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Hello!
I'm trying to run optitype in the cloud in a machine with 64GB of RAM with RNA Samples that are around 5GB each due to it being paired end. And the process is killed because it runs out of mem…
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Hello,
Optitype package (toolshed.g2.bx.psu.edu/repos/jjohnson/optitype/optitype/1.3.2) was installed into a local galaxy server from the toolshed. It was run on the paired-end data in the DNA mode…
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https://github.com/genome/docker-immuno_tools-cwl/blob/ef53b1e390a52280b362cd8a62237cd210ff4b71/optitype_script.sh#L55
Currently, our script provides 2 fastq files to Optitype as input, which resul…
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I'm running OptiType through a docker container (set up with 16GB memory on a 32GB Mac), and the initial mapping steps on my paired-end FASTQ data is failing, I suspect due to memory:
$ docker …
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When I use `hlarp` to compare HLA type from different samples for the same patient, I get output for each sample name separately. Is there a way to force `hlarp` to ignore the sample description in th…
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```
0:00:00.56 Mapping dry_run_1_XT-NORMAL-R1-cat.fastq to GEN reference...
(' Signal handler called from ', 'subprocess.py', '_eintr_retry_call', 476)
(' Waiting...',)
(' Signal', 15, 'recieved, b…
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After #423 is done, we can consider using a better aligner that doesn't suffer from the following:
> You can use any read mapper to do this step, although we suggest you use RazerS3. Its only drawb…
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conda create -n optitype python=2.7.3
conda install -n optitype -c bioconda optitype
conda activate optitype
bam=/home/ry/analysis/data/optitype/bam
raw=/home/ry/analysis/data/optitype/raw
fastq=…
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```
$ razers3 --help
Illegal instruction
```
See https://github.com/FRED-2/OptiType/issues/90
Downgrading to an older version helps. Not sure what the problem is.
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I'm getting the following error message. Any idea what is causing it?
```
mapping with 8 threads...
0:01:18.24 Mapping filtered_fished.fastq to GEN reference...
0:01:45.95 Generating binar…