abooker10 commented 1 year ago

Hi dada2 team-

Thank you for creating with workflow! I am trying to use dada2 to analyze 18S PacBio data. I edited the dada2_pacbio18S.yaml and job_submission.sh file to my specific locations on Charlie.

`#!/usr/bin/bash

PBS -N run_dada2_pipeline

PBS -q devel

PBS -l ncpus=4,mem=5gb

PBS -l walltime=2:00:00

PBS -M abooker@bigelow.org

PBS -m abe

module load dada2 data_path=/mnt/storage/labs/martinez_nfs/ECOHAB_Kb_virus/Data/PacBio/Kb_stocks_lysates_18S Rscript $data_path"/dada2_pacbio.R" $data_path"/dada2_pacbio18S.yaml" `

When I run the above script I get an error output Error: unexpected '{' in: " # input basenames - so all we need to do is match fq_files <- sapply(names(fq_files){" Execution halted

Full error file attached. run_dada2_pipeline.e2671544.txt

Any suggestions on how to resolve the error? Here is the edited yaml file I am using. dada2_pacbio18S.yaml.txt

Thanks for any input, Anne

btupper commented 1 year ago

Perhaps we should dial up a zoom session. It's hard to discern what the issue is from the traceback of the error.

abooker10 commented 1 year ago

A zoom session works for me. I can meet Wed (11/8) anytime before 11:15am and after 1pm. Or I can meet Thursday (11/9) anytime before 1pm and after 3:30pm.

thank you! Anne