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Hi,
First of all, thank you for this wonderful tool.
I used CTAT_Mutations v3.2.0 in Conda environment and I am wondering why 'subprocess.CalledProcessError' is happening.
the command line is:
…
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Hi,
After downloading the library and the supplementary library as instructed in the wiki, I tried to run (see command below) and I got a segmentation fault regarding a missing file (see below) Howev…
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Hi,
I am building a custom genome library for GENCODE ver 36. However, I encountered a problem that indicates there's no "gencode.v36.annotation.gtf.revised.custom.gtf".
I used the latest docker…
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Hi,
is the plug'n play variant of the library available for gencode v44 somewhere or is a manual build the only alternative?
thanks
koen.
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Hi,
I was running the software according to the wiki but realized that the --ctat_genome_lib argument is missing from the example :) No issue with running the program, just thought that it should b…
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Hello,
I am now using AWS EC2 server and docker as well, pull the image (+build dockerfile), and used the command like below.
docker run --rm -v /home/ec2-user/ctat/testing:/data -v /home/ec2-us…
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Hi,
I try to run ctat-mutations on your test samples at our server using singularity script, I got the error below.
My server admin said the error is from the singularity container. Could you ple…
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Hi,
I am running the latest version of your pipeline (3.3.1) and it got stuck in a couple of occasions.
The most relevant, for the moment, is the Annotate CRAVAT, since cravat is reporting an erro…
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Hi!
I am executing the the mutation lib integration utility using the singularity image `ctat_mutations.v3.0.1.simg`.
I used the command:
`singularity exec -e -B /home/RNAseq_project/trinity_ca…
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Hi,
I tried to run STAR-Fusion using docker.
I entered command lines as below on Mac terminal.
Fastqfiles and GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz file are in the same directo…