The bioBakery help forum

Error in filter_and_trim.R from biobakery_workflows 16s

hi, I’m trying to run a conda installation of biobakery_workflows,

biobakery_workflows 16s --input a --output tmp --method dada2 --dada-db gg --bypass-primers-removal

and getting the following errors… thanks for any suggestions!

raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `/gpfs/fs1/sfw2/biobakery/b1/lib/python3.9/site-packages/biobakery_workflows/Rscripts/filter_and_trim.
R --input_dir=a --output_dir=tmp --filtered_dir=filtered_input --maxee=1 --trun
c_len_max=200 --readcounts_tsv_path=/gpfs/fs2/scratch/hstern2/c/raw_data/tmp/Read_counts_after_filtering.tsv --readcounts_
rds_path=/gpfs/fs2/scratch/hstern2/c/raw_data/tmp/Read_counts_filt.rds --reads_plotF=/gpfs/fs2/scratch/hstern2/c/raw_data/tmp/FWD_read_p
lot.png --reads_plotR=/gpfs/fs2/scratch/hstern2/c/raw_data/tmp/REV_read_plot.png --pair_id=_R1_001 --threads
=1’ failed.

Err:

Loading required package: Rcpp

Error in $<-.data.frame(*tmp*, “minScore”, value = Inf) :

replacement has 1 row, data has 0

Calls: → $<- → $<-.data.frame

In addition: Warning message:

In min(anndf$minScore) : no non-missing arguments to min; returning Inf

Execution halted

Hello, Thank you for including the traceback error message. If your DADA2 method run fails in the filter and trim portion of the workflow it is likely due to the length or quality of the reads. I would first check to make sure that your fastq files don’t contain any reads of < 10nt in length. If that is not the case then try adjusting the --trunc-len-max <200> option to fit the length of your reads.

Thank you,
Lauren