# Chimera.uchime broken in 1.32.0 **URL:** \ **Category:** mothur bugs\ **Created:** [October 7, 2013, 7:09pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529 "2013-10-07T19:09:59Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![adamc83](https://avatars.discourse-cdn.com/v4/letter/a/48db29/32.png) [@adamc83](https://forum.mothur.org/u/adamc83)\ **Post date:** [October 7, 2013, 7:09pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/1 "2013-10-07T19:09:59Z")
Something isnt working in chimera.uchime or related code in version 1.32.0. I get a ton of errors like this: ```nohighlight [ERROR]: Your count table contains a sequence named RUN1_1_1101_18820_16351 with a total=0. Please correct. ``` But the corresponding entries in my count\_file definitely dont total to zero: ```nohighlight RUN1_1_1101_18820_16351 62 51 5 1 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ``` The same batch file runs without problem on 1.31.2, and I’ve had the same error in two different data sets. I am loosely following the MiSeq SOP, with my own data sets. Let me know if you need me to provide data to reproduce this issue. ---
**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:** [October 8, 2013, 5:13pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/2 "2013-10-08T17:13:44Z")
In version 1.32.0, we added an error flag in the count table to catch tables that where not made by mothur and had zero totals. Zero totals caused issues in some of mothur’s commands because mothur expects a representative sequence to at least represent itself. When chimera.uchime runs with a count table and dereplicate=t, it can create a temporary table with 0 counts, but then adjusts the table and prints it. Mothur is complaining about the temporary table. Thanks for reporting the issue. We will release a patch for this later this week, but in the meantime as a work around you could run the SOP with names and groups files, and then create the count table after the chimera.uchime command. ---
**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:** [October 16, 2013, 5:22pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/3 "2013-10-16T17:22:50Z")
Version 1.32.1 is up on the wiki and it includes the fix for this bug. ---
**Author:** ![jonls](https://avatars.discourse-cdn.com/v4/letter/j/c0e974/32.png) [@jonls](https://forum.mothur.org/u/jonls)\ **Post date:** [October 23, 2013, 3:39pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/4 "2013-10-23T15:39:09Z")
I had the same problem in 1.32.0 and I have updated to 1.32.1 now, however I am still running into errors like the following: ```nohighlight [ERROR]: M00763_18_000000000-A6DEW_1_1101_23407_24535/ab=21/ is not in your count table. Please correct. ``` It seems that the temporary table has “/ab=X/” added to the identifiers. Any idea why that happens? ---
**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:** [October 23, 2013, 8:29pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/5 "2013-10-23T20:29:00Z")
I am not seeing that error on our end. Could you post the chimera.uchime command you ran and the OS you are running mothur on? ---
**Author:** ![jonls](https://avatars.discourse-cdn.com/v4/letter/j/c0e974/32.png) [@jonls](https://forum.mothur.org/u/jonls)\ **Post date:** [October 23, 2013, 8:47pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/6 "2013-10-23T20:47:52Z")
Sure, the command I am trying to run is: ```nohighlight chimera.uchime(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=T, reference=silva.gold.ng.fasta, processors=8) ``` on a Linux system. I am following the guide here: [http://www.mothur.org/wiki/MiSeq\_SOP](http://www.mothur.org/wiki/MiSeq_SOP), so the input files to chimera.uchime are produced by the pre.cluster command. Let me know if I can provide any more info. ---
**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:** [October 25, 2013, 12:04pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/7 "2013-10-25T12:04:17Z")
Mothur should include an error message in this case. The command is not designed to be run this way. You can run it with the silva sequences as the reference, or use the abundance information in the count table to check the less abundant sequences against the more abundant, but not both. If you are following the MISeq SOP just leave off the silva reference and run the command. ---
**Author:** ![jonls](https://avatars.discourse-cdn.com/v4/letter/j/c0e974/32.png) [@jonls](https://forum.mothur.org/u/jonls)\ **Post date:** [October 25, 2013, 6:02pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/8 "2013-10-25T18:02:20Z")
Thanks, I will try that. So if I wanted to run chimera.uchime with a reference I would just leave out the count parameter? ---
**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:** [October 28, 2013, 11:51am UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/9 "2013-10-28T11:51:59Z")
Yes, that is correct. ---
**Author:** ![maasha](https://avatars.discourse-cdn.com/v4/letter/m/5fc32e/32.png) [@maasha](https://forum.mothur.org/u/maasha)\ **Post date:** [November 21, 2013, 9:15am UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/10 "2013-11-21T09:15:22Z")
I am seeing the same error following the MiSeq SOP: ```nohighlight [ERROR]: Your count table contains a sequence named M01168_77_000000000-A59UE_1_2114_9814_8689 with a total=0. Please correct. [ERROR]: Your count table contains a sequence named M01168_77_000000000-A59UE_1_2114_2857_10432 with a total=0. Please correct. [ERROR]: Your count table contains a sequence named M01168_77_000000000-A59UE_1_2114_13028_17777 with a total=0. Please correct. [ERROR]: Your count table contains a sequence named M01168_77_000000000-A59UE_1_2114_12343_20096 with a total=0. Please correct. [ERROR]: Your count table contains a sequence named M01168_77_000000000-A59UE_1_2114_6961_21614 with a total=0. Please correct. [ERROR]: Your count table contains a sequence named M01168_77_000000000-A59UE_1_2114_16376_26587 with a total=0. Please correct. ... ``` The command used was: ```nohighlight chimera.uchime(fasta=jt.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=jt.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t) ``` Mothur v.1.32.0 ---
**Author:** ![jonls](https://avatars.discourse-cdn.com/v4/letter/j/c0e974/32.png) [@jonls](https://forum.mothur.org/u/jonls)\ **Post date:** [November 21, 2013, 2:27pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/11 "2013-11-21T14:27:09Z")
> [@maasha](#): > > I am seeing the same error following the MiSeq SOP […] Mothur v.1.32.0 I believe the bug was fixed in v.1.32.1 so you would have to update your program to avoid running into that problem. ---
**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:** [November 21, 2013, 2:36pm UTC](https://forum.mothur.org/t/chimera-uchime-broken-in-1-32-0/1529/12 "2013-11-21T14:36:43Z")
> [@westcott](#): > > In version 1.32.0, we added an error flag in the count table to catch tables that where not made by mothur and had zero totals. Zero totals caused issues in some of mothur’s commands because mothur expects a representative sequence to at least represent itself. When chimera.uchime runs with a count table and dereplicate=t, it can create a temporary table with 0 counts, but then adjusts the table and prints it. Mothur is complaining about the temporary table. Thanks for reporting the issue. We will release a patch for this later this week, but in the meantime as a work around you could run the SOP with names and groups files, and then create the count table after the chimera.uchime command. This is fixed in the current version, 1.32.1, [Redirecting…](http://www.mothur.org/wiki/Download_mothur).