Alexandros Vasilikopoulos comments

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                                            Alexandros Vasilikopoulos

ERROR: ID=FUN_003286 has no CDS features, removing gene model

Hi I am having the same issue (key error in funannotate update) and I tried to see if the error is fixed but I get another error. I installed the...

ERROR: ID=FUN_003286 has no CDS features, removing gene model

Problem fixed. Thanks!

Restart after crash of the PASA training terminates normally

Where is this PASA log file located in the directory structure? Its name? thanks

Restart after crash of the PASA training terminates normally

Ok so here are the last lines of the /training/pasa/pasa-assembly.log: ``` [Thu Sep 15 11:32:25 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/extract_FL_transdecoder_entries.pl trinity.fasta.clean.transdecoder.gff3 > trinity.fasta.clean.transdecoder.gff3.fl_accs [Thu Sep 15 11:32:26 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/update_fli_status.dbi...

Bcftools norm prints only the header

this was caused by wrong input vcf

Bcftools norm prints only the header

Hello, I tested again and indeed there seems to be an issue that is only for one of my 2 test cases though. This is running in a pipeline in...

Adding functional annotation to reduced gff3 file

Hello, thanks for your reply. The problem is that I only have a modified gff and corresponding assembly fasta. however, the "funannotate predict" script requires the whole output dir of...

Sambamba slice - 94 Segmentation fault (core dumped)

I ended up using ```sambamba view``` instead ..

Difference between --atom-overlaps and --multi-overlaps

I assume that the dot then means something unknown but by definition different than 1 since otherwise it would not appear as a variant. From what I understand when splitting...