Triplet NAA not found

[Babita Singh]

Hi Loris,

I am getting this warning message and there is no output file generation. I am attaching the log file created and following is the log displayed on terminal:

13:10:13 INFO: Using HG19 as reference genome
13:10:13 INFO: Running analysis
Parsing elements 'annotation.bed':
 100% 181370/181370
 [00:12<00:00, 14829.24it/s]
13:10:53 INFO: Mapping mutations
* [0 muts]
********** [1000000 muts]
********** [2000000 muts]
********** [3000000 muts]
********** [4000000 muts]
********** [5000000 muts]
********** [6000000 muts]
********** [7000000 muts]
*          [7194736 muts]
13:16:23 INFO: Using precomputed signatures
13:16:23 INFO: Correcting signatures
13:16:23 WARNING: Triplet NAA not found
13:16:23 WARNING: Triplet NAA not found
13:16:23 WARNING: Triplet NAA not found
13:16:23 INFO: Pickles generated. Exiting

I am using following command to run:

oncodrivefml -i $src_path/mutations.tab -e $src_path/annotation.bed --type noncoding --sequencing wgs -o output_dir/ --no-indels

Can you please suggest what could be the error?

Thanks, Babita

[Iker]

The warning is because we do not have a precomputed value for that triplet. However, of your mutations has that context.

I am not sure why you do not have any output. Are you also passing the --generate-pickle flag?