imielinski
commented
1 year ago Hi – sorry about this, can you try with this is a known issue with the syntax of the base aggregate function changing in R 4.2 in a bit of a non-backward compatible way.
Can you try with R 4.1 or earlier? We have to update our code to be compatible with R 4.2 but unfortunately this issue affects several parts of our code base.
Marcin
Running: jba manta/manta.tumor.svs.hg38.vcf cov.rds --field ratio --purity 0.7 --outdir $PWD/jabba --name test --cores 8 --gurobi TRUE The cov.rds file contains the column ratio which is the ratio of the fragCounter values for tumor/normal.
After about 2h it produces the error: . .. . JaBbA 2023-02-16 22:28:39: Number of gaps with nonzero width: 12516 JaBbA 2023-02-16 22:28:39: Number of segments before gap filtering: 14982 JaBbA 2023-02-16 22:28:40: 5987 segments produced after gap filtering JaBbA 2023-02-16 22:28:40: creating karyograph JaBbA 2023-02-16 22:30:03: WARNING: big karyograph > 50000 nodes, may take longer to finish. JaBbA 2023-02-16 22:30:41: Definining coverage good quality nodes as >=50% bases covered by non-NA and non-Inf values in +/-100KB region JaBbA 2023-02-16 22:30:41: Hard setting 58.258246 Mb of the genome to NA that didn't pass our quality threshold JaBbA 2023-02-16 22:30:41: Using loess to fit mean to variance relationship in segments with greater than 1 bins JaBbA 2023-02-16 23:10:31: Using ppgrid to estimate purity ploidy JaBbA 2023-02-16 23:10:31: setting up ppgrid matrices ..
.. . JaBbA 2023-02-16 23:11:36: Built gGraph with 1181150 nodes, 1759858 edges, purity 0.7, and ploidy 1.25 Error in aggregate.formula(...) : argument 'x' is missing -- it has been renamed from 'formula' Calls: suppressPackageStartupMessages ... vaggregate -> aggregate -> aggregate -> aggregate.formula In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted I have tried with different purities an different variations of the cov.rds file but the error is the same R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting" Thanks in advance for your help
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
--
This message is for the recipient’s use only, and may contain confidential, privileged or protected information. Any unauthorized use or dissemination of this communication is prohibited. If you received this message in error, please immediately notify the sender and destroy all copies of this message. The recipient should check this email and any attachments for the presence of viruses, as we accept no liability for any damage caused by any virus transmitted by this email.
Running:
The cov.rds file contains the column
ratiowhich is the ratio of the fragCounter values for tumor/normal.After about 2h it produces the error:
I have tried with different purities an different variations of the cov.rds file but the error is the same
Thanks in advance for your help