Henri

I ended up doing this, concatenating all R1 files into a single R1 file. and for R2 the same. pigz -cd fw*.fastq.gz |awk '{print (NR%4 == 1) ? "@" ++i...

Just a dumb question, you sure you removed all the previous output? If so, look at the headers yourself first in the working directory. On Sat, 26 Jun 2021, 02:32...

I posted the complete list of the files in my post, I just checked again. Here are some contents of files in the update_misc/pasa folder: └─ $ ▶ head /update_misc/pasa/pasa_killer.input...

I ran the command separately, and that does reveal a new error: ``` .... * [Mon Jul 5 07:55:49 2021] Running CMD: /venv/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi -G /dev/shm/funannotate_tmp_plant/funannotate/update_misc/genome.fa --CPU 1 -M 'plant_softmasked_copy_pasa' >...

I often get thousands of contigs with plants, even those with n50 in tens of mB's. And in my experience, only the minus L parameter for purging has a significant...

In my case actually all plant assemblies resulted in plastid contigs, although the chloroplast always end up in 10-1000 copies. The cp is almost always 150kb, but most contigs are...

I would make a kmer plot of your hifi data first. I think this should always be done, users should see already peaks at expected coverage prior running hifiasm. Genomscope...

I am surprised that genomescope was able to fit the model at all, I think you can ignore the predicted genome sizes, since you do not see a clear peak(s)....

Could it be an alignment issue in this view? The AT from the duplex fits with read2 revcomp a bit to the right. Without seeing more bases to the right,...