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