 at 11:40 AM ConcettaDe4 @.***> wrote:

OK! I have one more question, it seems that the GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play.tar.gz library have the latest genome release, that is gencode version 33 compared to the other library. It is right? If yes, it is the same also for the fusion_annot_lib.gz?

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[ConcettaDe4]

OK! thank you for help and your suggest.

Best,

Concetta