Closed SuanyQuesada closed 2 years ago
Dear, thank you to use BITE! Which operating system are you using to run Treemix_bootstrap.sh script?
Hi! I am using ubuntu 18.04
Another question, which is the version of export function and bash?
The header of the bash script is this: #License: GPLv3 or later #Modification date: 2017-05-10 . And the name of the folder is BITE_1.2.0007 Thank you!
Thank you for your answer. However I'm interested to know the version of the export command installed in your Ubuntu machine.
Hi, the version of the export command in my pc is: "GNU bash, version 4.4.20(1)-release (x86_64-pc-linux-gnu)" Thank you!
Thank you for your answer. Please try to run the "Treemix_bootstrap.sh" script using bash instead sh.
Hi, Thank you for your answer. I ran the "Treemiz_bootstrap.sh" using bash and this ran, but now the script does not make all the gzip files of the bootstrap directory. I do not what is my new mistake..... Thank you in advice ! Have a nice day!
The command line was: bash BITE-master/BITE_1.2.0007/BITE/inst/scripts/treemix_scripts/Treemix_bootstrap.sh populations2.treemix.gz 3 6 500 NoOutgroup 10 /home/suany/Downloads/phylip-3.697/exe/consense pru
The error message was:
RUNNING TREEMIX RUNNING TREEMIX: DONE gzip: bootstrap/pru_treemix_bootrep_1.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_2.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_3.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_4.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_5.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_6.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_7.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_8.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_9.treeout.gz: No such file or directory gzip: bootstrap/pru_treemix_bootrep_10.treeout.gz: No such file or directory Boostrap procedure: DONE Phylip - consensus tree construction: START Phylip - consensus tree construction: DONE RUNNING TREEMIX with Consensus tree ERROR: Input Newick string with 1 populations. Input file has 9 RUNNING TREEMIX: DONE TreeMix - Bootstrap Analysis --> DONE
Dear Suany, it seems that the script is not able to do the bootstrap procedure. I know that others run the script with BASH and, apparently, they did not have problems. The bootstrap folder was created? I suggest to download and install the last version of the R package. After that, use the treemix.script function in R to save the Treemix_bootstrap.sh in your working directory. After that, run Treemix_bootstrap.sh again. I hope this will solve your problem
I am just starting to use treemix and I want to use BITE, but when I run the bash script "Treemix_bootstrap.sh" I got the error "54: export: Illegal option -f" . If I delete that line in the bash, I got emplty files... What can I do?? Thank you so much!
The line command was= sh ./BITE-master/BITE_1.2.0007/BITE/inst/scripts/treemix_scripts/Treemix_bootstrap.sh populations2.treemix.gz 3 6 500 NoOutgroup 10 ./ pru
RUNNING TREEMIX ./BITE-master/BITE_1.2.0007/BITE/inst/scripts/treemix_scripts/Treemix_bootstrap.sh: 54: export: Illegal option -f
Have a nice day!