Khi Pin, Chua

@atfdh By any chance the primers are already removed in your reads? I'm assuming these are standard F27 and R1492 primers for full-length 16S?

Thanks @roylejw . Will file this under enhancement. The picrust2 part is definitely an oversight as I don't test skip_nb with picrust. Thanks for catching that.

Hi @LuyangSong please open a separate ticket for this issue and share `.nextflow.log` for troubleshooting. Thank you.

Thanks @splaisan for reporting this!

Hi @ewissel , did you mean that you ran the same exact command, but with different samples and it's causing the error? Can you go into the directory `/ceph/.../all_raw_fqs/work/85/3a3d48e4f5f3e45d5fe4deb0ae1aee` and...

@ewissel You run the `bash .command.run` command in the work folder, not the `nf_conda` folder. ``` cd /ceph/.../all_raw_fqs/work/85/3a3d48e4f5f3e45d5fe4deb0ae1aee conda activate $HOME/nf_conda/*qiime* bash .command.run ``` To verify if the soft-links exist,...

@ewissel , I am confused. You said the command output nothing, but the following messages: ``` ls: cannot access /ceph/.../emily/databases/GTDB_bac120_arc53_ssu_r207_fullTaxo.fa.gz: No such file or directory ls: cannot access /ceph/.../emily/databases/RefSeq_16S_6-11-20_RDPv16_fullTaxo.fa.gz: No...

Did you modify the path names manually? In the last comment the Silva database has a path of `/ceph/sharedfs/.../emily/databases/silva_nr99_v138.1_wSpecies_train_set.fa.gz` whereas all the other databases files are in `/ceph/.../emily/databases/` (No `sharedfs`)....