# Very long runtime (\>20 hours) for feature-classifier extract-reads with SILVA 138.2 in QIIME 2 2026.4 **URL:** \ **Category:** Technical Support\ **Created:** [July 12, 2026, 5:41am UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243 "2026-07-12T05:41:01Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![ttssuu](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ttssuu/32/21867_2.png) [@ttssuu](https://forum.qiime2.org/u/ttssuu)\ **Post date:** [July 12, 2026, 5:41am UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243/1 "2026-07-12T05:41:01Z")
Hello, I am experiencing an unusually long runtime when running `qiime feature-classifier extract-reads` with SILVA 138.2 on QIIME 2 2026.4. My command is: ```auto qiime feature-classifier extract-reads \ --i-sequences silva-138.2-dna-seqs.qza \ --p-f-primer CCTACGGGNGGCWGCAG \ --p-r-primer GACTACHVGGGTATCTAATCC \ --p-max-length 600 \ --o-reads silva-138.2-99-V3V4.qza ``` ### Environment - QIIME 2: 2026.4 - Python: 3.12.13 - OS: Ubuntu on WSL2 - CPU: Intel Core i9 - RAM: 80 GB ### Input data The reference sequences were generated using RESCRIPt: ```auto qiime rescript reverse-transcribe \ --i-rna-sequences silva-138.2-seqs.qza \ --o-dna-sequences silva-138.2-dna-seqs.qza ``` The input artifact contains approximately **510,495 sequences**. ### What I observed - Running the same command on a test dataset containing only **100 sequences** finishes within a few seconds. - On the full dataset, the process continues for **more than 20 hours**. - During execution: - CPU usage stays around **100–103%** - Memory usage remains stable at about **1.2 GB** - I/O wait is **0%** - No output artifact (`silva-138.2-99-V3V4.qza`) is created while the process is running. - Using `--verbose` does not produce any progress messages. Current process status: ```auto ELAPSED 21:53:02 %CPU 102 TIME 22:26:53 RSS 1244088 KB ``` Disk space and memory are sufficient. ### Question Is this runtime expected for approximately 510k SILVA sequences, or could this indicate a performance issue in `feature-classifier extract-reads` in QIIME 2 2026.4? Has anyone observed similar behavior? Thank you for any suggestions. ---
**Author:** ![ttssuu](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ttssuu/32/21867_2.png) [@ttssuu](https://forum.qiime2.org/u/ttssuu)\ **Post date:** [July 12, 2026, 11:36am UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243/2 "2026-07-12T11:36:24Z")
**Additional information:** I tested the exact same input artifact and command on a Mac (QIIME 2 2026.4), and `feature-classifier extract-reads` completed successfully in a reasonable amount of time. The issue only occurs on my Ubuntu WSL2 environment, where the process runs for over 20 hours with ~100% CPU utilization and no output produced. ---
**Author:** ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Post date:** [July 12, 2026, 6:13pm UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243/3 "2026-07-12T18:13:28Z")
If you want to post the artifacts to the forum publicly, we can take a look at the history and see what could have caused this. > [@ttssuu](#): > > on a Mac (QIIME 2 2026.4 > ... > my Ubuntu WSL2 environment I also have run Qiime2 using WSL2 and using a Mac, and I find the mac to be _much_ faster! * * * Oh, there's a function of `rescript` that does this with vsearch and it's much faster! It's even multi-threaded, so make sure to use that too! Try that and report back: > **[rescript extract-seq-segments - rescript - Microbiome marker gene analysis with...](https://amplicon-docs.qiime2.org/en/stable/references/plugins/rescript/#q2-action-rescript-extract-seq-segments)** > > Reference sequence annotation and curation pipeline. ---
**Author:** ![ttssuu](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ttssuu/32/21867_2.png) [@ttssuu](https://forum.qiime2.org/u/ttssuu)\ **Post date:** [July 14, 2026, 6:48am UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243/4 "2026-07-14T06:48:23Z")
Hi Colin, Thank you for your suggestion. I prepared a zip file containing the input artifacts and environment information: - command.txt - conda-list.txt - cpu-info.txt - md5sum.txt - qiime-info.txt - silva-138.2-dna-seqs.qza - silva-138.2-seqs.qza The file is available here: > **[dataset.zip is available for download](https://www.transfernow.net/en/cld?utm_source=20260714Sk3Mei0p&utm_medium=FyLaxaIC)** > > Click to access the dataset.zip (384 MB) download with TransferNow The download link will be available for one week. Could you please take a look at the artifacts and let me know if you can identify what might be causing the issue on my WSL2 environment? Thank you very much for your help. ---
**Author:** ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Post date:** [July 15, 2026, 9:46pm UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243/5 "2026-07-15T21:46:47Z")
Thank you for this detailed information! I was able to get this working on my laptop. Full writeup on GitHub: > **[q2-forums/34243 at main · colinbrislawn/q2-forums](https://github.com/colinbrislawn/q2-forums/tree/main/34243)** > > main/34243 Remarkably, the vsearch accelerated [`rescript extract-seq-segments`](https://amplicon-docs.qiime2.org/en/stable/references/plugins/rescript/#q2-plugin-rescript) takes just as long as the built-in `feature-classifier extract-reads` feature, at about 5 minutes each. EDIT: I'm not sure I really answered your question as this also works on your mac. I don't have access to my WSL2 machine, right now! I'll have to check later or wait for someone else to test this on WSL2 ---
**Author:** ![ttssuu](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ttssuu/32/21867_2.png) [@ttssuu](https://forum.qiime2.org/u/ttssuu)\ **Post date:** [July 17, 2026, 8:16am UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243/6 "2026-07-17T08:16:11Z")
> [@colinbrislawn](#): > > feature-classifier extract-reads Hi Colin, I tried the `rescript extract-seq-segments` approach, and it worked perfectly. In the end, I wasn't able to get `feature-classifier extract-reads` to work, so I'll use the RESCRIPt approach instead. Thanks so much for your helpful suggestion! ---
**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\ **Post date:** [August 17, 2026, 2:16pm UTC](https://forum.qiime2.org/t/very-long-runtime-20-hours-for-feature-classifier-extract-reads-with-silva-138-2-in-qiime-2-2026-4/34243/7 "2026-08-17T14:16:16Z")
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