# Single-end biobakery\_16S workflow

**URL:** <https://forum.biobakery.org/t/single-end-biobakery-16s-workflow/3140>\
**Category:** bioBakery workflows\
**Created:** [February 16, 2022, 1:55pm UTC](https://forum.biobakery.org/t/single-end-biobakery-16s-workflow/3140 "2022-02-16T13:55:27Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![kennyyeo13](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kennyyeo13/32/1171_2.png) [@kennyyeo13](https://forum.biobakery.org/u/kennyyeo13)\
**Post date:** [February 16, 2022, 1:55pm UTC](https://forum.biobakery.org/t/single-end-biobakery-16s-workflow/3140/1 "2022-02-16T13:55:27Z")

</div>

Hi, I am having trouble running single-end data using biobakery\_workflows 16s. I was wondering if it is because of the file identifier. How do I specify that my files are single-ended?

This is the anadama.log

2022-02-17 00:18:41,588 LoggerReporter started INFO: Beginning AnADAMA run with 10 tasks.  
2022-02-17 00:18:41,591 LoggerReporter started INFO: Workflow description = A workflow for 16S sequencing data  
2022-02-17 00:18:41,591 LoggerReporter started INFO: Workflow version = 0.1  
2022-02-17 00:18:41,591 LoggerReporter started INFO: Workflow configuration options  
2022-02-17 00:18:41,591 LoggerReporter started INFO: method = dada2  
2022-02-17 00:18:41,591 LoggerReporter started INFO: dada\_db = gg  
2022-02-17 00:18:41,591 LoggerReporter started INFO: usearch\_db = /Users/kennyyeo/biobakery\_workflows\_databases/green\_genes\_fasta\_db/97\_otus.fasta,/Users/kennyyeo/biobakery\_workflows\_databases/green\_genes\_taxonomy\_db/97\_otu\_taxonomy.txt  
2022-02-17 00:18:41,591 LoggerReporter started INFO: bypass\_functional\_profiling = False  
2022-02-17 00:18:41,592 LoggerReporter started INFO: barcode\_file =  
2022-02-17 00:18:41,592 LoggerReporter started INFO: dual\_barcode\_file =  
2022-02-17 00:18:41,592 LoggerReporter started INFO: input\_extension = fastq.gz  
2022-02-17 00:18:41,592 LoggerReporter started INFO: threads = 5  
2022-02-17 00:18:41,592 LoggerReporter started INFO: pair\_identifier = \_R1\_001  
2022-02-17 00:18:41,592 LoggerReporter started INFO: index\_identifier = \_I1\_001  
2022-02-17 00:18:41,592 LoggerReporter started INFO: min\_pred\_qc\_score = 15  
2022-02-17 00:18:41,592 LoggerReporter started INFO: maxee = 1  
2022-02-17 00:18:41,593 LoggerReporter started INFO: trunc\_len\_max = 200  
2022-02-17 00:18:41,593 LoggerReporter started INFO: min\_size = 2  
2022-02-17 00:18:41,593 LoggerReporter started INFO: bypass\_primers\_removal = False  
2022-02-17 00:18:41,593 LoggerReporter started INFO: fwd\_primer = ACACTGACGACATGGTTCTACAAGAGTTTGATCCTGGCTCAG  
2022-02-17 00:18:41,593 LoggerReporter started INFO: rev\_primer = TACGGTAGCAGAGACTTGGTCTATTACCGCGGCTGCTGG  
2022-02-17 00:18:41,593 LoggerReporter started INFO: minoverlap = 20  
2022-02-17 00:18:41,593 LoggerReporter started INFO: maxmismatch = 0  
2022-02-17 00:18:41,594 LoggerReporter started INFO: percent\_identity = 0.97  
2022-02-17 00:18:41,594 LoggerReporter started INFO: bypass\_msa = False  
2022-02-17 00:18:41,594 LoggerReporter started INFO: picrust\_version = 1  
2022-02-17 00:18:41,594 LoggerReporter started INFO: output = /Volumes/Seagate/16S\_analysis/done/PRJNA587786/output3  
2022-02-17 00:18:41,594 LoggerReporter started INFO: input = /Volumes/Seagate/16S\_analysis/done/PRJNA587786/fastq\_16s  
2022-02-17 00:18:41,594 LoggerReporter started INFO: config = None  
2022-02-17 00:18:41,594 LoggerReporter started INFO: jobs = 1  
2022-02-17 00:18:41,594 LoggerReporter started INFO: grid\_jobs = 0  
2022-02-17 00:18:41,594 LoggerReporter started INFO: grid = None  
2022-02-17 00:18:41,594 LoggerReporter started INFO: grid\_partition =  
2022-02-17 00:18:41,594 LoggerReporter started INFO: grid\_benchmark = off  
2022-02-17 00:18:41,594 LoggerReporter started INFO: grid\_options = None  
2022-02-17 00:18:41,595 LoggerReporter started INFO: grid\_environment = None  
2022-02-17 00:18:41,595 LoggerReporter started INFO: grid\_scratch = None  
2022-02-17 00:18:41,595 LoggerReporter started INFO: dry\_run = False  
2022-02-17 00:18:41,595 LoggerReporter started INFO: skip\_nothing = False  
2022-02-17 00:18:41,595 LoggerReporter started INFO: quit\_early = False  
2022-02-17 00:18:41,595 LoggerReporter started INFO: until\_task = None  
2022-02-17 00:18:41,595 LoggerReporter started INFO: exclude\_task = None  
2022-02-17 00:18:41,595 LoggerReporter started INFO: target = None  
2022-02-17 00:18:41,595 LoggerReporter started INFO: exclude\_target = None  
2022-02-17 00:18:41,595 LoggerReporter started INFO: log\_level = INFO  
2022-02-17 00:18:42,339 LoggerReporter log\_event INFO: task 0, filter\_and\_trim : ready and waiting for resources  
2022-02-17 00:18:42,339 LoggerReporter log\_event INFO: task 0, filter\_and\_trim : starting to run  
2022-02-17 00:18:42,339 LoggerReporter task\_command INFO: Executing with shell: /Users/kennyyeo/opt/miniconda3/lib/python3.8/site-packages/biobakery\_workflows/Rscripts/filter\_and\_trim.R --input\_dir=/Volumes/Seagate/16S\_analysis/done/PRJNA587786/fastq\_16s --output\_dir=/Volumes/Seagate/16S\_analysis/done/PRJNA587786/output3 --filtered\_dir=filtered\_input --maxee=1 --trunc\_len\_max=200 --readcounts\_tsv\_path=/Volumes/Seagate/16S\_analysis/done/PRJNA587786/output3/Read\_counts\_after\_filtering.tsv --readcounts\_rds\_path=/Volumes/Seagate/16S\_analysis/done/PRJNA587786/output3/Read\_counts\_filt.rds --reads\_plotF=/Volumes/Seagate/16S\_analysis/done/PRJNA587786/output3/FWD\_read\_plot.png --reads\_plotR=/Volumes/Seagate/16S\_analysis/done/PRJNA587786/output3/REV\_read\_plot.png --pair\_id=\_R1\_001 --threads=5  
2022-02-17 00:18:53,134 LoggerReporter task\_failed ERROR: task 0, filter\_and\_trim : Failed! Error message : Error executing action 0. Original Exception:  
Traceback (most recent call last):  
File “/Users/kennyyeo/opt/miniconda3/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally  
action\_func(task)  
File “/Users/kennyyeo/opt/miniconda3/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh  
ret = \_sh(s, \*\*kwargs)  
File “/Users/kennyyeo/opt/miniconda3/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh  
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))  
anadama2.util.ShellException: [Errno 1] Command `/Users/kennyyeo/opt/miniconda3/lib/python3.8/site-packages/biobakery_workflows/Rscripts/filter_and_trim.R --input_dir=/Volumes/Seagate/16S_analysis/done/PRJNA587786/fastq_16s --output_dir=/Volumes/Seagate/16S_analysis/done/PRJNA587786/output3 --filtered_dir=filtered_input --maxee=1 --trunc_len_max=200 --readcounts_tsv_path=/Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/Read_counts_after_filtering.tsv --readcounts_rds_path=/Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/Read_counts_filt.rds --reads_plotF=/Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/FWD_read_plot.png --reads_plotR=/Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/REV_read_plot.png --pair_id=_R1_001 --threads=5' failed. Out: b'[1] \xe2\x80\x981.22.0\xe2\x80\x99\ninput_dir \t /Volumes/Seagate/16S_analysis/done/PRJNA587786/fastq_16s \noutput_dir \t /Volumes/Seagate/16S_analysis/done/PRJNA587786/output3 \nfiltered_dir \t filtered_input \nmaxee \t 1 \ntrunc_len_max \t 200 \nreadcounts_tsv_path \t /Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/Read_counts_after_filtering.tsv \nreadcounts_rds_path \t /Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/Read_counts_filt.rds \nreads_plotF \t /Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/FWD_read_plot.png \nreads_plotR \t /Volumes/Seagate/16S_analysis/done/PRJNA587786/output3/REV_read_plot.png \npair_id \t _R1_001 \nthreads \t 5 \nSRR10418970_I1_001.fastq.gz\nSRR10418971_I1_001.fastq.gz\nSRR10418972_I1_001.fastq.gz\nSRR10418973_I1_001.fastq.gz\nSRR10418974_I1_001.fastq.gz\nSRR10418975_I1_001.fastq.gz\nSRR10418976_I1_001.fastq.gz\nSRR10418977_I1_001.fastq.gz\nSRR10418978_I1_001.fastq.gz\nSRR10418979_I1_001.fastq.gz\nSRR10418980_I1_001.fastq.gz\nSRR10418981_I1_001.fastq.gz\nSRR10418982_I1_001.fastq.gz\nSRR10418983_I1_001.fastq.gz\nSRR10418984_I1_001.fastq.gz\nSRR10418985_I1_001.fastq.gz\nSRR10418986_I1_001.fastq.gz\nSRR10418987_I1_001.fastq.gz\nSRR10418988_I1_001.fastq.gz\nSRR10418989_I1_001.fastq.gz\nSRR10418990_I1_001.fastq.gz\nSRR10418991_I1_001.fastq.gz\nSRR10418992_I1_001.fastq.gz\nSRR10418993_I1_001.fastq.gz\nSRR10418994_I1_001.fastq.gz\nSRR10418995_I1_001.fastq.gz\nSRR10418996_I1_001.fastq.gz\nSRR10418997_I1_001.fastq.gz\nSRR10418998_I1_001.fastq.gz\nSRR10418999_I1_001.fastq.gz\nSRR10419000_I1_001.fastq.gz\nSRR10419001_I1_001.fastq.gz\nSRR10419002_I1_001.fastq.gz\nSRR10419003_I1_001.fastq.gz\nSRR10419004_I1_001.fastq.gz\nSRR10419005_I1_001.fastq.gz\nSRR10419006_I1_001.fastq.gz\nSRR10419007_I1_001.fastq.gz\nSRR10419008_I1_001.fastq.gz\nSRR10419009_I1_001.fastq.gz\nSRR10419010_I1_001.fastq.gz\nSRR10419011_I1_001.fastq.gz\nSRR10419012_I1_001.fastq.gz\nSRR10419013_I1_001.fastq.gz\nSRR10419014_I1_001.fastq.gz\nSRR10419015_I1_001.fastq.gz\nSRR10419016_I1_001.fastq.gz\nSRR10419017_I1_001.fastq.gz\nSRR10419018_I1_001.fastq.gz\nSRR10419019_I1_001.fastq.gz\nSRR10419020_I1_001.fastq.gz\nSRR10419021_I1_001.fastq.gz\nSRR10419022_I1_001.fastq.gz\nSRR10419023_I1_001.fastq.gz\nSRR10419024_I1_001.fastq.gz\nSRR10419025_I1_001.fastq.gz\nSRR10419026_I1_001.fastq.gz\nSRR10419027_I1_001.fastq.gz\nSRR10419028_I1_001.fastq.gz\nSRR10419029_I1_001.fastq.gz\nSRR10419030_I1_001.fastq.gz\nSRR10419031_I1_001.fastq.gz\nSRR10419032_I1_001.fastq.gz\nSRR10419033_I1_001.fastq.gz\nSRR10419034_I1_001.fastq.gz\nSRR10419035_I1_001.fastq.gz\nSRR10419036_I1_001.fastq.gz\nSRR10419037_I1_001.fastq.gz\nSRR10419038_I1_001.fastq.gz\nSRR10419039_I1_001.fastq.gz\nSRR10419040_I1_001.fastq.gz\nSRR10419041_I1_001.fastq.gz\nSRR10419042_I1_001.fastq.gz\n[1] TRUE\n' Err: b'Loading required package: Rcpp\nError in `$\<-.data.frame`(`_tmp_`, “minScore”, value = Inf) : \n replacement has 1 row, data has 0\nCalls: → $\<- → $\<-.data.frame\nIn addition: Warning message:\nIn min(anndf$minScore) : no non-missing arguments to min; returning Inf\nExecution halted\n’

2022-02-17 00:18:53,134 LoggerReporter task\_failed ERROR: task 2, learn\_error\_rates : Failed! Error message : Task failed because parent task `0' failed 2022-02-17 00:18:53,134	LoggerReporter	task_failed	ERROR: task 3, dereplicate_and_merge : Failed! Error message : Task failed because parent task `2’ failed  
2022-02-17 00:18:53,134 LoggerReporter task\_failed ERROR: task 4, construct\_sequence\_table : Failed! Error message : Task failed because parent task `3' failed 2022-02-17 00:18:53,134	LoggerReporter	task_failed	ERROR: task 6, clustalo_nonchimera : Failed! Error message : Task failed because parent task `4’ failed  
2022-02-17 00:18:53,134 LoggerReporter task\_failed ERROR: task 8, fasttree : Failed! Error message : Task failed because parent task `6' failed 2022-02-17 00:18:53,134	LoggerReporter	task_failed	ERROR: task 9, assign_taxonomy : Failed! Error message : Task failed because parent task `4’ failed  
2022-02-17 00:18:53,134 LoggerReporter finished ERROR: AnADAMA run finished with errors.

Thanks for the help!