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
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
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.