tetedange13

Hi @drpatelh, Thanks a lot for `viralrecon` ! I recently found out I could have the use of such option to hard-clip primers and my case is a bit similar...

Hi @drpatelh, Yup, for what I saw produced FASTQ are identical with both `fgbio ClipBam` and `ngsutilsj` Just to precise Peter's implementation, I could not manage to make `fgbio` **v2.0.1**...

Hi @chriswyatt1 , Yep sorry I messed up with my different versions, but I confirm that **this issue occurs well with v2.5 too** => I actually use `viralrecon-2.4` in production,...

Hi @ashbig, Not an author of CNVkit, but indeed it looks like a segmentation failure To be sure I well understood your case: * You are expecting an amplification of...

Hi @HeejunJang, In my experience this is due to conda struggling to find compatible packages within a single channel 1. What is your conda version (output of `conda --version`) 1....

Hi @jlchen5, It is better to install CNVkit inside its own fresh _conda_ environment => Try : `conda install -n cnvkit -c conda-forge -c bioconda cnvkit` Your error is probably...

Hi @CKZan , Are you really running CNVkit v0.9.1? => It is currently at v0.9.9, so please update and see if you still got this issue ? Hope this helps...

Hi @CKZan, Thanks for updating ! If I understand correctly : 1. Your initial issue was that you got "excessive loss call" => What do you mean by that ?...

Hi @etal, I already had a branch adressing this on my fork of CNVkit, I will submit a PR as soon as possible ! Have a nice day. Felix.

This adress #666 too (even if already closed) Kind regards, Felix.