issue/bug getting root to tip variation #8
Description
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....