husamia

I think you might be better off building it yourself with index_gff and download the gff3 from the table browser. And may not work on entire genome due to issues,...

How about we suggest in the specifications a reference to the source of the base calls such as the software release date, training model, and instrument?

The source is not required at the moment. In the example is in silico source i.e. program. but for example if the caller is detecting somatic variants in cancerous tissue...

> Hi husamia, > > Based on your log, the index file you downloaded seems to be incomplete! > > The reference size is 4354060288 in your log which should...

> If you are using linux cmd line, you can use below command to download large file. > > * -c option restarts download from where it stopped., -T is...

Thanks. The file Homo_sapiens_assembly38.fasta.suffixarray_uint64_L0_PARAMETERS URL isn't listed in the downloads but I downloaded it anyway. I am having alot of trouble getting Docker to run on the Apple M Studio....

> Are you still having other seg fault problem even though you have the valid index files? I guess it should have resolved the issue. > > Based on what...

I am not getting segmentation fault. your right it was the files incomplete. but I am now trying to figure out why it's getting killed ``` # time bwa-meme mem...

cat output_dir_full/logs/L1522785992-normal.validate.snakemake.batch-39.log.txt ``` `2022-05-26 21:00:07,691 [INFO] MAVIS: 3.0.0 2022-05-26 21:00:07,692 [INFO] hostname: 7aa05bbe492b 2022-05-26 21:00:07,692 [INFO] arguments 2022-05-26 21:00:07,692 [INFO] command= 'validate' 2022-05-26 21:00:07,692 [INFO] config= '/app/mavis/output_dir_full/config.json' 2022-05-26 21:00:07,692 [INFO]...

I tested this model with the free Google colab GPU with latest guppy and it worked great. Saved me so much time. Here is a guide [https://gist.github.com/sirselim/13f70ae69f2a512e7d9e1f00f9704f53](url)