abundance | samtools view: failed to add PG line to the header about metagem HOT 2 OPEN

Hi Kunal, thanks again for reporting this issue and apologies for my delay in responding.

I believe that this problem occurs due to the fact that contig headers are not guaranteed to be unique across MAGs. It is unlikely, but evidently it is possible that two different contigs are assembled with the same node_length_coverage values across different genomes from the same sample, in which case you will see those errors you have reported.
I will have to think about the best way to deal with this in the future, but for now you can simply add a unique MAG ID at the start of each contig header when concatenating MAGs to avoid this issue.

Instead of using cat, use a loop to append MAG ID at the start of each contig e.g. assuming your mags for a given sample are in subfolder mags with .fa extension:

ls mags|grep ".fa"|while read genome;do paste mags/$genome| sed "s/>/>${genome%.*}_/g";done > sample.fa

Best wishes,
Francisco

from metagem.

Hi Francisco,

Thank you very much for your reply and the detailed explanation.
Thanks a lot
Kunal

from metagem.