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!