# Parsimony **URL:** \ **Category:** mothur bugs\ **Created:** [February 27, 2013, 4:54pm UTC](https://forum.mothur.org/t/parsimony/1241 "2013-02-27T16:54:54Z")\ **Posts on this page:** 14\ **Page:** 1
**Author:** ![juliacope](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@juliacope](https://forum.mothur.org/u/juliacope)\ **Post date:** [February 27, 2013, 4:54pm UTC](https://forum.mothur.org/t/parsimony/1241/1 "2013-02-27T16:54:54Z")
Hello, I am trying to run parsimony on a small dataset. I know that the groups file contains the groups indicated. Either way I try to run the command I encounter an error. The count method tells me none of my groups are present and goes into a scrolling output that I have to force close. count.seqs(name=final\_a\_bacdups.names, group=a\_bacdups.pick.happy.groups) parsimony(tree=final\_a\_bacdups.an.thetayc.0.03.ave.tre, count=final\_a\_bacdups.count\_table) The group method comes up with a seg fault. parsimony(tree=final\_a\_bacdups.an.thetayc.0.03.ave.tre, group=a\_bacdups.pick.happy.groups Any help would be greatly appreciated. Logs are below. -Julia * * * mothur v.1.29.2 Last updated: 2/26/2013 by Patrick D. Schloss Department of Microbiology & Immunology University of Michigan [pschloss@umich.edu](mailto:pschloss@umich.edu) [http://www.mothur.org](http://www.mothur.org) When using, please cite: Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. Distributed under the GNU General Public License Type ‘help()’ for information on the commands that are available Type ‘quit()’ to exit program mothur \> set.dir(input=/Users/julia/Desktop/bacdupsworking) Mothur’s directories: inputDir=/Users/julia/Desktop/bacdupsworking/ mothur \> set.dir(output=/Users/julia/Desktop/bacdupsworking) Mothur’s directories: outputDir=/Users/julia/Desktop/bacdupsworking/ mothur \> set.dir(tempdefault=/Users/julia/Desktop/bacdupsworking) Mothur’s directories: tempDefault=/Users/julia/Desktop/bacdupsworking/ mothur \> count.seqs(name=final\_a\_bacdups.names, group=a\_bacdups.pick.happy.groups) Unable to open final\_a\_bacdups.names. Trying default /Users/julia/Desktop/bacdupsworking/final\_a\_bacdups.names Unable to open a\_bacdups.pick.happy.groups. Trying default /Users/julia/Desktop/bacdupsworking/a\_bacdups.pick.happy.groups Total number of sequences: 12784 Output File Names: /Users/julia/Desktop/bacdupsworking/final\_a\_bacdups.count\_table mothur \> parsimony(tree=final\_a\_bacdups.an.thetayc.0.03.ave.tre, count=final\_a\_bacdups.count\_table) Unable to open final\_a\_bacdups.an.thetayc.0.03.ave.tre. Trying default /Users/julia/Desktop/bacdupsworking/final\_a\_bacdups.an.thetayc.0.03.ave.tre Unable to open final\_a\_bacdups.count\_table. Trying default /Users/julia/Desktop/bacdupsworking/final\_a\_bacdups.count\_table Using 1 processors. [ERROR]: STYS3\_2\_ is not in your count table. Please correct. Segmentation fault nat-10-200-52-30:mothur1.29.2 julia$ * * * Mac version Using ReadLine Running 64Bit Version mothur v.1.29.2 Last updated: 2/26/2013 by Patrick D. Schloss Department of Microbiology & Immunology University of Michigan [pschloss@umich.edu](mailto:pschloss@umich.edu) [http://www.mothur.org](http://www.mothur.org) When using, please cite: Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. Distributed under the GNU General Public License Type ‘help()’ for information on the commands that are available Type ‘quit()’ to exit program Interactive Mode mothur \> set.dir(input=/Users/julia/Desktop/bacdupsworking) Mothur's directories: inputDir=/Users/julia/Desktop/bacdupsworking/ mothur \> set.dir(output=/Users/julia/Desktop/bacdupsworking) Mothur’s directories: outputDir=/Users/julia/Desktop/bacdupsworking/ mothur \> set.dir(tempdefault=/Users/julia/Desktop/bacdupsworking) Mothur’s directories: tempDefault=/Users/julia/Desktop/bacdupsworking/ mothur \> parsimony(tree=final\_a\_bacdups.an.thetayc.0.03.ave.tre, group=a\_bacdups.pick.happy.groups) Unable to open final\_a\_bacdups.an.thetayc.0.03.ave.tre. Trying default /Users/julia/Desktop/bacdupsworking/final\_a\_bacdups.an.thetayc.0.03.ave.tre Unable to open a\_bacdups.pick.happy.groups. Trying default /Users/julia/Desktop/bacdupsworking/a\_bacdups.pick.happy.groups Using 1 processors. [ERROR]: Your group file does not contain HVYS5\_. Please correct. [ERROR]: Your group file does not contain HVYS5\_2\_. Please correct. [ERROR]: Your group file does not contain HVYS5\_3\_. Please correct. [ERROR]: Your group file does not contain STYS3\_. Please correct. [ERROR]: Your group file does not contain STYS3\_2\_. Please correct. Removing group: HVYS5\_ because all sequences have been removed. Removing group: HVYS5\_2\_ because all sequences have been removed. Removing group: HVYS5\_3\_ because all sequences have been removed. Removing group: STYS3\_ because all sequences have been removed. Removing group: STYS3\_2\_ because all sequences have been removed. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. error with lc [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. error with lc [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. error with lc [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. [ERROR]: Your count table does not have group info. Please correct. error with lc \<------- This is repeated until the memory fills or I lose patience. ---
**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:** [February 27, 2013, 5:51pm UTC](https://forum.mothur.org/t/parsimony/1241/2 "2013-02-27T17:51:15Z")
Do your group names contain ‘:’ characters? ---
**Author:** ![juliacope](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@juliacope](https://forum.mothur.org/u/juliacope)\ **Post date:** [February 27, 2013, 6:51pm UTC](https://forum.mothur.org/t/parsimony/1241/3 "2013-02-27T18:51:33Z")
No, no colons. My list of groups is: HVYS5\_ HVYS5\_2\_ HVYS5\_3\_ STYS3\_ STYS3\_2\_ ---
**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:** [March 1, 2013, 2:11pm UTC](https://forum.mothur.org/t/parsimony/1241/4 "2013-03-01T14:11:17Z")
Could you send your input files and logfile to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) so I can try to track down the issue for you? ---
**Author:** ![juliacope](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@juliacope](https://forum.mothur.org/u/juliacope)\ **Post date:** [March 1, 2013, 2:37pm UTC](https://forum.mothur.org/t/parsimony/1241/5 "2013-03-01T14:37:57Z")
Logs and files sent. ---
**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:** [March 1, 2013, 3:46pm UTC](https://forum.mothur.org/t/parsimony/1241/6 "2013-03-01T15:46:19Z")
Your tree file shows the relationships between your groups, but your groupfile relates your sequences to their groups. You want to use a design file for the group file input with the parsimony command when your tree relates group. The design file tells mothur the treatments the groups belong to. Here’s an example from the Schloss SOP, [http://www.mothur.org/wiki/Schloss\_SOP#Analysis](http://www.mothur.org/wiki/Schloss_SOP#Analysis). mouse.sex\_time.design contains: F003D000 F003Early F003D002 F003Early F003D004 F003Early F003D006 F003Early F003D008 F003Early F003D142 F003Late F003D144 F003Late F003D146 F003Late F003D148 F003Late F003D150 F003Late parsimony(tree=final.an.thetayc.0.03.ave.tre, group=mouse.sex\_time.design, groups=all) Kindly, Sarah ---
**Author:** ![ghaida\_ali](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@ghaida\_ali](https://forum.mothur.org/u/ghaida_ali)\ **Post date:** [August 27, 2014, 8:36am UTC](https://forum.mothur.org/t/parsimony/1241/7 "2014-08-27T08:36:24Z")
Hello, I am also facing the same problem. I am trying to run parsimony and unifrac command, mothur\>parsimony(tree=final.an.unique\_list.braycurtis.0.03.tre, group=mucus.design, groups=all) when i run them i get error with lc. I used both the current database and old for greengenes formated database, and i still get error with lc. I really need a help, i dont know why i get this error, your help is much appreciate it. Ghaida ---
**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:** [August 28, 2014, 5:54pm UTC](https://forum.mothur.org/t/parsimony/1241/8 "2014-08-28T17:54:15Z")
Can you send us the files you are inputting to the command, the actual command syntax you are entering, and the url for this post? Thanks! Pat [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) ---
**Author:** ![ghaida\_ali](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@ghaida\_ali](https://forum.mothur.org/u/ghaida_ali)\ **Post date:** [August 31, 2014, 8:06am UTC](https://forum.mothur.org/t/parsimony/1241/9 "2014-08-31T08:06:31Z")
I have attached the files to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) ---
**Author:** ![ghaida\_ali](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@ghaida\_ali](https://forum.mothur.org/u/ghaida_ali)\ **Post date:** [September 8, 2014, 11:48am UTC](https://forum.mothur.org/t/parsimony/1241/10 "2014-09-08T11:48:47Z")
Hello, I didn’t heard anything from you about my data, I would like to know if there is any problem with it or what? Thank you and hope to hear from you soon. Ghiada ---
**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:** [September 10, 2014, 6:31pm UTC](https://forum.mothur.org/t/parsimony/1241/11 "2014-09-10T18:31:57Z")
You are getting the following errors… ```nohighlight mothur > parsimony(tree=final.an.unique_list.braycurtis.0.03.tre, group=design.file.txt) Using 1 processors. [ERROR]: Your group file does not contain AD1. Please correct. [ERROR]: Your group file does not contain AD2. Please correct. [ERROR]: Your group file does not contain AD3. Please correct. [ERROR]: Your group file does not contain AD4. Please correct. [ERROR]: Your group file does not contain AD5. Please correct. [ERROR]: Your group file does not contain AD6. Please correct. [ERROR]: Your group file does not contain AD7. Please correct. [ERROR]: Your group file does not contain AD8. Please correct. [ERROR]: Your group file does not contain AD9. Please correct. [ERROR]: Your group file does not contain S1. Please correct. [ERROR]: Your group file does not contain S2. Please correct. [ERROR]: Your group file does not contain S3. Please correct. [ERROR]: Your group file does not contain S4. Please correct. [ERROR]: Your group file does not contain S5. Please correct. [ERROR]: Your group file does not contain S6. Please correct. [ERROR]: Your group file does not contain S7. Please correct. [ERROR]: Your group file does not contain S8. Please correct. [ERROR]: Your group file does not contain S9. Please correct. Name: AD9 is not in your groupfile, and will be disregarded. [ERROR]: Your count table contains more than 1 sequence named AD9, sequence names must be unique. Please correct. error with lc ``` When I look at your design file you have group names like S01, S02, etc - not S1, S2. If you can fix this I think you’ll be in good shape. pat ---
**Author:** ![ghaida\_ali](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@ghaida\_ali](https://forum.mothur.org/u/ghaida_ali)\ **Post date:** [September 11, 2014, 2:07pm UTC](https://forum.mothur.org/t/parsimony/1241/12 "2014-09-11T14:07:05Z")
ok, i will do it and will let you know:) Thank you for your help ---
**Author:** ![ghaida\_ali](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@ghaida\_ali](https://forum.mothur.org/u/ghaida_ali)\ **Post date:** [September 24, 2014, 9:21am UTC](https://forum.mothur.org/t/parsimony/1241/13 "2014-09-24T09:21:02Z")
Hello, I renamed the samples instead of S01,S02,etc to S1,S2,etc… but I still have the same message mothur \> parsimony(tree=final.an.unique\_list.braycurtis.0.03.tre, group=design.file.txt) Using 1 processors. [ERROR]: Your group file does not contain AD1. Please correct. [ERROR]: Your group file does not contain AD2. Please correct. [ERROR]: Your group file does not contain AD3. Please correct. [ERROR]: Your group file does not contain AD4. Please correct. [ERROR]: Your group file does not contain AD5. Please correct. [ERROR]: Your group file does not contain AD6. Please correct. [ERROR]: Your group file does not contain AD7. Please correct. [ERROR]: Your group file does not contain AD8. Please correct. [ERROR]: Your group file does not contain AD9. Please correct. [ERROR]: Your group file does not contain S1. Please correct. [ERROR]: Your group file does not contain S2. Please correct. [ERROR]: Your group file does not contain S3. Please correct. [ERROR]: Your group file does not contain S4. Please correct. [ERROR]: Your group file does not contain S5. Please correct. [ERROR]: Your group file does not contain S6. Please correct. [ERROR]: Your group file does not contain S7. Please correct. [ERROR]: Your group file does not contain S8. Please correct. [ERROR]: Your group file does not contain S9. Please correct. Name: AD9 is not in your groupfile, and will be disregarded. [ERROR]: Your count table contains more than 1 sequence named AD9, sequence names must be unique. Please correct. error with lc In my file design the first column refers to sample name and the second column refers to the group that each sample belong to For example: AD1,AD2,etc … belongs to AD group Also, I looked into my count table file and I didn’t see that AD9 have more than 1 sequence. So, what do you think the problem is. Your help is much appreciated. Thank you again Hope to hear from you soon ---
**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:** [September 24, 2014, 1:26pm UTC](https://forum.mothur.org/t/parsimony/1241/14 "2014-09-24T13:26:19Z")
Are you using our current version? I am not seeing that error. mothur \> parsimony(tree=final.an.unique\_list.braycurtis.0.03.tre, group=design.file.txt) Using 1 processors. \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*# **#** # **#** # **#** # **#** # **#** # Comparing to random:|||||||||||||||||||||||||||||||||||||||||||||||||||| * * * Tree# Groups ParsScore ParsSig 1 AD-ADF-RS-RSF 5 \<0.001 Kindly, Sarah