# Dist.shared with subsampling hangs in 1.41.3 **URL:** \ **Category:** mothur bugs\ **Created:** [April 23, 2019, 1:50pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844 "2019-04-23T13:50:40Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![CDP23](https://avatars.discourse-cdn.com/v4/letter/c/bbce88/32.png) [@CDP23](https://forum.mothur.org/u/CDP23)\ **Post date:** [April 23, 2019, 1:50pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/1 "2019-04-23T13:50:40Z")
Hi, I’m a new user of mothur and I’m trying to run the following using Ubuntu 18.04: dist.shared (shared = my.shared, calc = thetayc - jclass, sumbsample = 3648, processors = 10) This is taking 15+ hours to complete, so I’m assuming it’s hanging. However, if I run sub.sample(shared = my.shared, size = 3648) then dist.shared (shared = my.0.03.subsample.shared, calc = thetayc - jclass, processors = 10) this works fine. Is this a known issue / appropriate work around? Thanks ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [April 25, 2019, 12:40pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/2 "2019-04-25T12:40:30Z")
Hi, No that is not an appropriate work-around. Running `sub.sample` and then `dist.shared` is the same as running `dist.shared` with `iters=1`. You might try running the original `dist.shared` function call with `iters=100`. How many samples do you have and how many OTUs are there? Is anything outputted to the screen? pat ---
**Author:** ![CDP23](https://avatars.discourse-cdn.com/v4/letter/c/bbce88/32.png) [@CDP23](https://forum.mothur.org/u/CDP23)\ **Post date:** [April 25, 2019, 1:49pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/3 "2019-04-25T13:49:44Z")
Hi Pat, I have 50 samples. I have one sample with 106 OTUs and the rest range from 3648 to approx 40000. The only output to the screen is that the 106 OTU sample is being eliminated. Thanks ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [April 29, 2019, 4:57pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/4 "2019-04-29T16:57:44Z")
Can you try it with fewer iterations? ---
**Author:** ![CDP23](https://avatars.discourse-cdn.com/v4/letter/c/bbce88/32.png) [@CDP23](https://forum.mothur.org/u/CDP23)\ **Post date:** [May 9, 2019, 3:03pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/5 "2019-05-09T15:03:52Z")
Hi Pat, I tried this and received the same output. After 10+ hours it still hadn’t progressed passed the first sample. Any advice appreciated ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [May 9, 2019, 3:43pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/6 "2019-05-09T15:43:17Z")
Can you send the shared file to us at [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) and in the email provide the url to this thread? Thanks Pat ---
**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\ **Post date:** [May 13, 2019, 4:58pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/7 "2019-05-13T16:58:59Z")
Thanks for sending your files and reporting this issue. The slow down was caused by the way we were removing otus that had no members after the subsampling. I have modified how mothur removes the OTUs to greatly reduce the time required to eliminate them. You can download the updated version here, [https://github.com/mothur/mothur/releases/tag/v1.42.1](https://github.com/mothur/mothur/releases/tag/v1.42.1). ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [May 23, 2019, 4:59pm UTC](https://forum.mothur.org/t/dist-shared-with-subsampling-hangs-in-1-41-3/19844/8 "2019-05-23T16:59:00Z")
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