RuntimeError

[pengxi1209]

Hello, when I was using OncodriveFML with hg19 as the reference, I encountered an error: "RuntimeError: Sequence 'UN_GL000228' not found in genome build 'hg19' (/datasets/genomereference/hg19-20190201/UN_GL000228.txt)". How can I resolve this issue?
my code is oncodrivefml -i paad.txt.gz -e cds.tsv.gz -s wgs -c oncodrivefml_v2.conf -o result --force

[pengxi1209]

Additionally, could you please tell me how to obtain the hg38 cds.tsv.gz file? I couldn't find it on UCSC or Ensembl.

[FedericaBrando]

Hi, could you try re-download the genome reference with the following steps:

1. Remove the ~/.bgdata folder
2. Downloading the cadd scores:

   bgdata get genomicscores/caddpack/1.0

3. Downloading the genome reference:

   bgdata get datasets/genomereference/hg19

4. export BGDATA_LOCAL=~/.bgdata and BGDATA_OFFLINE=TRUE environment variables
5. run the example.

Additionally, could you please tell me how to obtain the hg38 cds.tsv.gz file? I couldn't find it on UCSC or Ensembl.

You can build it yourself, following this structure https://oncodrivefml.readthedocs.io/en/latest/files.html#regions-file-format and pass it to OncodriveFML.

[pengxi1209]

Thank you very much for your patient answer. I downloaded the CADD score and genomereference/hg19 and hg38 correctly, and successfully ran the example to obtain the result file(ex_paad-oncodrivefml.html; ex_paad-oncodrivefml.png; ex_paad-oncodrivefml.tsv.gz).

However, when running my own data, it was not smooth. Since my paad.txt.gz is based on hg38, I need the cds.tsv.gz of hg38. I have carefully read the detailed information about each column in the file format in the link you sent me before, but I still don't know how to obtain the data for each column.

I tried to select "Chromosome/scaffold name" "Gene start (bp)" "Gene end (bp)" "Gene stable ID" "Gene name"
in the ensemble database and built a list of more than 70000 rows, while your example 'cds.tsv.gz' of hg19 has 200000 lines, so when I run it with the cds.tsv.gz of hg38, which has over 70000 lines, many warnings appear: "background mismatch at position xxxx", and ultimately, no result file similar to the example was obtained.