-
I tried to run the example data provided in the git repo and got the following error. I am using the trinityfusion.v0.4.0.simg.
* Running CMD: /usr/local/bin/STAR --runThreadN 4 --genomeDir /mn…
-
`/DATA1/Softwares/CTAT-SPLICING.v0.0.3.FULL/CTAT-SPLICING.v0.0.3/STAR_to_cancer_introns.py --SJ_tab_file ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA_star_SJ.out.tab --chimJ_file ./0710-0496_10_R1_RNA/0…
-
Hello,
I am trying to run CTAT mutations to find variants in my RNA-seq patient samples using singularity in a high performance cluster. I have not been able to run the test or any sample, could you…
-
[1-ERROR]
_____________________________________________
CMD: **annotate_with_cravat**: **oc** run \~/Pipline/Hematological_Disease/Fastqs/NDX551335/20240802_E200019755_BeiJingDiAnT7_C_1/00.mergeRawF…
-
I am running Docker to create a new CTAT resource lib. Here is my command:
```
docker run -v `pwd`:/data --rm trinityctat/starfusion /bin/bash -c "chmod 770 /usr/local/src/STAR-Fusion/ctat-genome-…
-
i am seeing the error:
```
Error, cmd: bash -c "set -euxo pipefail; cat /refbuild/GRCh37/starfusion/../annotation/Homo_sapiens.GRCh37.75.gtf | egrep 'IG_V_gene|IG_C_gene|IG_D_gene|IG_J_gene' | awk '…
-
### Description of feature
https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/VirusInsertionFinder/ctat_vif.v1.0.1.simg
We just threw the docker image in.
-
The Intro to Stats course contains CTAT activity instances that the digest tool does not handle correctly. While the digest tool will successfully convert the course and create a digest, the ingest i…
-
Hi, I am running the CTAT-mutations (v3.2.0) pipeline, the library version is StarFv1.10. I used the commamd:
$ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15 \
--genome_lib_dir ~/…
-
I'm running the CTAT-mutations pipeline, and I get the following warning messages that appear during the SNP-eff step. The script stops running at this point, even though I have allocated 50 hours of …