issue/bug getting root to tip variation

[crcardenas]

I have the following slurm script:

#!/bin/sh
#SBATCH --job-name=sorta_date           # job name
#SBATCH --mem=10000                     # 10 gb of ram
#SBATCH --ntasks=1                      # number of tasks
#SBATCH --cpus-per-task=1               # cores each task needs
#SBATCH --partition=public-cpu          # partition
#SBATCH --time=02:00:00                 # max two hours 

module load GCC/11.3.0 OpenMPI/4.1.4 phyx/1.3 Anaconda3

SD="SortaDate/src"
REROOT="rerooted/"
SPECIESTREE="noflank_parti-gene_30p.rr.treefile"

printf "get root to tip variation\n"
python ${SD}/get_var_length.py ${REROOT} --flend .rr.treefile --outf analysis/var --outg GCA905333025_gen,SRR2083676_tra,SRR921609_tra,SRR2083695_tra,SRR10334043_uce,SRR10334056_uce

# get bipartition support
printf "get bipartition support\n"
python ${SD}/get_bp_genetrees.py --flend .rr.treefile ${REROOT} ${SPECIESTREE} --outf analysis/bp

# get good genes
printf "combine_results\n"
python ${SD}/combine_results.py analysis/var analysis/bp --outf analysis/comb

# get good genes
printf "get good genes\n"
python ${SD}/get_good_genes.py analysis/comb --max 200 --order 3,1,2 --outf analysis/good_genes

Running it gives me a similar error to this closed topic.

$ cat slurm-6074476.out
get root to tip variation
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
Error: this really only works with nexus or newick. Exiting.
Error: this really only works with nexus or newick. Exiting.
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
Error: this really only works with nexus or newick. Exiting.
directory: rerooted
file ending for trees: .rr.treefile
outgroups: GCA905333025_gen,SRR2083676_tra,SRR921609_tra,SRR2083695_tra,SRR10334043_uce,SRR10334056_uce
phyx location: 
outfile: analysis/var
get bipartition support
directory: rerooted
file ending for trees: .rr.treefile
species tree: noflank_parti-gene_30p.rr.treefile
phyx location: 
outfile: analysis/bp
combine_results
outfile: analysis/comb
get good genes
order: bipartition root-to-tip variance treelength
outfile: analysis/good_genes
Traceback (most recent call last):
  File "/home/users/c/cardenac/phylo/2023_adephaga/SORTADATE/SortaDate/src/get_good_genes.py", line 41, in <module>
    tuples.append((spls[0],float(spls[1]),float(spls[2]),-float(spls[-1])))
IndexError: list index out of range

I looked at the var file, and indeed there are empty lines"

...
trimalauto_30p_ENSMPTG00005025653.rr.treefile	0.0205059	10.0266
trimalauto_30p_ENSMPTG00005027711.rr.treefile	0.0325183	17.8281
trimalauto_30p_uce194347.rr.treefile	0.0577492	12.7498
trimalauto_30p_ENSMPTG00005020600.rr.treefile		
trimalauto_30p_ENSMPTG00005022173.rr.treefile	0.0850962	40.1361
trimalauto_30p_ENSMPTG00005025359.rr.treefile	0.0842451	22.3873
...	

Trying to make a copy of the files in a new directory didn't help and returned a similar error. I checked the treefiles (newick format) and they look fine. I was able to successfully run it without indicating out groups. But I still need accurate variation... so I removed those trees from the run. ( for i in $(cat analysis/var | tr " " "\t" | awk '{if ($2=="") print;}'); do echo mv rerooted/${i} rerooted_removed/${i}; done)

However, there were still some warnings/errors in the slurm out file

get root to tip variation
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
free(): double free detected in tcache 2
directory: rerooted/
file ending for trees: .rr.treefile
outgroups: GCA905333025_gen,SRR2083676_tra,SRR921609_tra,SRR2083695_tra,SRR10334043_uce,SRR10334056_uce
phyx location: 
outfile: analysis/var
get bipartition support
directory: rerooted/
file ending for trees: .rr.treefile
species tree: noflank_parti-gene_30p.rr.treefile
phyx location: 
outfile: analysis/bp
combine_results
outfile: analysis/comb
get good genes
order: bipartition root-to-tip variance treelength
outfile: analysis/good_genes

So I am not sure if the fact I'm running phyx as a module on a slurm cluster is the problem.

I think it could be because I'm not sure how to indicate where phyx lives, but I loaded it as a module (the --loc parameter). Its in my paths ...:/opt/ebsofts/phyx/1.3-foss-2022a/bin:.... but just running a pxrr --help throws an error.

python /opt/ebsofts/phyx/1.3-foss-2022a/bin/pxrr --help
SyntaxError: Non-UTF-8 code starting with '\xd2' in file /opt/ebsofts/phyx/1.3-foss-2022a/bin/pxrr on line 2, but no encoding declared; see https://python.org/dev/peps/pep-0263/ for details

While, of course, without indicating the bin in my paths python pxrr --help works fine.

I would try running it on my computer, but I had an issue installing phyx....