# Understanding min sequence length of F and R/ quality scores and how it is impacting dada2 downstream **URL:** https://forum.qiime2.org/t/understanding-min-sequence-length-of-f-and-r-quality-scores-and-how-it-is-impacting-dada2-downstream/33191 **Category:** User Support **Tags:** dada2 **Created:** [May 24, 2025, 3:04pm UTC](https://forum.qiime2.org/t/understanding-min-sequence-length-of-f-and-r-quality-scores-and-how-it-is-impacting-dada2-downstream/33191 "2025-05-24T15:04:27Z") **Posts on this page:** 1 **Showing post:** 3
### Author: ![KaraS](https://forum.qiime2.org/user_avatar/forum.qiime2.org/karas/32/15832_2.png) [@KaraS](https://forum.qiime2.org/u/KaraS) #### Post date: [May 26, 2025, 5:15am UTC](https://forum.qiime2.org/t/understanding-min-sequence-length-of-f-and-r-quality-scores-and-how-it-is-impacting-dada2-downstream/33191/3 "2025-05-26T05:15:12Z")
R version 3.5.1 (2018-07-02) Loading required package: Rcpp DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4 1. Filtering The filter removed all reads: /var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/filt\_f/428\_138\_L001\_R1\_001.fastq.gz and /var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/filt\_r/428\_139\_L001\_R2\_001.fastq.gz not written. The filter removed all reads: /var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/filt\_f/296-2\_96\_L001\_R1\_001.fastq.gz and /var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/filt\_r/296-2\_97\_L001\_R2\_001.fastq.gz not written. Some input samples had no reads pass the filter. .........................................................................................................................................x....................x................................................................................................. 2. Learning Error Rates 289560551 total bases in 1067489 reads from 4 samples will be used for learning the error rates. 244454981 total bases in 1067489 reads from 4 samples will be used for learning the error rates. 3. Denoise remaining samples ..................................................................................................................................................................................................................................................Error in dada(drpR, err = errR, multithread = multithread, verbose = FALSE) : Invalid derep$quals matrix. Quality values must be positive integers. Execution halted Traceback (most recent call last): File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2\_dada2/\_denoise.py", line 257, in denoise\_paired run\_commands([cmd]) File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2\_dada2/\_denoise.py", line 36, in run\_commands subprocess.run(cmd, check=True) File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run\_dada\_paired.R', '/var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/forward', '/var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/reverse', '/var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/output.tsv.biom', '/var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/track.tsv', '/var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/filt\_f', '/var/folders/yp/gmbd6\_256wnbb6qyf3s3v\_6r0000gn/T/tmpkg09sibn/filt\_r', '0', '229', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in **call** results = action(\*\*arguments) File "\", line 2, in denoise\_paired File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound\_callable output\_types, provenance) File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable\_executor_ output\_views = self.\_callable(\*\*view\_args) File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2\_dada2/\_denoise.py", line 272, in denoise\_paired " and stderr to learn more." % e.returncode) Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more. --- _[View the full topic](https://forum.qiime2.org/t/understanding-min-sequence-length-of-f-and-r-quality-scores-and-how-it-is-impacting-dada2-downstream/33191)._