Error at "gene_tree2" step

[Jiffin Paulose]

Francesco,

I've been able to get as far as the 2nd gene tree step. 

My input is as follows: 

python phylophlan2.py -i input/klebsiella-aerogenes/ -d phylophlan -f supertree_aa.cfg -t a --diversity low --accurate --maas phylophlan.tsv --submat pfasum60 --subsample phylophlan --scoring_function trident --mutation_rates --nproc 8 --output_folder output --verbose

supertree_aa.confg is as follows:

[db_aa]

program_name = diamond

params = makedb

threads = --threads

input = --in

output = --db

version = version

command_line = #program_name# #params# #threads# #input# #output#

[db_dna]

program_name = makeblastdb

params = -parse_seqids -dbtype nucl

input = -in

output = -out

version = -version

command_line = #program_name# #params# #input# #output#

[map_dna]

program_name = diamond

params = blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0

input = --query

database = --db

output = --out

version = version

command_line = #program_name# #params# #input# #database# #output#

[map_aa]

program_name = diamond

params = blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0

input = --query

database = --db

output = --out

version = version

command_line = #program_name# #params# #input# #database# #output#

[msa]

program_name = mafft

params = --quiet --anysymbol --auto

version = --version

command_line = #program_name# #params# #input# > #output#

environment = TMPDIR=/tmp

[trim]

program_name = trimal

params = -gappyout

input = -in

output = -out

version = --version

command_line = #program_name# #params# #input# #output#

[gene_tree1]

program_name = FastTree

params = -quiet -mlacc 2 -slownni -spr 4 -fastest -mlnni 4 -no2nd -lg

output = -out

command_line = #program_name# #params# #output# #input#

[gene_tree2]

program_name = raxmlHPC

params = -p 1989

database = -t

input = -s

output_path = -w

output = -n

version = -v

model = -m

command_line = #program_name# #model# #params# #database# #output_path# #input# #output#

[tree1]

program_name = java -jar /home/jiffin/tools/ASTRAL/Astral/astral.5.6.3.jar

input = -i

output = -o

version = -i /home/jiffin/tools/ASTRAL/Astral/test_data/song_mammals.424.gene.tre

command_line = #program_name# #input# #output#

After the gene trees are built, I get the following error:

[e] starting tree "output/klebsiella-aerogenes_phylophlan/tmp/gene_tree1_polytomiesp0058.tre" not found in "output/klebsiella-aerogenes_phylophlan/tmp/gene_tree1_polytomies", built from "output/klebsiella-aerogenes_phylophlan/tmp/sub/p0058.aln"

At first I though this was acceptable, but then the script exits with the following error:

Gene trees already refined

Merging gene trees

Gene trees merged into "output/klebsiella-aerogenes_phylophlan/tmp/gene_trees.tre" in 0s

Building phylogeny "output/klebsiella-aerogenes_phylophlan/tmp/gene_trees.tre"

[e] Command '['java', '-jar', '/home/jiffin/tools/ASTRAL/Astral/astral.5.6.3.jar', '-i', 'output/klebsiella-aerogenes_phylophlan/tmp/gene_trees.tre', '-o', '/home/jiffin/phylophlan/output/klebsiella-aerogenes_phylophlan/klebsiella-aerogenes.tre']' returned non-zero exit status 1

[e] error while executing

    command_line: java -jar /home/jiffin/tools/ASTRAL/Astral/astral.5.6.3.jar -i output/klebsiella-aerogenes_phylophlan/tmp/gene_trees.tre -o /home/jiffin/phylophlan/output/klebsiella-aerogenes_phylophlan/klebsiella-aerogenes.tre

           stdin: None

          stdout: None

             env: None

The merged gene_trees.tre file is empty

For every file generated in the previous step.  It appears that the script is looking for, for example "output/klebsiella-aerogenes_phylophlan/tmp/gene_tree1_polytomiesp0058.tre", within the tmp directory, but that file is located in "output/klebsiella-aerogenes_phylophlan/tmp/gene_tree1_polytomies/"  so there is a "/" missing or something .

As far as I can tell, the file location is mismatched as the file is in the directory of gene_tree1_polytomies.  I tried looking through the script to see where the file is called, but I haven't had an luck.

[Francesco Asnicar]

Many thanks for reporting this.

I actually tried (a while back) the gene tree pipeline and never encountered that problem, but I think I figured out where the problem is. It should be fixed now with the "e4cd8e5" commit.

Can you update your version and give it a try?

Many thanks,

Francesco

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